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Daco L, Colling G, Matthies D. Clinal variation in quantitative traits but not in evolutionary potential along elevational and latitudinal gradients in the widespread Anthyllis vulneraria. AMERICAN JOURNAL OF BOTANY 2024; 111:e16360. [PMID: 38888183 DOI: 10.1002/ajb2.16360] [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: 09/14/2023] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 06/20/2024]
Abstract
PREMISE Strong elevational and latitudinal gradients allow the study of genetic differentiation in response to similar environmental changes. However, it is uncertain whether the environmental changes along the two types of gradients result in similar genetically based changes in quantitative traits. Peripheral arctic and alpine populations are thought to have less evolutionary potential than more central populations do. METHODS We studied quantitative traits of the widespread Anthyllis vulneraria in a common garden. Plants originated from 20 populations along a 2000-m elevational gradient from the lowlands to the elevational limit of the species in the Alps, and from 20 populations along a 2400-km latitudinal gradient from the center of the distribution of the species in Central Europe to its northern distributional margin. RESULTS Most traits showed similar clinal variations with elevation and latitude of origin, and the magnitude of all measured traits in relation to mean annual temperature was similar. Higher QST values than FST values in several traits indicated diversifying selection, but for others QST was smaller than FST. Genetic diversity of quantitative traits and neutral molecular markers was not correlated. Plasticity in response to favorable conditions declined with elevation and less strongly with latitude of origin, but the evolvability of traits did not. CONCLUSIONS The clinal variation suggests adaptive differentiation of quantitative traits along the two gradients. The evolutionary potential of peripheral populations is not necessarily reduced, but lower plasticity may threaten their survival under rapidly changing climatic conditions.
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Affiliation(s)
- Laura Daco
- Musée national d'histoire naturelle, 25 rue Münster, Luxembourg, L-2160, Luxembourg
- Department of Biology, University of Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany
- Fondation faune-flore, 24 rue Münster, Luxembourg, L-2160, Luxembourg
| | - Guy Colling
- Musée national d'histoire naturelle, 25 rue Münster, Luxembourg, L-2160, Luxembourg
| | - Diethart Matthies
- Department of Biology, University of Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany
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2
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López-Goldar X, Agrawal AA. Tissue and toxin-specific divergent evolution in plant defense Evolución divergente específica de tejido y toxina en defensa de plantas. Evolution 2023; 77:2431-2441. [PMID: 37656826 DOI: 10.1093/evolut/qpad155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 08/07/2023] [Accepted: 08/30/2023] [Indexed: 09/03/2023]
Abstract
A major predicted constraint on the evolution of anti-herbivore defense in plants is the nonindependent expression of traits mediating resistance. Since herbivore attack can be highly variable across plant tissues, we hypothesized that correlations in toxin expression within and between plant tissues may limit population differentiation and, thus, plant adaptation. Using full-sib families from two nearby (<1 km) common milkweed (Asclepias syriaca) populations, we investigated genetic correlations among 28 distinct cardenolide toxins within and between roots, leaves, and seeds and examined signatures of tissue-specific divergent selection between populations by QST-FST comparisons. The prevalence, direction, and strength of genetic correlations among cardenolides were tissue specific, and concentrations of individual cardenolides were moderately correlated between tissues; nonetheless, the direction and strength of correlations were population specific. Population divergence in the cardenolide chemistry was stronger in roots than in leaves and seeds. Divergent selection on individual cardenolides was tissue and toxin specific, except for a single highly toxic cardenolide (labriformin), that showed divergent selection across all plant tissues. Heterogeneous evolution of cardenolides within and between tissues across populations appears possible due to their highly independent expression. This independence may be common in nature, especially in specialized interactions in which distinct herbivores feed on different plant tissues.
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Affiliation(s)
- Xosé López-Goldar
- Department of Entomology, Michigan State University, East Lansing, MI, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Anurag A Agrawal
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
- Department of Entomology, Cornell University, Ithaca, NY, USA
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3
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Walisch TJ, Colling G, Hermant S, Matthies D. Molecular and quantitative genetic variation within and between populations of the declining grassland species Saxifraga granulata. Ecol Evol 2022; 12:e9462. [PMID: 36415877 PMCID: PMC9674452 DOI: 10.1002/ece3.9462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 09/06/2022] [Accepted: 10/04/2022] [Indexed: 11/21/2022] Open
Abstract
Formerly common plant species are expected to be particularly susceptible to recent habitat fragmentation. We studied the population genetics of 19 recently fragmented Saxifraga granulata populations (max. distance 61 km) in Luxembourg and neighboring Germany using RAPD markers and a common garden experiment. We assessed (1) the relationships between plant fitness, quantitative genetic variation, molecular genetic variation, and population size; and (2) the relative importance of genetic drift and selection in shaping genetic variation. Molecular genetic diversity was high but did not correlate with population size, habitat conditions, or plant performance. Genetic differentiation was low (F ST = 0.079 ± 0.135), and there was no isolation by distance. Longevity, clonality, and the long-lived seed bank of S. granulata may have prevented strong genetic erosion and genetic differentiation among populations. However, genetic distinctness increased with decreasing genetic diversity indicating that random genetic drift occurred in the studied populations. Quantitative and molecular genetic variations were correlated, and their differentiation (Q ST vs. F ST) among S. granulata populations was similar, suggesting that mainly random processes have shaped the quantitative genetic differentiation among populations. However, pairwise quantitative genetic distances increased with geographic and climatic distances, even when adjusted for molecular genetic distances, indicating diversifying selection. Our results indicate that long-lived clonal species may be buffered at least temporarily against the negative effects of fragmentation. The relationship between quantitative genetic and geographic distance may be a more sensitive indicator of selection than Q ST-F ST differences.
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Affiliation(s)
- Tania J. Walisch
- Musée National d'Histoire NaturelleLuxembourg CityLuxembourg
- Department of BiologyPhilipps‐Universität MarburgMarburgGermany
| | - Guy Colling
- Musée National d'Histoire NaturelleLuxembourg CityLuxembourg
| | - Sylvie Hermant
- Musée National d'Histoire NaturelleLuxembourg CityLuxembourg
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4
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Climate-Driven Adaptive Differentiation in Melia azedarach: Evidence from a Common Garden Experiment. Genes (Basel) 2022; 13:genes13111924. [DOI: 10.3390/genes13111924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/10/2022] [Accepted: 10/19/2022] [Indexed: 11/04/2022] Open
Abstract
Studies of local adaptation in populations of chinaberry (Melia azedarach L.) are important for clarifying patterns in the population differentiation of this species across its natural range. M. azedarach is an economically important timber species, and its phenotype is highly variable across its range in China. Here, we collected M. azedarach seeds from 31 populations across its range and conducted a common garden experiment. We studied patterns of genetic differentiation among populations using molecular markers (simple sequence repeats) and data on phenotypic variation in six traits collected over five years. Our sampled populations could be subdivided into two groups based on genetic analyses, as well as patterns of isolation by distance and isolation by environment. Significant differentiation in growth traits was observed among provenances and families within provenances. Geographic distance was significantly correlated with the quantitative genetic differentiation (QST) in height (HEIT) and crown breadth. Climate factors were significantly correlated with the QST for each trait. A total of 23 climatic factors were examined. There was a significant effect of temperature on all traits, and minimum relative humidity had a significant effect on the survival rate over four years. By comparing the neutral genetic differentiation (FST) with the QST, the mode of selection acting on survival rate varied, whereas HEIT and the straightness of the main trunk were subject to the same mode of selection. The variation in survival rate was consistent with the variation in genetic differentiation among populations, which was indicative of local adaptation. Overall, our findings provide new insights into the responses of the phenological traits of M. azedarach to changes in the climate conditions of China.
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5
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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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6
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Spatiotemporal Variation in Gross Primary Productivity and Their Responses to Climate in the Great Lakes Region of Sub-Saharan Africa during 2001–2020. SUSTAINABILITY 2022. [DOI: 10.3390/su14052610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The impacts of climate on spatiotemporal variations of eco-physiological and bio-physical factors have been widely explored in previous research, especially in dry areas. However, the understanding of gross primary productivity (GPP) variations and its interactions with climate in humid and semi-humid areas remains unclear. Based on hyperspectral satellite remotely sensed vegetation phenology processes and related indices and the re-analysed climate datasets, we investigated the seasonal and inter-annual variability of GPP by using different light-use efficiency (LUE) models including the Carnegie-Ames-Stanford Approaches (CASA) model, vegetation photosynthesis models (VPMChl and VPMCanopy) and Moderate Resolution Imaging Spectroradiometer (MODIS) GPP products (MOD17A2H) during 2001–2020 over the Great Lakes region of Sub-Saharan Africa (GLR-SSA). The models’ validation against the in situ GPP-based upscaled observations (GPP-EC) indicated that these three models can explain 82%, 79% and 80% of GPP variations with root mean square error (RMSE) values of 5.7, 8.82 and 10.12 g C·m−2·yr−1, respectively. The spatiotemporal variations of GPP showed that the GLR-SSA experienced: (i) high GPP values during December-May; (ii) high annual GPP increase during 2002–2003, 2011–2013 and 2015–2016 and annual decreasing with a marked alternation in other years; (iii) evergreen broadleaf forests having the highest GPP values while grasslands and croplands showing lower GPP values. The spatial correlation between GPP and climate factors indicated 60% relative correlation between precipitation and GPP and 65% correction between surface air temperature and GPP. The results also showed high GPP values under wet conditions (in rainy seasons and humid areas) that significantly fell by the rise of dry conditions (in long dry season and arid areas). Therefore, these results showed that climate factors have potential impact on GPP variability in this region. However, these findings may provide a better understanding of climate implications on GPP variability in the GLR-SSA and other tropical climate zones.
