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Sertse D, Fetene A, Leon J, You FM, Cloutier S, McCartney CA. Tracing post-domestication historical events and screening pre-breeding germplasm from large gene pools in wheat in the absence of phenotype data. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:237. [PMID: 39340687 DOI: 10.1007/s00122-024-04738-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 09/04/2024] [Indexed: 09/30/2024]
Abstract
Wheat, particularly common wheat (Triticum aestivum L.), is a major crop accounting for 25% of the world cereal production and thriving in diverse ecogeographic regions. Its adaptation to diverse environments arises from its three distinct genomes adapted to different environments and post-domestication anthropogenic interventions. In search of key genomic regions revealing historic events and breeding significance to common wheat, we performed genome scan and genome-environment association (GEA) analyses using high-marker density genotype datasets. Whole-genome scans revealed highly differentiated regions on chromosomes 2A, 3B, and 4A. In-depth analyses corroborated our previous prediction of the 4A differentiated region signifying the separation between Spelt/Macha and other wheat types. Individual chromosome scans captured key introgressions, including one from T. timopheevii and one from Thinopyrum ponticum on 2B and 3D, respectively, as well as known genes such as Vrn-A1 on 5A. GEA highlighted loci linked to latitude-induced environmental variations, influencing traits such as photoperiodism and responses to abiotic stress. Variation at the Vrn-A1 locus on 5A assigned accessions to two haplotypes (6% and 94%). Further analysis on Vrn-A1 coding gene revealed four subgroups of the major haplotype, while the minor haplotype remained undifferentiated. Analyses at differentiated loci mostly dichotomized the population, illustrating the possibility of isolating pre-breeding materials with desirable traits from large gene pools in the absence of phenotype data. Given the current availability of broad genetic data, the genome-scan-GEA hybrid can be an efficient and cost-effective approach for pinpointing environmentally resilient pre-breeding germplasm from vast gene pools, including gene banks regardless of trait characterization.
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Affiliation(s)
- Demissew Sertse
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada.
| | - Aramde Fetene
- Department of Environmental Planning and Landscape Design, EiABC, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jen Leon
- Department of Plant Breeding, University of Bonn, Bonn, Germany
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Curt A McCartney
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada.
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Gamba D, Vahsen ML, Maxwell TM, Pirtel N, Romero S, Van Ee JJ, Penn A, Das A, Ben-Zeev R, Baughman O, Blaney CS, Bodkins R, Budha-Magar S, Copeland SM, Davis-Foust SL, Diamond A, Donnelly RC, Dunwiddie PW, Ensing DJ, Everest TA, Hoitink H, Holdrege MC, Hufbauer RA, Juzėnas S, Kalwij JM, Kashirina E, Kim S, Klisz M, Klyueva A, Langeveld M, Lutfy S, Martin D, Merkord CL, Morgan JW, Nagy DU, Ott JP, Puchalka R, Pyle LA, Rasran L, Rector BG, Rosche C, Sadykova M, Shriver RK, Stanislavschi A, Starzomski BM, Stone RL, Turner KG, Urza AK, VanWallendael A, Wegenschimmel CA, Zweck J, Brown CS, Leger EA, Blumenthal DM, Germino MJ, Porensky LM, Hooten MB, Adler PB, Lasky JR. Local adaptation to climate facilitates a global invasion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.12.612725. [PMID: 39345363 PMCID: PMC11429938 DOI: 10.1101/2024.09.12.612725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Local adaptation may facilitate range expansion during invasions, but the mechanisms promoting destructive invasions remain unclear. Cheatgrass ( Bromus tectorum ), native to Eurasia and Africa, has invaded globally, with particularly severe impacts in western North America. We sequenced 307 genotypes and conducted controlled experiments. We found that diverse lineages invaded North America, where long-distance gene flow is common. Ancestry and phenotypic clines in the native range predicted those in the invaded range, indicating pre-adapted genotypes colonized different regions. Common gardens showed directional selection on flowering time that reversed between warm and cold sites, potentially maintaining clines. In the Great Basin, genomic predictions of strong local adaptation identified sites where cheatgrass is most dominant. Preventing new introductions that may fuel adaptation is critical for managing ongoing invasions.