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7
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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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Valencia-Montoya WA, Flaven E, Pouzadoux J, Imbert E, Cheptou PO. Rapid divergent evolution of an annual plant across a latitudinal gradient revealed by seed resurrection. Evolution 2021; 75:2759-2772. [PMID: 34558662 DOI: 10.1111/evo.14364] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 08/05/2021] [Accepted: 08/13/2021] [Indexed: 11/29/2022]
Abstract
Global change is expected to drive short-term evolution of natural populations. However, it remains unclear whether different populations are changing in unison. Here, we study contemporary evolution of growth-related and reproductive traits of three populations of Cyanus segetum facing warming and pollinator decline across a latitudinal gradient in France. We resurrected stored seeds sampled up to 24 years apart from northern, central-western, and southern populations and conducted an in situ common-garden experiment. To disentangle neutral from selection-driven differentiation, we calculated neutral genetic differentiation (FST ) and quantitative trait differentiation (QST ) between temporal samples. We found that phenotypic evolution was divergent across populations exhibiting different trends for rosette size, date of flowering, and capitula size. By measuring seed set as a proxy of fitness, we showed that samples with larger mean capitula size outperformed samples with smaller mean capitula size in the western and southern populations. Regression of traits on seed set showed that flowering date and capitula size are the primary determinants of fitness, and QST -FST comparisons indicated that natural selection has likely contributed to the shifts in flowering phenology and rosette size. These findings outline the potential for rescue of natural populations through contemporary evolution and emphasize the complex interplay between spatial and temporal variation in species' responses to global change.
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Affiliation(s)
- Wendy A Valencia-Montoya
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valery Montpellier, EPHE, Montpellier, 34090, France.,Current Address: Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, 02138
| | - Elodie Flaven
- ISEM, University of Montpellier, Montpellier, 34000, France
| | | | - Eric Imbert
- ISEM, University of Montpellier, Montpellier, 34000, France
| | - Pierre-Olivier Cheptou
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valery Montpellier, EPHE, Montpellier, 34090, France
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9
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Govaert L, De Meester L, Rousseaux S, Declerck SAJ, Pantel JH. Measuring the contribution of evolution to community trait structure in freshwater zooplankton. OIKOS 2021. [DOI: 10.1111/oik.07885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Lynn Govaert
- Leibniz Inst. für Gewässerökologie und Binnenfischerei (IGB) Berlin Germany
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven Leuven Belgium
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Zurich Switzerland
- Swiss Federal Inst. of Aquatic Science and Technology, Dept of Aquatic Ecology Dübendorf Switzerland
- URPP Global Change and Biodiversity, Univ. of Zurich Zurich Switzerland
| | - Luc De Meester
- Leibniz Inst. für Gewässerökologie und Binnenfischerei (IGB) Berlin Germany
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven Leuven Belgium
- Inst. of Biology, Freie Univ. Berlin Berlin Germany
| | - Sarah Rousseaux
- Leibniz Inst. für Gewässerökologie und Binnenfischerei (IGB) Berlin Germany
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven Leuven Belgium
- Natuurinvest, Maatschappelijke zetel Brussel, Herman Teirlinckgebouw Brussel Belgium
| | - Steven A. J. Declerck
- Leibniz Inst. für Gewässerökologie und Binnenfischerei (IGB) Berlin Germany
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven Leuven Belgium
- Dept of Aquatic Ecology, Netherlands Inst. of Ecology (NIOO‐KNAW) Wageningen the Netherlands
| | - Jelena H. Pantel
- Leibniz Inst. für Gewässerökologie und Binnenfischerei (IGB) Berlin Germany
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven Leuven Belgium
- Dept of Computer Science, Mathematics and Environmental Science, The American Univ. of Paris Paris France
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10
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Inoue K, Inoue Y, Oe T, Nishimura M. Genomic imprinting variances of beef carcass traits and physiochemical characteristics in Japanese Black cattle. Anim Sci J 2021; 92:e13504. [PMID: 33458906 DOI: 10.1111/asj.13504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/26/2020] [Accepted: 12/17/2020] [Indexed: 01/15/2023]
Abstract
The objective of this study was to estimate variance components related to imprinting for carcass traits and physiochemical characteristics in Japanese Black cattle. The carcass records obtained from 4,220 Japanese Black feedlot cattle included carcass weight (CW), rib eye area (REA), rib thickness, subcutaneous fat thickness, and beef marbling score (BMS), and the physiochemical characteristics were fat, moisture, glycogen per proportion of moisture content, oleic acid, and monounsaturated fatty acids (MUFA). To detect gametic effects, an imprinting model was fitted. High additive heritabilities were estimated for all traits (from 0.516 for glycogen to 0.853 for fat) and were reduced in Mendelian heritability. The range of the differences was from 0.002 (CW) to 0.331 (fat and moisture), and the reductions were due to their imprinting variances. The ratio of the imprinting variance to the total additive genetic variance for REA (0.374), BMS (0.291), fat (0.387), moisture (0.388), and MUFA (0.337) were large (p < 0.05). These imprinting variances were due to the maternal contribution and suggested the existence of maternally expressed genomic imprinting effects on the traits in Japanese Black cattle. Therefore, maternal gametic effects should be considered in breeding programs for Japanese Black cattle.
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Affiliation(s)
- Keiichi Inoue
- National Livestock Breeding Center, Nishigo, Fukushima, Japan
| | - Yoshinobu Inoue
- Tottori Prefectural Livestock Research Center, Kotoura, Tottori, Japan
| | - Toshiaki Oe
- Tottori Prefecture Department of Agriculture, Forestry and Fishery Agricultural Advancement Strategy Administration Livestock Division, Tottori, Tottori, Japan
| | - Masami Nishimura
- Tottori Prefectural Livestock Research Center, Kotoura, Tottori, Japan
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11
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Abstract
Distinguishing which traits have evolved under natural selection, as opposed to neutral evolution, is a major goal of evolutionary biology. Several tests have been proposed to accomplish this, but these either rely on false assumptions or suffer from low power. Here, I introduce an approach to detecting selection that makes minimal assumptions and only requires phenotypic data from ∼10 individuals. The test compares the phenotypic difference between two populations to what would be expected by chance under neutral evolution, which can be estimated from the phenotypic distribution of an F2 cross between those populations. Simulations show that the test is robust to variation in the number of loci affecting the trait, the distribution of locus effect sizes, heritability, dominance, and epistasis. Comparing its performance to the QTL sign test-an existing test of selection that requires both genotype and phenotype data-the new test achieves comparable power with 50- to 100-fold fewer individuals (and no genotype data). Applying the test to empirical data spanning over a century shows strong directional selection in many crops, as well as on naturally selected traits such as head shape in Hawaiian Drosophila and skin color in humans. Applied to gene expression data, the test reveals that the strength of stabilizing selection acting on mRNA levels in a species is strongly associated with that species' effective population size. In sum, this test is applicable to phenotypic data from almost any genetic cross, allowing selection to be detected more easily and powerfully than previously possible.
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Affiliation(s)
- Hunter B Fraser
- Department of Biology, Stanford University, Stanford, CA 94305
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12
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Marin S, Gibert A, Archambeau J, Bonhomme V, Lascoste M, Pujol B. Potential adaptive divergence between subspecies and populations of snapdragon plants inferred from Q ST -F ST comparisons. Mol Ecol 2020; 29:3010-3021. [PMID: 32652730 PMCID: PMC7540467 DOI: 10.1111/mec.15546] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 11/30/2022]
Abstract
Phenotypic divergence among natural populations can be explained by natural selection or by neutral processes such as drift. Many examples in the literature compare putatively neutral (FST ) and quantitative genetic (QST ) differentiation in multiple populations to assess their evolutionary signature and identify candidate traits involved with local adaptation. Investigating these signatures in closely related or recently diversified species has the potential to shed light on the divergence processes acting at the interspecific level. Here, we conducted this comparison in two subspecies of snapdragon plants (eight populations of Antirrhinum majus pseudomajus and five populations of A. m. striatum) in a common garden experiment. We also tested whether altitude was involved with population phenotypic divergence. Our results identified candidate phenological and morphological traits involved with local adaptation. Most of these traits were identified in one subspecies but not the other. Phenotypic divergence increased with altitude for a few biomass-related traits, but only in A. m. striatum. These traits therefore potentially reflect A. m. striatum adaptation to altitude. Our findings imply that adaptive processes potentially differ at the scale of A. majus subspecies.
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Affiliation(s)
- Sara Marin
- PSL Université Paris, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France.,Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse Midi-Pyrénées, CNRS, Toulouse, France
| | - Anaïs Gibert
- PSL Université Paris, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | | | - Vincent Bonhomme
- Institut des Sciences de l'Évolution (ISEM), Montpellier Cedex, France
| | - Mylène Lascoste
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse Midi-Pyrénées, CNRS, Toulouse, France
| | - Benoit Pujol
- PSL Université Paris, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France.,Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse Midi-Pyrénées, CNRS, Toulouse, France
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13
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Li Z, Löytynoja A, Fraimout A, Merilä J. Effects of marker type and filtering criteria on Q ST- F ST comparisons. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190666. [PMID: 31827824 PMCID: PMC6894560 DOI: 10.1098/rsos.190666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 09/16/2019] [Indexed: 06/10/2023]
Abstract
Comparative studies of quantitative and neutral genetic differentiation (Q ST-F ST tests) provide means to detect adaptive population differentiation. However, Q ST-F ST tests can be overly liberal if the markers used deflate F ST below its expectation, or overly conservative if methodological biases lead to inflated F ST estimates. We investigated how marker type and filtering criteria for marker selection influence Q ST-F ST comparisons through their effects on F ST using simulations and empirical data on over 18 000 in silico genotyped microsatellites and 3.8 million single-locus polymorphism (SNP) loci from four populations of nine-spined sticklebacks (Pungitius pungitius). Empirical and simulated data revealed that F ST decreased with increasing marker variability, and was generally higher with SNPs than with microsatellites. The estimated baseline F ST levels were also sensitive to filtering criteria for SNPs: both minor alleles and linkage disequilibrium (LD) pruning influenced F ST estimation, as did marker ascertainment. However, in the case of stickleback data used here where Q ST is high, the choice of marker type, their genomic location, ascertainment and filtering made little difference to outcomes of Q ST-F ST tests. Nevertheless, we recommend that Q ST-F ST tests using microsatellites should discard the most variable loci, and those using SNPs should pay attention to marker ascertainment and properly account for LD before filtering SNPs. This may be especially important when level of quantitative trait differentiation is low and levels of neutral differentiation high.
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Affiliation(s)
- Zitong Li
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki 00014, Finland
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Antoine Fraimout
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki 00014, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki 00014, Finland
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14
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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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15
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Dávalos LM, Lancaster WC, Núñez-Novas MS, León YM, Lei B, Flanders J, Russell AL. A coalescent-based estimator of genetic drift, and acoustic divergence in the Pteronotus parnellii species complex. Heredity (Edinb) 2019; 122:417-427. [PMID: 30120366 PMCID: PMC6460761 DOI: 10.1038/s41437-018-0129-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/04/2018] [Accepted: 07/06/2018] [Indexed: 01/12/2023] Open
Abstract
Determining the processes responsible for phenotypic variation is one of the central tasks of evolutionary biology. While the importance of acoustic traits for foraging and communication in echolocating mammals suggests adaptation, the seldom-tested null hypothesis to explain trait divergence is genetic drift. Here we derive FST values from multi-locus coalescent isolation-with-migration models, and couple them with estimates of quantitative trait divergence, or PST, to test drift as the evolutionary process responsible for phenotypic divergence in island populations of the Pteronotus parnellii species complex. Compared to traditional comparisons of PST to FST, the migration-based estimates of FST are unidirectional instead of bidirectional, simultaneously integrate variation among loci and individuals, and posterior densities of PST and FST can be compared directly. We found the evolution of higher call frequencies is inconsistent with genetic drift for the Hispaniolan population, despite many generations of isolation from its Puerto Rican counterpart. While the Hispaniolan population displays dimorphism in call frequencies, the higher frequency of the females is incompatible with sexual selection. Instead, cultural drift toward higher frequencies among Hispaniolan females might explain the divergence. By integrating Bayesian coalescent and trait analyses, this study demonstrates a powerful approach to testing genetic drift as the default evolutionary mechanism of trait differentiation between populations.
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Affiliation(s)
- Liliana M Dávalos
- Department of Ecology and Evolution and Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Winston C Lancaster
- Department of Biological Sciences, California State University, Sacramento, CA, 95819, USA
- Department of Biology, University of Alabama, Birmingham, AL, 35294, USA
| | - Miguel S Núñez-Novas
- Museo Nacional de Historia Natural Profesor Eugenio De Jesús Marcano. César Nicolás Penson Street esq. Máximo Gómez, Plaza de la Cultura, Santo Domingo, Dominican Republic
| | - Yolanda M León
- Instituto Tecnológico de Santo Domingo y Grupo Jaragua, Santo Domingo, Dominican Republic
| | - Bonnie Lei
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Microsoft, One Microsoft Way, Redmond, WA, 98052, USA
| | - Jon Flanders
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
- Bat Conservation International, 500 North Capital of Texas Highway, Austin, TX, 78746, USA
| | - Amy L Russell
- Department of Biology, Grand Valley State University, Allendale, MI, 49401, USA.
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16
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Marshall MM, Batten LC, Remington DL, Lacey EP. Natural selection contributes to geographic patterns of thermal plasticity in Plantago lanceolata. Ecol Evol 2019; 9:2945-2963. [PMID: 30891228 PMCID: PMC6405498 DOI: 10.1002/ece3.4977] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 01/09/2019] [Accepted: 01/17/2019] [Indexed: 01/01/2023] Open
Abstract
A long-standing debate in evolutionary biology concerns the relative importance of different evolutionary forces in explaining phenotypic diversification at large geographic scales. For example, natural selection is typically assumed to underlie divergence along environmental gradients. However, neutral evolutionary processes can produce similar patterns. We collected molecular genetic data from 14 European populations of Plantago lanceolata to test the contributions of natural selection versus neutral evolution to population divergence in temperature-sensitive phenotypic plasticity of floral reflectance. In P. lanceolata, reflectance plasticity is positively correlated with latitude/altitude. We used population pairwise comparisons between neutral genetic differentiation (F ST and Jost's D) and phenotypic differentiation (P ST) to assess the contributions of geographic distance and environmental parameters of the reproductive season in driving population divergence. Data are consistent with selection having shaped large-scale geographic patterns in thermal plasticity. The aggregate pattern of P ST versus F ST was consistent with divergent selection. F ST explained thermal plasticity differences only when geographic distance was not included in the model. Differences in the extent of cool reproductive season temperatures, and not overall temperature variation, explained plasticity differences independent of distance. Results are consistent with the hypothesis that thermal plasticity is adaptive where growing seasons are shorter and cooler, that is, at high latitude/altitude.
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Affiliation(s)
- Matthew M. Marshall
- Department of BiologyUniversity of North Carolina at GreensboroGreensboroNorth Carolina
| | - Leslie C. Batten
- Department of BiologyUniversity of North Carolina at GreensboroGreensboroNorth Carolina
| | - David L. Remington
- Department of BiologyUniversity of North Carolina at GreensboroGreensboroNorth Carolina
| | - Elizabeth P. Lacey
- Department of BiologyUniversity of North Carolina at GreensboroGreensboroNorth Carolina
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17
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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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18
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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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19
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Iglesias PP, Soto IM, Soto EM, Calderón L, Hurtado J, Hasson E. Rapid divergence of courtship song in the face of neutral genetic homogeneity in the cactophilic fly Drosophila buzzatii. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Patricia P Iglesias
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Buenos Aires, Argentina
| | - Ignacio M Soto
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Buenos Aires, Argentina
| | - Eduardo M Soto
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Buenos Aires, Argentina
| | - Luciano Calderón
- CONICET-Instituto de Biología Agrícola de Mendoza (IBAM), Mendoza, Argentina
| | - Juan Hurtado
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Buenos Aires, Argentina
| | - Esteban Hasson
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Buenos Aires, Argentina
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20
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Abbott JM, DuBois K, Grosberg RK, Williams SL, Stachowicz JJ. Genetic distance predicts trait differentiation at the subpopulation but not the individual level in eelgrass, Zostera marina. Ecol Evol 2018; 8:7476-7489. [PMID: 30151164 PMCID: PMC6106171 DOI: 10.1002/ece3.4260] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 03/29/2018] [Accepted: 05/15/2018] [Indexed: 11/08/2022] Open
Abstract
Ecological studies often assume that genetically similar individuals will be more similar in phenotypic traits, such that genetic diversity can serve as a proxy for trait diversity. Here, we explicitly test the relationship between genetic relatedness and trait distance using 40 eelgrass (Zostera marina) genotypes from five sites within Bodega Harbor, CA. We measured traits related to nutrient uptake, morphology, biomass and growth, photosynthesis, and chemical deterrents for all genotypes. We used these trait measurements to calculate a multivariate pairwise trait distance for all possible genotype combinations. We then estimated pairwise relatedness from 11 microsatellite markers. We found significant trait variation among genotypes for nearly every measured trait; however, there was no evidence of a significant correlation between pairwise genetic relatedness and multivariate trait distance among individuals. However, at the subpopulation level (sites within a harbor), genetic (FST) and trait differentiation were positively correlated. Our work suggests that pairwise relatedness estimated from neutral marker loci is a poor proxy for trait differentiation between individual genotypes. It remains to be seen whether genomewide measures of genetic differentiation or easily measured "master" traits (like body size) might provide good predictions of overall trait differentiation.