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Garrido-Bautista J, Comas M, Jowers MJ, Smith S, Penn DJ, Bakkali M, Moreno-Rueda G. Fine-scale genetic structure and phenotypic divergence of a passerine bird population inhabiting a continuous Mediterranean woodland. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240601. [PMID: 39253402 PMCID: PMC11382889 DOI: 10.1098/rsos.240601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 09/11/2024]
Abstract
Genetic differentiation between populations inhabiting ecologically different habitats might appear because of limited dispersal and gene flow, which may lead to patterns of phenotypic divergence and local adaptation. In this study, we use dispersal, genotypic (24 microsatellite loci) and phenotypic (body size and clutch size) data to analyse patterns of genetic structuring and phenotypic divergence in a blue tit (Cyanistes caeruleus) population inhabiting a continuous and heterogeneous woodland along a valley. The two slopes of the valley differ in their forest formations and environmental conditions. Findings showed that most blue tits reproduced within their natal slope. Accordingly, microsatellite analyses revealed that populations of blue tits established in the two slopes show subtle genetic differentiation. The two genetic populations diverged in clutch size, exceeding the level of differentiation expected based on genetic drift, hence suggesting divergent selection (or other processes promoting divergence) on this life-history trait. Our findings reveal that restricted dispersal and spatial heterogeneity may lead to genetic differentiation among bird populations at a surprisingly small scale. In this respect, it is worth highlighting that such differentiation occurs for an organism with high dispersal capacity and within a continuous woodland. Moreover, we show that small-scale ecological differences, together with limited gene flow, can result in selection favouring different phenotypes even within the same continuum population.
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Affiliation(s)
| | - Mar Comas
- Department of Zoology, University of Granada, Granada 18071, Spain
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
| | - Michael J Jowers
- Department of Zoology, University of Granada, Granada 18071, Spain
| | - Steve Smith
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine Vienna, Vienna 1160, Austria
| | - Dustin J Penn
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine Vienna, Vienna 1160, Austria
| | - Mohammed Bakkali
- Department of Genetics, Faculty of Sciences, University of Granada, Granada 18071, Spain
| | - Gregorio Moreno-Rueda
- Department of Zoology, University of Granada, Granada 18071, Spain
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
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4
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de la Mata R, Mollá-Morales A, Méndez-Vigo B, Torres-Pérez R, Oliveros JC, Gómez R, Marcer A, Castilla AR, Nordborg M, Alonso-Blanco C, Picó FX. Variation and plasticity in life-history traits and fitness of wild Arabidopsis thaliana populations are not related to their genotypic and ecological diversity. BMC Ecol Evol 2024; 24:56. [PMID: 38702598 PMCID: PMC11067129 DOI: 10.1186/s12862-024-02246-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/25/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Despite its implications for population dynamics and evolution, the relationship between genetic and phenotypic variation in wild populations remains unclear. Here, we estimated variation and plasticity in life-history traits and fitness of the annual plant Arabidopsis thaliana in two common garden experiments that differed in environmental conditions. We used up to 306 maternal inbred lines from six Iberian populations characterized by low and high genotypic (based on whole-genome sequences) and ecological (vegetation type) diversity. RESULTS Low and high genotypic and ecological diversity was found in edge and core Iberian environments, respectively. Given that selection is expected to be stronger in edge environments and that ecological diversity may enhance both phenotypic variation and plasticity, we expected genotypic diversity to be positively associated with phenotypic variation and plasticity. However, maternal lines, irrespective of the genotypic and ecological diversity of their population of origin, exhibited a substantial amount of phenotypic variation and plasticity for all traits. Furthermore, all populations harbored maternal lines with canalization (robustness) or sensitivity in response to harsher environmental conditions in one of the two experiments. CONCLUSIONS Overall, we conclude that the environmental attributes of each population probably determine their genotypic diversity, but all populations maintain substantial phenotypic variation and plasticity for all traits, which represents an asset to endure in changing environments.
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Affiliation(s)
- Raul de la Mata
- Departamento de Biología Evolutiva, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, 41092, Spain
- Faculty of Forestry, Institute of Dehesa Research (INDEHESA), Universidad de Extremadura, 10600, Plasencia, Spain
| | | | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Rafael Torres-Pérez
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Juan Carlos Oliveros
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - Rocío Gómez
- Departamento de Biología Evolutiva, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, 41092, Spain
| | - Arnald Marcer
- CREAF, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain
- Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain
| | - Antonio R Castilla
- Department of Plant Biology, Ecology, and Evolution, College of Arts and Sciences, Oklahoma State University, Stillwater, OK, 74078-3031, USA
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, 1030, Vienna, Austria
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049, Madrid, Spain
| | - F Xavier Picó
- Departamento de Biología Evolutiva, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, 41092, Spain.