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Affiliation(s)
- Jessica M. Abbott
- Center for Population BiologyUniversity of CaliforniaDavisCalifornia
- Department of Evolution and EcologyUniversity of CaliforniaDavisCalifornia
- Institute for Wildlife StudiesArcataCalifornia
| | - Katherine DuBois
- Department of Evolution and EcologyUniversity of CaliforniaDavisCalifornia
- Bodega Marine LaboratoryBodega BayCalifornia
| | - Richard K. Grosberg
- Center for Population BiologyUniversity of CaliforniaDavisCalifornia
- Department of Evolution and EcologyUniversity of CaliforniaDavisCalifornia
| | - Susan L. Williams
- Department of Evolution and EcologyUniversity of CaliforniaDavisCalifornia
- Bodega Marine LaboratoryBodega BayCalifornia
| | - John J. Stachowicz
- Center for Population BiologyUniversity of CaliforniaDavisCalifornia
- Department of Evolution and EcologyUniversity of CaliforniaDavisCalifornia
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21
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Josephs EB. Determining the evolutionary forces shaping G × E. THE NEW PHYTOLOGIST 2018; 219:31-36. [PMID: 29574919 DOI: 10.1111/nph.15103] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 02/09/2018] [Indexed: 06/08/2023]
Abstract
Contents Summary 31 I. Introduction 31 II. The maintenance of genetic variation for plasticity 32 III. Why is there environmental variation for genetic effects? 33 IV. Conclusions 35 Acknowledgements 35 References 35 SUMMARY: Phenotypic plasticity is common in nature, yet we lack a comprehensive understanding of the evolutionary forces that shape genetic variation for plasticity. This endeavor is especially important because variation for plasticity will result in genotype-by-environment interactions (G × E), a crucial component of variation in quantitative traits. Here, I review our understanding of the evolutionary forces shaping G × E, focusing specifically on: what evolutionary forces maintain variation for plasticity; and what forces maintain different genetic architectures across environments. My specific goal is to show that genomic data can be leveraged to explain the maintenance of G × E by contrasting patterns of genetic variation for plasticity with neutral expectations.
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Affiliation(s)
- Emily B Josephs
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
- Center for Population Biology, University of California, Davis, CA, 95616, USA
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22
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Dubuc-Messier G, Caro SP, Perrier C, van Oers K, Réale D, Charmantier A. Gene flow does not prevent personality and morphological differentiation between two blue tit populations. J Evol Biol 2018; 31:1127-1137. [PMID: 29791058 DOI: 10.1111/jeb.13291] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 05/02/2018] [Accepted: 05/13/2018] [Indexed: 11/28/2022]
Abstract
Understanding the causes and consequences of population phenotypic divergence is a central goal in ecology and evolution. Phenotypic divergence among populations can result from genetic divergence, phenotypic plasticity or a combination of the two. However, few studies have deciphered these mechanisms for populations geographically close and connected by gene flow, especially in the case of personality traits. In this study, we used a common garden experiment to explore the genetic basis of the phenotypic divergence observed between two blue tit (Cyanistes caeruleus) populations inhabiting contrasting habitats separated by 25 km, for two personality traits (exploration speed and handling aggression), one physiological trait (heart rate during restraint) and two morphological traits (tarsus length and body mass). Blue tit nestlings were removed from their population and raised in a common garden for up to 5 years. We then compared adult phenotypes between the two populations, as well as trait-specific Qst and Fst . Our results revealed differences between populations similar to those found in the wild, suggesting a genetic divergence for all traits. Qst -Fst comparisons revealed that the trait divergences likely result from dissimilar selection patterns rather than from genetic drift. Our study is one of the first to report a Qst -Fst comparison for personality traits and adds to the growing body of evidence that population genetic divergence is possible at a small scale for a variety of traits including behavioural traits.
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Affiliation(s)
- Gabrielle Dubuc-Messier
- Centre d'Écologie Fonctionnelle et Évolutive, Unité Mixte de Recherche CNRS 5175, Montpellier, France.,Département des sciences biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Samuel P Caro
- Centre d'Écologie Fonctionnelle et Évolutive, Unité Mixte de Recherche CNRS 5175, Montpellier, France.,Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Charles Perrier
- Centre d'Écologie Fonctionnelle et Évolutive, Unité Mixte de Recherche CNRS 5175, Montpellier, France
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Denis Réale
- Département des sciences biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Anne Charmantier
- Centre d'Écologie Fonctionnelle et Évolutive, Unité Mixte de Recherche CNRS 5175, Montpellier, France.,Département des sciences biologiques, Université du Québec à Montréal, Montréal, QC, Canada
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23
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Hämälä T, Mattila TM, Savolainen O. Local adaptation and ecological differentiation under selection, migration, and drift in Arabidopsis lyrata. Evolution 2018; 72:1373-1386. [PMID: 29741234 DOI: 10.1111/evo.13502] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/03/2018] [Indexed: 12/19/2022]
Abstract
How the balance between selection, migration, and drift influences the evolution of local adaptation has been under intense theoretical scrutiny. Yet, empirical studies that relate estimates of local adaptation to quantification of gene flow and effective population sizes have been rare. Here, we conducted a reciprocal transplant trial, a common garden trial, and a whole-genome-based demography analysis to examine these effects among Arabidopsis lyrata populations from two altitudinal gradients in Norway. Demography simulations indicated that populations within the two gradients are connected by gene flow (0.1 < 4Ne m < 11) and have small effective population sizes (Ne < 6000), suggesting that both migration and drift can counteract local selection. However, the three-year field experiments showed evidence of local adaptation at the level of hierarchical multiyear fitness, attesting to the strength of differential selection. In the lowland habitat, local superiority was associated with greater fecundity, while viability accounted for fitness differences in the alpine habitat. We also demonstrate that flowering time differentiation has contributed to adaptive divergence between these locally adapted populations. Our results show that despite the estimated potential of gene flow and drift to hinder differentiation, selection among these A. lyrata populations has resulted in local adaptation.
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Affiliation(s)
- Tuomas Hämälä
- Department of Ecology and Genetics, University of Oulu, FI-90014 Oulu, Finland
- Biocenter Oulu, University of Oulu, FI-90014 Oulu, Finland
| | - Tiina M Mattila
- Department of Ecology and Genetics, University of Oulu, FI-90014 Oulu, Finland
| | - Outi Savolainen
- Department of Ecology and Genetics, University of Oulu, FI-90014 Oulu, Finland
- Biocenter Oulu, University of Oulu, FI-90014 Oulu, Finland
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24
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Mäkinen H, Sävilammi T, Papakostas S, Leder E, Vøllestad LA, Primmer CR. Modularity Facilitates Flexible Tuning of Plastic and Evolutionary Gene Expression Responses during Early Divergence. Genome Biol Evol 2018; 10:77-93. [PMID: 29293993 PMCID: PMC5758911 DOI: 10.1093/gbe/evx278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2017] [Indexed: 12/14/2022] Open
Abstract
Gene expression changes have been recognized as important drivers of adaptation to changing environmental conditions. Little is known about the relative roles of plastic and evolutionary responses in complex gene expression networks during the early stages of divergence. Large gene expression data sets coupled with in silico methods for identifying coexpressed modules now enable systems genetics approaches also in nonmodel species for better understanding of gene expression responses during early divergence. Here, we combined gene coexpression analyses with population genetics to separate plastic and population (evolutionary) effects in expression networks using small salmonid populations as a model system. We show that plastic and population effects were highly variable among the six identified modules and that the plastic effects explained larger proportion of the total eigengene expression than population effects. A more detailed analysis of the population effects using a QST - FST comparison across 16,622 annotated transcripts revealed that gene expression followed neutral expectations within modules and at the global level. Furthermore, two modules showed enrichment for genes coding for early developmental traits that have been previously identified as important phenotypic traits in thermal responses in the same model system indicating that coexpression analysis can capture expression patterns underlying ecologically important traits. We suggest that module-specific responses may facilitate the flexible tuning of expression levels to local thermal conditions. Overall, our study indicates that plasticity and neutral evolution are the main drivers of gene expression variance in the early stages of thermal adaptation in this system.
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Affiliation(s)
| | | | | | - Erica Leder
- Department of Biology, University of Turku, Finland
- Natural History Museum, University of Oslo, Norway
| | - Leif A Vøllestad
- Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Craig R Primmer
- Department of Biosciences, University of Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Finland
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25
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Seeholzer GF, Brumfield RT. Isolation by distance, not incipient ecological speciation, explains genetic differentiation in an Andean songbird (Aves: Furnariidae:
Cranioleuca antisiensis,
Line‐cheeked Spinetail) despite near threefold body size change across an environmental gradient. Mol Ecol 2017; 27:279-296. [DOI: 10.1111/mec.14429] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/18/2017] [Accepted: 11/02/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Glenn F. Seeholzer
- Museum of Natural Science and Department of Biological Sciences Louisiana State University Baton Rouge LA USA
| | - Robb T. Brumfield
- Museum of Natural Science and Department of Biological Sciences Louisiana State University Baton Rouge LA USA
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26
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Singh A, Roy S. High altitude population of Arabidopsis thaliana is more plastic and adaptive under common garden than controlled condition. BMC Ecol 2017; 17:39. [PMID: 29237449 PMCID: PMC5729231 DOI: 10.1186/s12898-017-0149-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 12/06/2017] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Population differentiation and their adaptation to a particular environment depend on their ability to respond to a new environment. This, in turn is governed to an extent, by the degree of phenotypic plasticity exhibited by the populations. The populations of same species inhabiting different climatic conditions may differ in their phenotypic plasticity. Himalayan populations of Arabidopsis thaliana originating from a steep altitude are exposed to different climatic conditions ranging from sub-tropical to temperate. Thus they might have experienced different selection pressures during evolution and may respond differently under common environmental condition. RESULTS Phenotypic plasticity and differentiation of natural populations of A. thaliana grown under common garden and controlled conditions were determined. A total of seventeen morphological traits, their plasticity, association between traits and environment were performed using 45 accessions from three populations. Plants from different altitudes differed in phenotypes, their selection and fitness under two conditions. Under both the conditions lower altitude population was characterized by higher leaf count and larger silique than higher and middle altitude population. Flowering time of high altitude population increased while that of low and medium altitude decreased under controlled condition compared to open field. An increase in seed weight and germination was observed for all the population under open field than controlled. Rosette area was under divergent selection in both the condition. The heritability of lower altitude population was the highest under both the conditions, where as it was the least for higher altitude population further indicating that the high altitude populations are more responsive towards phenotypic changes under new environmental conditions. Ninety-nine percent of variability in traits and their plasticity co-varied with the altitude of their origin. The population of high altitude was more plastic and differentiated as compared to the lower altitude one. CONCLUSIONS Arabidopsis thaliana population native to different altitudes of the west Himalaya responds differently when grown under common environments. The success of high altitude population is more in common garden than the controlled conditions. The significant variability in phenotype and its association with altitude of origin predicts for non-random genetic differentiation among the populations.
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Affiliation(s)
- Akanksha Singh
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001 India
| | - Sribash Roy
- Genetics and Molecular Biology Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001 India
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27
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Firmat C, Delzon S, Louvet JM, Parmentier J, Kremer A. Evolutionary dynamics of the leaf phenological cycle in an oak metapopulation along an elevation gradient. J Evol Biol 2017; 30:2116-2131. [PMID: 28977711 DOI: 10.1111/jeb.13185] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 09/20/2017] [Accepted: 09/26/2017] [Indexed: 01/18/2023]
Abstract
It has been predicted that environmental changes will radically alter the selective pressures on phenological traits. Long-lived species, such as trees, will be particularly affected, as they may need to undergo major adaptive change over only one or a few generations. The traits describing the annual life cycle of trees are generally highly evolvable, but nothing is known about the strength of their genetic correlations. Tight correlations can impose strong evolutionary constraints, potentially hampering the adaptation of multivariate phenological phenotypes. In this study, we investigated the evolutionary, genetic and environmental components of the timing of leaf unfolding and senescence within an oak metapopulation along an elevation gradient. Population divergence, estimated from in situ and common-garden data, was compared to expectations under neutral evolution, based on microsatellite markers. This approach made it possible (1) to evaluate the influence of genetic correlation on multivariate local adaptation to elevation and (2) to identify traits probably exposed to past selective pressures due to the colder climate at high elevation. The genetic correlation was positive but very weak, indicating that genetic constraints did not shape the local adaptation pattern for leaf phenology. Both spring and fall (leaf unfolding and senescence, respectively) phenology timings were involved in local adaptation, but leaf unfolding was probably the trait most exposed to climate change-induced selection. Our data indicated that genetic variation makes a much smaller contribution to adaptation than the considerable plastic variation displayed by a tree during its lifetime. The evolutionary potential of leaf phenology is, therefore, probably not the most critical aspect for short-term population survival in a changing climate.
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Affiliation(s)
- C Firmat
- INRA, URP3F, Lusignan, France.,INRA, UMR 1202 BIOGECO, University of Bordeaux, Cestas, France
| | - S Delzon
- INRA, UMR 1202 BIOGECO, University of Bordeaux, Cestas, France
| | - J-M Louvet
- INRA, UMR 1202 BIOGECO, University of Bordeaux, Cestas, France
| | - J Parmentier
- INRA, UE 0393, Unité Expérimentale Arboricole, Centre de Recherche Bordeaux-Aquitaine, Toulenne, France
| | - A Kremer
- INRA, UMR 1202 BIOGECO, University of Bordeaux, Cestas, France
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28
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Michalski SG, Malyshev AV, Kreyling J. Trait variation in response to varying winter temperatures, diversity patterns and signatures of selection along the latitudinal distribution of the widespread grassland plant Arrhenatherum elatius. Ecol Evol 2017; 7:3268-3280. [PMID: 28480024 PMCID: PMC5415536 DOI: 10.1002/ece3.2936] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 01/20/2017] [Accepted: 03/03/2017] [Indexed: 01/17/2023] Open
Abstract
Across Europe, genetic diversity can be expected to decline toward the North because of stochastic and selective effects which may imply diminished phenotypic variation and less potential for future genetic adaptations to environmental change. Understanding such latitudinal patterns can aid provenance selection for breeding or assisted migration approaches. In an experiment simulating different winter temperatures, we assessed quantitative trait variation, genetic diversity, and differentiation for natural populations of the grass Arrhenatherum elatius originating from a large latitudinal gradient. In general, populations from the North grew smaller and had a lower flowering probability. Toward the North, the absolute plastic response to the different winter conditions as well as heritability for biomass production significantly declined. Genetic differentiation in plant height and probability of flowering were very strong and significantly higher than under neutral expectations derived from SNP data, suggesting adaptive differentiation. Differentiation in biomass production did not exceed but mirrored patterns for neutral genetic differentiation, suggesting that migration‐related processes caused the observed clinal trait variation. Our results demonstrate that genetic diversity and trait differentiation patterns for A. elatius along a latitudinal gradient are likely shaped by both local selection and genetic drift.
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Affiliation(s)
- Stefan G Michalski
- Department of Community Ecology (BZF) Helmholtz Centre for Environmental Research UFZ Halle Germany
| | - Andrey V Malyshev
- Institute for Botany and Landscape Ecology Ernst Moritz Arndt University Greifswald Greifswald Germany
| | - Juergen Kreyling
- Institute for Botany and Landscape Ecology Ernst Moritz Arndt University Greifswald Greifswald Germany
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29
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Milano ER, Kenney AM, Juenger TE. Adaptive differentiation in floral traits in the presence of high gene flow in scarlet gilia (
Ipomopsis aggregata
). Mol Ecol 2016; 25:5862-5875. [DOI: 10.1111/mec.13752] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 10/21/2022]
Affiliation(s)
- Elizabeth R. Milano
- Department of Integrative Biology The University of Texas at Austin 1 University Station C0930 Austin TX 78712 USA
| | - Amanda M. Kenney
- Department of Biological Sciences St. Edward's University 3001 S. Congress Ave. Austin TX 78704 USA
| | - Thomas E. Juenger
- Department of Integrative Biology The University of Texas at Austin 1 University Station C0930 Austin TX 78712 USA
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30
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Guo B, Lu D, Liao WB, Merilä J. Genomewide scan for adaptive differentiation along altitudinal gradient in the Andrew's toadBufo andrewsi. Mol Ecol 2016; 25:3884-900. [PMID: 27289071 DOI: 10.1111/mec.13722] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 06/02/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Baocheng Guo
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; P.O. Box 65 Helsinki FI-00014 Finland
| | - Di Lu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education); China West Normal University; Nanchong 637009 China
| | - Wen Bo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education); China West Normal University; Nanchong 637009 China
| | - Juha Merilä
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; P.O. Box 65 Helsinki FI-00014 Finland
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31
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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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32
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Causes and consequences of intra-specific variation in vertebral number. Sci Rep 2016; 6:26372. [PMID: 27210072 PMCID: PMC4876516 DOI: 10.1038/srep26372] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/28/2016] [Indexed: 11/09/2022] Open
Abstract
Intraspecific variation in vertebral number is taxonomically widespread. Much scientific attention has been directed towards understanding patterns of variation in vertebral number among individuals and between populations, particularly across large spatial scales and in structured environments. However, the relative role of genes, plasticity, selection, and drift as drivers of individual variation and population differentiation remains unknown for most systems. Here, we report on patterns, causes and consequences of variation in vertebral number among and within sympatric subpopulations of pike (Esox lucius). Vertebral number differed among subpopulations, and common garden experiments indicated that this reflected genetic differences. A QST-FST comparison suggested that population differences represented local adaptations driven by divergent selection. Associations with fitness traits further indicated that vertebral counts were influenced both by stabilizing and directional selection within populations. Overall, our study enhances the understanding of adaptive variation, which is critical for the maintenance of intraspecific diversity and species conservation.