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5
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Alruiz JM, Peralta-Maraver I, Cavieres G, Bozinovic F, Rezende EL. Fitness surfaces and local thermal adaptation in Drosophila along a latitudinal gradient. Ecol Lett 2024; 27:e14405. [PMID: 38623056 DOI: 10.1111/ele.14405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 03/01/2024] [Accepted: 03/03/2024] [Indexed: 04/17/2024]
Abstract
Local adaptation is commonly cited to explain species distribution, but how fitness varies along continuous geographical gradients is not well understood. Here, we combine thermal biology and life-history theory to demonstrate that Drosophila populations along a 2500 km latitudinal cline are adapted to local conditions. We measured how heat tolerance and viability rate across eight populations varied with temperature in the laboratory and then simulated their expected cumulative Darwinian fitness employing high-resolution temperature data from their eight collection sites. Simulations indicate a trade-off between annual survival and cumulative viability, as both mortality and the recruitment of new flies are predicted to increase in warmer regions. Importantly, populations are locally adapted and exhibit the optimal combination of both traits to maximize fitness where they live. In conclusion, our method is able to reconstruct fitness surfaces employing empirical life-history estimates and reconstructs peaks representing locally adapted populations, allowing us to study geographic adaptation in silico.
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Affiliation(s)
- José M Alruiz
- Departamento de Ecología, Facultad de Ciencias Biológicas, Center of Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ignacio Peralta-Maraver
- Departamento de Ecología e Instituto del Agua, Universidad de Granada, Granada, Spain
- Research Unit Modeling Nature (MNat), Universidad de Granada, Granada, Spain
| | - Grisel Cavieres
- Departamento de Ecología, Facultad de Ciencias Biológicas, Center of Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Francisco Bozinovic
- Departamento de Ecología, Facultad de Ciencias Biológicas, Center of Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Enrico L Rezende
- Departamento de Ecología, Facultad de Ciencias Biológicas, Center of Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, Santiago, Chile
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6
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Yang Z, Zhao A, Teng M, Li M, Wang H, Wang X, Liu Z, Zeng Q, Hu L, Hu J, Bao Z, Huang X. Signatures of selection in Mulinia lateralis underpinning its rapid adaptation to laboratory conditions. Evol Appl 2024; 17:e13657. [PMID: 38357357 PMCID: PMC10866071 DOI: 10.1111/eva.13657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
The dwarf surf clam, Mulinia lateralis, is considered as a model species for bivalves because of its rapid growth and short generation time. Recently, successful breeding of this species for multiple generations in our laboratory revealed its acquisition of adaptive advantages during artificial breeding. In this study, 310 individuals from five different generations were genotyped with 22,196 single nucleotide polymorphisms (SNPs) with the aim of uncovering the genetic basis of their adaptation to laboratory conditions. Results revealed that M. lateralis consistently maintained high genetic diversity across generations, characterized by high observed heterozygosity (H o: 0.2733-0.2934) and low levels of inbreeding (F is: -0.0244-0.0261). Population analysis indicated low levels of genetic differentiation among generations of M. lateralis during artificial breeding (F st <0.05). In total, 316 genomic regions exhibited divergent selection, with 168 regions under positive selection. Furthermore, 227 candidate genes were identified in the positive selection regions, which have functions including growth, stress resistance, and reproduction. Notably, certain selection signatures with significantly higher F st value were detected in genes associated with male reproduction, such as GAL3ST1, IFT88, and TSSK2, which were significantly upregulated during artificial breeding. This suggests a potential role of sperm-associated genes in the rapid evolutionary response of M. lateralis to selection in laboratory conditions. Overall, our findings highlight the phenotypic and genetic changes, as well as selection signatures, in M. lateralis during artificial breeding. This contributes to understanding their adaptation to laboratory conditions and underscores the potential for using this species to explore the adaptive evolution of bivalves.