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33
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Côte J, Roussel JM, Le Cam S, Guillaume F, Evanno G. Adaptive divergence in embryonic thermal plasticity among Atlantic salmon populations. J Evol Biol 2016; 29:1593-601. [PMID: 27177256 DOI: 10.1111/jeb.12896] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 05/02/2016] [Accepted: 05/10/2016] [Indexed: 11/28/2022]
Abstract
In the context of global changes, the long-term viability of populations of endangered ectotherms may depend on their adaptive potential and ability to cope with temperature variations. We measured responses of Atlantic salmon embryos from four populations to temperature variations and used a QST -FST approach to study the adaptive divergence among these populations. Embryos were reared under two experimental conditions: a low temperature regime at 4 °C until eyed-stage and 10 °C until the end of embryonic development and a high temperature regime with a constant temperature of 10 °C throughout embryonic development. Significant variations among populations and population × temperature interactions were observed for embryo survival, incubation time and length. QST was higher than FST in all but one comparison suggesting an important effect of divergent selection. QST was also higher under the high-temperature treatment than at low temperature for length and survival due to a higher variance among populations under the stressful warmer treatment. Interestingly, heritability was lower for survival under high temperature in relation to a lower additive genetic variance under that treatment. Overall, these results reveal an adaptive divergence in thermal plasticity in embryonic life stages of Atlantic salmon suggesting that salmon populations may differentially respond to temperature variations induced by climate change. These results also suggest that changes in temperature may alter not only the adaptive potential of natural populations but also the selection regimes among them.
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Affiliation(s)
- J Côte
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, Rennes, France.,Agrocampus Ouest, UMR ESE, Rennes, France.,UMR 5174 EDB (Laboratoire Evolution et Diversité Biologique), CNRS, Université Toulouse III Paul Sabatier, Toulouse, France
| | - J-M Roussel
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, Rennes, France.,Agrocampus Ouest, UMR ESE, Rennes, France
| | - S Le Cam
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, Rennes, France.,Agrocampus Ouest, UMR ESE, Rennes, France
| | - F Guillaume
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - G Evanno
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, Rennes, France.,Agrocampus Ouest, UMR ESE, Rennes, France
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34
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Bertrand JAM, Delahaie B, Bourgeois YXC, Duval T, García-Jiménez R, Cornuault J, Pujol B, Thébaud C, Milá B. The role of selection and historical factors in driving population differentiation along an elevational gradient in an island bird. J Evol Biol 2016; 29:824-36. [DOI: 10.1111/jeb.12829] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 01/10/2016] [Indexed: 01/31/2023]
Affiliation(s)
- J. A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique; UMR 5174; Université Paul Sabatier; Toulouse 3 - Centre National de la Recherche Scientifique (CNRS) - École Nationale de Formation Agronomique (ENFA); Toulouse Cedex 9 France
| | - B. Delahaie
- Laboratoire Évolution et Diversité Biologique; UMR 5174; Université Paul Sabatier; Toulouse 3 - Centre National de la Recherche Scientifique (CNRS) - École Nationale de Formation Agronomique (ENFA); Toulouse Cedex 9 France
| | - Y. X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique; UMR 5174; Université Paul Sabatier; Toulouse 3 - Centre National de la Recherche Scientifique (CNRS) - École Nationale de Formation Agronomique (ENFA); Toulouse Cedex 9 France
| | - T. Duval
- Hémisphères; Poindimié New Caledonia
| | - R. García-Jiménez
- National Museum of Natural Sciences; Spanish National Research Council (CSIC); Madrid Spain
| | - J. Cornuault
- Laboratoire Évolution et Diversité Biologique; UMR 5174; Université Paul Sabatier; Toulouse 3 - Centre National de la Recherche Scientifique (CNRS) - École Nationale de Formation Agronomique (ENFA); Toulouse Cedex 9 France
| | - B. Pujol
- Laboratoire Évolution et Diversité Biologique; UMR 5174; Université Paul Sabatier; Toulouse 3 - Centre National de la Recherche Scientifique (CNRS) - École Nationale de Formation Agronomique (ENFA); Toulouse Cedex 9 France
| | - C. Thébaud
- Laboratoire Évolution et Diversité Biologique; UMR 5174; Université Paul Sabatier; Toulouse 3 - Centre National de la Recherche Scientifique (CNRS) - École Nationale de Formation Agronomique (ENFA); Toulouse Cedex 9 France
| | - B. Milá
- National Museum of Natural Sciences; Spanish National Research Council (CSIC); Madrid Spain
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35
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Howell PE, Lundrigan B, Scribner KT. Environmental and genealogical effects on emergence of cranial morphometric variability in reintroduced American martens. J Mammal 2016. [DOI: 10.1093/jmammal/gyw008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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36
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Monceau K. The next meeting for animal personality: population genetics. ETHOL ECOL EVOL 2015. [DOI: 10.1080/03949370.2014.984345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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37
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Wood JLA, Tezel D, Joyal D, Fraser DJ. Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish. Evolution 2015. [PMID: 26207947 DOI: 10.1111/evo.12733] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
How population size influences quantitative genetic variation and differentiation among natural, fragmented populations remains unresolved. Small, isolated populations might occupy poor quality habitats and lose genetic variation more rapidly due to genetic drift than large populations. Genetic drift might furthermore overcome selection as population size decreases. Collectively, this might result in directional changes in additive genetic variation (VA ) and trait differentiation (QST ) from small to large population size. Alternatively, small populations might exhibit larger variation in VA and QST if habitat fragmentation increases variability in habitat types. We explored these alternatives by investigating VA and QST using nine fragmented populations of brook trout varying 50-fold in census size N (179-8416) and 10-fold in effective number of breeders, Nb (18-135). Across 15 traits, no evidence was found for consistent differences in VA and QST with population size and almost no evidence for increased variability of VA or QST estimates at small population size. This suggests that (i) small populations of some species may retain adaptive potential according to commonly adopted quantitative genetic measures and (ii) populations of varying sizes experience a variety of environmental conditions in nature, however extremely large studies are likely required before any firm conclusions can be made.
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Affiliation(s)
- Jacquelyn L A Wood
- Department of Biology, Concordia University, Montreal, QC, H4B 2E5, Canada. .,Group for interuniversity research in limnology and aquatic environment (GRIL), Université du Québec à Trois-Rivières, Trois-Rivières, QC, G9A 5H7, Canada.