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Affiliation(s)
- Zujing Yang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Ang Zhao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Mingxuan Teng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Moli Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Hao Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Xuefeng Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Zhi Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding EngineeringSanya Oceanographic Institution, Ocean University of ChinaSanyaChina
| | - Liping Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- Yantai Marine Economic Research InstituteYantaiChina
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding EngineeringSanya Oceanographic Institution, Ocean University of ChinaSanyaChina
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding EngineeringSanya Oceanographic Institution, Ocean University of ChinaSanyaChina
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
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7
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Schmid M, Rueffler C, Lehmann L, Mullon C. Resource Variation Within and Between Patches: Where Exploitation Competition, Local Adaptation, and Kin Selection Meet. Am Nat 2024; 203:E19-E34. [PMID: 38207145 DOI: 10.1086/727483] [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] [Indexed: 01/13/2024]
Abstract
AbstractIn patch- or habitat-structured populations, different processes can favor adaptive polymorphism at different scales. While spatial heterogeneity can generate spatially disruptive selection favoring variation between patches, local competition can lead to locally disruptive selection promoting variation within patches. So far, almost all theory has studied these two processes in isolation. Here, we use mathematical modeling to investigate how resource variation within and between habitats influences the evolution of variation in a consumer population where individuals compete in finite patches connected by dispersal. We find that locally and spatially disruptive selection typically act in concert, favoring polymorphism under a wider range of conditions than when in isolation. But when patches are small and dispersal between them is low, kin competition inhibits the emergence of polymorphism, especially when the latter is driven by local competition for resources. We further use our model to clarify what comparisons between trait and neutral genetic differentiation (Q ST / F ST comparisons) can tell about the nature of selection. Overall, our results help us understand the interaction between two major drivers of polymorphism: locally and spatially disruptive selection, and how this interaction is modulated by the unavoidable effects of kin selection under limited dispersal.
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8
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Feoktistova NY, Meschersky IG, Karmanova TN, Gureeva AV, Surov AV. Allele Diversity of the Major Histocompatibility Complex in the Common Hamster (Cricetus cricetus) in Urban and Rural Populations. BIOL BULL+ 2022. [DOI: 10.1134/s1062359022050077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Shafer CL. A greater yellowstone ecosystem grizzly bear case study: genetic reassessment for managers. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01262-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractThere are five grizzly bear (Ursus arctos horribilis) populations in the lower 48 states of the United States. My goal in this Commentary was to ascertain whether genetic diversity is being lost from the isolated GYE grizzly bear population and to better understand any viability implications. I reviewed the scientific literature, including two key genetic studies that the US Fish and Wildlife Service (USFWS) relied upon for their 2007 and current 2017 GYE grizzly bear genetics policy. I discovered that some studies reveal a loss of heterozygosity in the GYE bear population, both historically and in recent decades. Some had a statistically significant depletion rate. My review took place periodically between 2010 and 2021 and indicates that the genome of the GYE grizzly bear population is too small for long-term adaptation. The paper includes a discussion about evolutionary adaptation which invokes time frames rarely considered by nature conservation planners. I also examined genetic statements in the USFWS’s 2017 GYE grizzly bear delisting regulations and highlighted those that seem incongruent with current scientific thought. If this paper is read by some scientists, land managers, administrators, environmentalists, and others with some genetics background, they will better understand some USFWS decisions and policy statements. This case study illustrates that land management agencies can provide a one-sided treatment of some science when writing regulations about genetics.
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10
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Cubry P, Oddou-Muratorio S, Scotti I, Lefèvre F. Interactions between microenvironment, selection and genetic architecture drive multiscale adaptation in a simulation experiment. J Evol Biol 2022; 35:451-466. [PMID: 35170114 PMCID: PMC9306464 DOI: 10.1111/jeb.13988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 11/28/2022]
Abstract
When environmental conditions differ both within and among populations, multiscale adaptation results from processes at both scales and interference across scales. We hypothesize that within-population environmental heterogeneity influences the chance of success of migration events, both within and among populations, and maintains within-population adaptive differentiation. We used a simulation approach to analyze the joint effects of environmental heterogeneity patterns, selection intensity and number of QTL controlling a selected trait on local adaptation in a hierarchical metapopulation design. We show the general effects of within-population environmental heterogeneity: (i) it increases occupancy rate at the margins of distribution ranges, under extreme environments and high levels of selection; (ii) it increases the adaptation lag in all environments; (iii) it impacts the genetic variance in each environment, depending on the ratio of within- to between-populations environmental heterogeneity; (iv) it reduces the selection-induced erosion of adaptive gene diversity. Most often, the smaller the number of QTL involved, the stronger are these effects. We also show that both within- and between-populations phenotypic differentiation (QST ) mainly results from covariance of QTL effects rather than QTL differentiation (FSTq ), that within-population QTL differentiation is negligible, and that stronger divergent selection is required to produce adaptive differentiation within populations than among populations. With a high number of QTL, when the difference between environments within populations exceeds the smallest difference between environments across populations, high levels of within-population differentiation can be reached, reducing differentiation among populations. Our study stresses the need to account for within-population environmental heterogeneity when investigating local adaptation.