| | - Defne Tezel
- Department of Biology, Concordia University, Montreal, QC, H4B 2E5, Canada
| | - Destin Joyal
- Department of Biology, Concordia University, Montreal, QC, H4B 2E5, Canada
| | - Dylan J Fraser
- Department of Biology, Concordia University, Montreal, QC, H4B 2E5, Canada.,Group for interuniversity research in limnology and aquatic environment (GRIL), Université du Québec à Trois-Rivières, Trois-Rivières, QC, G9A 5H7, Canada
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38
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Walisch TJ, Colling G, Bodenseh M, Matthies D. Divergent selection along climatic gradients in a rare central European endemic species, Saxifraga sponhemica. ANNALS OF BOTANY 2015; 115:1177-90. [PMID: 25862244 PMCID: PMC4648456 DOI: 10.1093/aob/mcv040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/31/2014] [Accepted: 03/02/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS The effects of habitat fragmentation on quantitative genetic variation in plant populations are still poorly known. Saxifraga sponhemica is a rare endemic of Central Europe with a disjunct distribution, and a stable and specialized habitat of treeless screes and cliffs. This study therefore used S. sponhemica as a model species to compare quantitative and molecular variation in order to explore (1) the relative importance of drift and selection in shaping the distribution of quantitative genetic variation along climatic gradients; (2) the relationship between plant fitness, quantitative genetic variation, molecular genetic variation and population size; and (3) the relationship between the differentiation of a trait among populations and its evolvability. METHODS Genetic variation within and among 22 populations from the whole distribution area of S. sponhemica was studied using RAPD (random amplified polymorphic DNA) markers, and climatic variables were obtained for each site. Seeds were collected from each population and germinated, and seedlings were transplanted into a common garden for determination of variation in plant traits. KEY RESULTS In contrast to previous results from rare plant species, strong evidence was found for divergent selection. Most population trait means of S. sponhemica were significantly related to climate gradients, indicating adaptation. Quantitative genetic differentiation increased with geographical distance, even when neutral molecular divergence was controlled for, and QST exceeded FST for some traits. The evolvability of traits was negatively correlated with the degree of differentiation among populations (QST), i.e. traits under strong selection showed little genetic variation within populations. The evolutionary potential of a population was not related to its size, the performance of the population or its neutral genetic diversity. However, performance in the common garden was lower for plants from populations with reduced molecular genetic variation, suggesting inbreeding depression due to genetic erosion. CONCLUSIONS The findings suggest that studies of molecular and quantitative genetic variation may provide complementary insights important for the conservation of rare species. The strong differentiation of quantitative traits among populations shows that selection can be an important force for structuring variation in evolutionarily important traits even for rare endemic species restricted to very specific habitats.
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Affiliation(s)
- Tania J Walisch
- Musée national d'histoire naturelle, Service biologie des populations et évolution, 25 rue Munster L-2160 Luxembourg, Pflanzenökologie, Fachbereich Biologie, Philipps-Universität Marburg, D-35032 Marburg, Germany and Fondation Faune-Flore, 24 rue Muünster, L-2160 Luxembourg Musée national d'histoire naturelle, Service biologie des populations et évolution, 25 rue Munster L-2160 Luxembourg, Pflanzenökologie, Fachbereich Biologie, Philipps-Universität Marburg, D-35032 Marburg, Germany and Fondation Faune-Flore, 24 rue Muünster, L-2160 Luxembourg Musée national d'histoire naturelle, Service biologie des populations et évolution, 25 rue Munster L-2160 Luxembourg, Pflanzenökologie, Fachbereich Biologie, Philipps-Universität Marburg, D-35032 Marburg, Germany and Fondation Faune-Flore, 24 rue Muünster, L-2160 Luxembourg
| | - Guy Colling
- Musée national d'histoire naturelle, Service biologie des populations et évolution, 25 rue Munster L-2160 Luxembourg, Pflanzenökologie, Fachbereich Biologie, Philipps-Universität Marburg, D-35032 Marburg, Germany and Fondation Faune-Flore, 24 rue Muünster, L-2160 Luxembourg
| | - Melanie Bodenseh
- Musée national d'histoire naturelle, Service biologie des populations et évolution, 25 rue Munster L-2160 Luxembourg, Pflanzenökologie, Fachbereich Biologie, Philipps-Universität Marburg, D-35032 Marburg, Germany and Fondation Faune-Flore, 24 rue Muünster, L-2160 Luxembourg
| | - Diethart Matthies
- Musée national d'histoire naturelle, Service biologie des populations et évolution, 25 rue Munster L-2160 Luxembourg, Pflanzenökologie, Fachbereich Biologie, Philipps-Universität Marburg, D-35032 Marburg, Germany and Fondation Faune-Flore, 24 rue Muünster, L-2160 Luxembourg
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39
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Ozerov MY, Himberg M, Aykanat T, Sendek DS, Hägerstrand H, Verliin A, Krause T, Olsson J, Primmer CR, Vasemägi A. Generation of a neutral F
ST
baseline for testing local adaptation on gill raker number within and between European whitefish ecotypes in the Baltic Sea basin. J Evol Biol 2015; 28:1170-83. [DOI: 10.1111/jeb.12645] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 01/17/2023]
Affiliation(s)
- M. Y. Ozerov
- Department of Biology; University of Turku; Turku Finland
| | - M. Himberg
- Faculty of Science and Engineering; Åbo Akademi University; Turku Finland
| | - T. Aykanat
- Department of Biology; University of Turku; Turku Finland
| | - D. S. Sendek
- State Research Institute on Lake and River Fisheries (GosNIORKh); St. Petersburg Russia
| | - H. Hägerstrand
- Faculty of Science and Engineering; Åbo Akademi University; Turku Finland
| | - A. Verliin
- Estonian Marine Institute; University of Tartu; Tartu Estonia
| | - T. Krause
- Institute of Agricultural and Environmental Sciences; Estonian University of Life Sciences; Tartu Estonia
| | - J. Olsson
- Department of Aquatic Resources; Institute for Coastal Research; Swedish University of Agricultural Sciences; Öregrund Sweden
| | - C. R. Primmer
- Department of Biology; University of Turku; Turku Finland
| | - A. Vasemägi
- Department of Biology; University of Turku; Turku Finland
- Institute of Agricultural and Environmental Sciences; Estonian University of Life Sciences; Tartu Estonia
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40
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Tibblin P, Forsman A, Koch-Schmidt P, Nordahl O, Johannessen P, Nilsson J, Larsson P. Evolutionary divergence of adult body size and juvenile growth in sympatric subpopulations of a top predator in aquatic ecosystems. Am Nat 2015; 186:98-110. [PMID: 26098342 DOI: 10.1086/681597] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Evolutionary theory predicts that different selective regimes may contribute to divergent evolution of body size and growth rate among populations, but most studies have focused on allopatric populations. Here, we studied five sympatric subpopulations of anadromous northern pike (Esox lucius) in the Baltic Sea subjected to allopatric habitats for a short period of their life cycle due to homing behavior. We report differences in adult body size among subpopulations that were in part due to variation in growth rate. Body size of emigrating juveniles also differed among subpopulations, and differences remained when individuals were reared in a common environment, thus indicating evolutionary divergence among subpopulations. Furthermore, a QST-FST comparison indicated that differences had evolved due to divergent selection rather than genetic drift, possibly in response to differences in selective mortality among spawning habitats during the allopatric life stage. Adult and juvenile size were negatively correlated across subpopulations, and reconstruction of growth trajectories of adult fishes suggested that body size differences developed gradually and became accentuated throughout the first years of life. These results represent rare evidence that sympatric subpopulations can evolve differences in key life-history traits despite being subjected to allopatric habitats during only a very short fraction of their life.
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Affiliation(s)
- Petter Tibblin
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, SE-391 82 Kalmar, Sweden
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41
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Barley AJ, Monnahan PJ, Thomson RC, Grismer LL, Brown RM. Sun skink landscape genomics: assessing the roles of micro-evolutionary processes in shaping genetic and phenotypic diversity across a heterogeneous and fragmented landscape. Mol Ecol 2015; 24:1696-712. [DOI: 10.1111/mec.13151] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 02/27/2015] [Accepted: 03/10/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Anthony J. Barley
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045 USA
| | - Patrick J. Monnahan
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045 USA
| | - Robert C. Thomson
- Department of Biology; University of Hawai'i at Mānoa; Honolulu HI 96822 USA
| | - L. Lee Grismer
- Department of Biology; La Sierra University; Riverside CA 92515 USA
| | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045 USA
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42
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Oubida RW, Gantulga D, Zhang M, Zhou L, Bawa R, Holliday JA. Partitioning of multivariate phenotypes using regression trees reveals complex patterns of adaptation to climate across the range of black cottonwood (Populus trichocarpa). FRONTIERS IN PLANT SCIENCE 2015; 6:181. [PMID: 25870603 PMCID: PMC4375981 DOI: 10.3389/fpls.2015.00181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 03/06/2015] [Indexed: 05/25/2023]
Abstract
Local adaptation to climate in temperate forest trees involves the integration of multiple physiological, morphological, and phenological traits. Latitudinal clines are frequently observed for these traits, but environmental constraints also track longitude and altitude. We combined extensive phenotyping of 12 candidate adaptive traits, multivariate regression trees, quantitative genetics, and a genome-wide panel of SNP markers to better understand the interplay among geography, climate, and adaptation to abiotic factors in Populus trichocarpa. Heritabilities were low to moderate (0.13-0.32) and population differentiation for many traits exceeded the 99th percentile of the genome-wide distribution of FST, suggesting local adaptation. When climate variables were taken as predictors and the 12 traits as response variables in a multivariate regression tree analysis, evapotranspiration (Eref) explained the most variation, with subsequent splits related to mean temperature of the warmest month, frost-free period (FFP), and mean annual precipitation (MAP). These grouping matched relatively well the splits using geographic variables as predictors: the northernmost groups (short FFP and low Eref) had the lowest growth, and lowest cold injury index; the southern British Columbia group (low Eref and intermediate temperatures) had average growth and cold injury index; the group from the coast of California and Oregon (high Eref and FFP) had the highest growth performance and the highest cold injury index; and the southernmost, high-altitude group (with high Eref and low FFP) performed poorly, had high cold injury index, and lower water use efficiency. Taken together, these results suggest variation in both temperature and water availability across the range shape multivariate adaptive traits in poplar.
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Affiliation(s)
| | | | | | | | | | - Jason A. Holliday
- *Correspondence: Jason A. Holliday, Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, 304 Cheatham Hall, Blacksburg, VA 24061, USA
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Luo Y, Widmer A, Karrenberg S. The roles of genetic drift and natural selection in quantitative trait divergence along an altitudinal gradient in Arabidopsis thaliana. Heredity (Edinb) 2015; 114:220-8. [PMID: 25293874 PMCID: PMC4815633 DOI: 10.1038/hdy.2014.89] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 07/29/2014] [Accepted: 08/19/2014] [Indexed: 02/02/2023] Open
Abstract
Understanding how natural selection and genetic drift shape biological variation is a central topic in biology, yet our understanding of the agents of natural selection and their target traits is limited. We investigated to what extent selection along an altitudinal gradient or genetic drift contributed to variation in ecologically relevant traits in Arabidopsis thaliana. We collected seeds from 8 to 14 individuals from each of 14 A. thaliana populations originating from sites between 800 and 2700 m above sea level in the Swiss Alps. Seed families were grown with and without vernalization, corresponding to winter-annual and summer-annual life histories, respectively. We analyzed putatively neutral genetic divergence between these populations using 24 simple sequence repeat markers. We measured seven traits related to growth, phenology and leaf morphology that are rarely reported in A. thaliana and performed analyses of altitudinal clines, as well as overall QST-FST comparisons and correlation analyses among pair-wise QST, FST and altitude of origin differences. Multivariate analyses suggested adaptive differentiation along altitude in the entire suite of traits, particularly when expressed in the summer-annual life history. Of the individual traits, a decrease in rosette leaf number in the vegetative state and an increase in leaf succulence with increasing altitude could be attributed to adaptive divergence. Interestingly, these patterns relate well to common within- and between-species trends of smaller plant size and thicker leaves at high altitude. Our results thus offer exciting possibilities to unravel the underlying mechanisms for these conspicuous trends using the model species A. thaliana.
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Affiliation(s)
- Y Luo
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
- ETH Zurich, ETH Zurich, Plant Ecological Genetics, Institute of Integrative Biology (IBZ), Universitätstrasse 16, Zurich, Switzerland
| | - A Widmer
- ETH Zurich, ETH Zurich, Plant Ecological Genetics, Institute of Integrative Biology (IBZ), Universitätstrasse 16, Zurich, Switzerland
| | - S Karrenberg
- ETH Zurich, ETH Zurich, Plant Ecological Genetics, Institute of Integrative Biology (IBZ), Universitätstrasse 16, Zurich, Switzerland
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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44
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Evidences of local adaptation in quantitative traits in Prosopis alba (Leguminosae). Genetica 2014; 143:31-44. [PMID: 25523543 DOI: 10.1007/s10709-014-9810-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 12/15/2014] [Indexed: 01/12/2023]
Abstract
Signals of selection on quantitative traits can be detected by the comparison between the genetic differentiation of molecular (neutral) markers and quantitative traits, by multivariate extensions of the same model and by the observation of the additive covariance among relatives. We studied, by three different tests, signals of occurrence of selection in Prosopis alba populations over 15 quantitative traits: three economically important life history traits: height, basal diameter and biomass, 11 leaf morphology traits that may be related with heat-tolerance and physiological responses and spine length that is very important from silvicultural purposes. We analyzed 172 G1-generation trees growing in a common garden belonging to 32 open pollinated families from eight sampling sites in Argentina. The multivariate phenotypes differ significantly among origins, and the highest differentiation corresponded to foliar traits. Molecular genetic markers (SSR) exhibited significant differentiation and allowed us to provide convincing evidence that natural selection is responsible for the patterns of morphological differentiation. The heterogeneous selection over phenotypic traits observed suggested different optima in each population and has important implications for gene resource management. The results suggest that the adaptive significance of traits should be considered together with population provenance in breeding program as a crucial point prior to any selecting program, especially in Prosopis where the first steps are under development.
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McKinney GJ, Varian A, Scardina J, Nichols KM. Genetic and morphological divergence in three strains of brook trout Salvelinus fontinalis commonly stocked in Lake Superior. PLoS One 2014; 9:e113809. [PMID: 25479612 PMCID: PMC4257586 DOI: 10.1371/journal.pone.0113809] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 10/30/2014] [Indexed: 11/19/2022] Open
Abstract
Fitness related traits often show spatial variation across populations of widely distributed species. Comparisons of genetic variation among populations in putatively neutral DNA markers and in phenotypic traits susceptible to selection (QST FST analysis) can be used to determine to what degree differentiation among populations can be attributed to selection or genetic drift. Traditionally, QST FST analyses require a large number of populations to achieve sufficient statistical power; however, new methods have been developed that allow QST FST comparisons to be conducted on as few as two populations if their pedigrees are informative. This study compared genetic and morphological divergence in three strains of brook trout Salvelinus fontinalis that were historically or currently used for stocking in the Lake Superior Basin. Herein we examined if morphological divergence among populations showed temporal variation, and if divergence could be attributed to selection or was indistinguishable from genetic drift. Multivariate QST FST analysis showed evidence for divergent selection between populations. Univariate analyses suggests that the pattern observed in the multivariate analyses was largely driven by divergent selection for length and weight, and moreover by divergence between the Assinica strain and each of the Iron River and Siskiwit strains rather than divergent selection between each population pair. While it could not be determined if divergence was due to natural selection or inadvertent artificial selection in hatcheries, selected differences were consistent with patterns of domestication commonly found in salmonids.
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Affiliation(s)
- Garrett J. McKinney
- Purdue University, Department of Biological Sciences, West Lafayette, Indiana, United States of America
| | - Anna Varian
- Purdue University, Department of Forestry and Natural Resources, West Lafayette, Indiana, United States of America
| | - Julie Scardina
- Purdue University, Department of Biological Sciences, West Lafayette, Indiana, United States of America
| | - Krista M. Nichols
- Purdue University, Department of Biological Sciences, West Lafayette, Indiana, United States of America
- * E-mail:
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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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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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48
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Shirk RY, Hamrick JL. Multivariate adaptation but no increase in competitive ability in invasive Geranium carolinianum L. (Geraniaceae). Evolution 2014; 68:2945-59. [PMID: 24931621 DOI: 10.1111/evo.12474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 06/02/2014] [Indexed: 11/26/2022]
Abstract
Adaptive evolution can affect the successful establishment of invasive species, but changes in selective pressures, loss of genetic variation in relevant traits, and/or altered trait correlations can make adaptation difficult to predict. We used a common-garden experiment to assess trait correlations and patterns of adaptation in the invasive plant, Geranium carolinianum, sampled across 20 populations in its native (United States) and invasive (China) ranges. We used multivariate QST - FST tests to determine if phenotypic differences between countries are attributable to adaptation. We also compared population-level variation within each country to assess whether local adaptation resulted in similar multivariate phenotypes in the United States and China. Between countries, most phenotypic differences are indistinguishable from genetic drift, although we detected a signature of adaptation to the colder, drier winters in China. There was no evidence for increases in invasive traits in China. Within countries, strong multivariate adaptation appears to be driven by latitudinal climatic variation in the United States, but not in China. Additionally, adaptive trait combinations as well as their underlying correlations differ between the two countries, indicating that adaptation in invasive populations does not parallel patterns in native populations due to differences in selection pressures, genetic constraints, or both.
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Affiliation(s)
- Rebecca Y Shirk
- Department of Plant Biology, 2502 Miller Plant Sciences, University of Georgia, Athens, Georgia, 30602.
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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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50
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Brommer JE, Hanski IK, Kekkonen J, Väisänen RA. Size differentiation in Finnish house sparrows follows Bergmann's rule with evidence of local adaptation. J Evol Biol 2014; 27:737-47. [DOI: 10.1111/jeb.12342] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/09/2014] [Accepted: 01/18/2014] [Indexed: 11/30/2022]
Affiliation(s)
- J. E. Brommer
- Department of Biology; University of Turku; Turku Finland
- Aronia Research and Development Institute; Åbo Akademi and Novia University of Applied Sciences; Ekenäs Finland
| | - I. K. Hanski
- Finnish Museum of Natural History; Helsinki Finland
| | - J. Kekkonen
- Department of Biosciences; University of Helsinki; Helsinki Finland
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