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Affiliation(s)
- Philippe Cubry
- Ecologie des Forêts Méditerranéennes, URFM, INRAE, Avignon, France.,DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
| | - Sylvie Oddou-Muratorio
- Ecologie des Forêts Méditerranéennes, URFM, INRAE, Avignon, France.,ECOBIOP, Université de Pau et des Pays de l'Adour, E2S UPPA, INRAE, Saint-Pée-sur-Nivelle, France
| | - Ivan Scotti
- Ecologie des Forêts Méditerranéennes, URFM, INRAE, Avignon, France
| | - François Lefèvre
- Ecologie des Forêts Méditerranéennes, URFM, INRAE, Avignon, France
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11
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Historical comparisons show evolutionary changes in drought responses in European plant species after two decades of climate change. Basic Appl Ecol 2022. [DOI: 10.1016/j.baae.2021.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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de Miguel M, Rodríguez-Quilón I, Heuertz M, Hurel A, Grivet D, Jaramillo-Correa JP, Vendramin GG, Plomion C, Majada J, Alía R, Eckert AJ, González-Martínez SC. Polygenic adaptation and negative selection across traits, years and environments in a long-lived plant species (Pinus pinaster Ait., Pinaceae). Mol Ecol 2022; 31:2089-2105. [PMID: 35075727 DOI: 10.1111/mec.16367] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 11/30/2021] [Accepted: 01/11/2022] [Indexed: 11/26/2022]
Abstract
A decade of genetic association studies in multiple organisms suggests that most complex traits are polygenic, i.e., they have a genetic architecture determined by numerous loci each with small effect-size. Thus, determining the degree of polygenicity and its variation across traits, environments and time is crucial to understand the genetic basis of phenotypic variation. We applied multilocus approaches to estimate the degree of polygenicity of fitness-related traits in a long-lived plant (Pinus pinaster Ait., maritime pine) and to analyze this variation across environments and years. We evaluated five categories of fitness-related traits (survival, height, phenology, functional, and biotic-stress response traits) in a clonal common-garden network, planted in contrasted environments (over 12,500 trees). Most of the analyzed traits showed evidence of local adaptation based on Qst -Fst comparisons. We further observed a remarkably stable degree of polygenicity, averaging 6% (range of 0-27%), across traits, environments and years. We detected evidence of negative selection, which could explain, at least partially, the high degree of polygenicity. Because polygenic adaptation can occur rapidly, our results suggest that current predictions on the capacity of natural forest tree populations to adapt to new environments should be revised, especially in the current context of climate change.
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Affiliation(s)
- Marina de Miguel
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France.,EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Isabel Rodríguez-Quilón
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | | | - Agathe Hurel
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | - Juan-Pablo Jaramillo-Correa
- Department of Evolutionary Ecology, Institute of Ecology, Universidad Nacional Autónoma de México, AP 70-275, México City, CDMX 04510, Mexico
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, Division of Florence, National Research Council, 50019, Sesto Fiorentino (FI), Italy
| | | | - Juan Majada
- Sección Forestal, SERIDA, Finca Experimental ''La Mata'', 33820, Grado, Principado de Asturias, Spain
| | - Ricardo Alía
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
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Contrasting environmental drivers of genetic and phenotypic divergence in an Andean poison frog (Epipedobates anthonyi). Heredity (Edinb) 2022; 128:33-44. [PMID: 34718332 PMCID: PMC8733028 DOI: 10.1038/s41437-021-00481-2] [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: 01/07/2021] [Revised: 10/17/2021] [Accepted: 10/18/2021] [Indexed: 01/03/2023] Open
Abstract
Phenotypic and genetic divergence are shaped by the homogenizing effects of gene flow and the differentiating processes of genetic drift and local adaptation. Herein, we examined the mechanisms that underlie phenotypic (size and color) and genetic divergence in 35 populations (535 individuals) of the poison frog Epipedobates anthonyi along four elevational gradients (0-1800 m asl) in the Ecuadorian Andes. We found phenotypic divergence in size and color despite relatively low genetic divergence at neutral microsatellite loci. Genetic and phenotypic divergence were both explained by landscape resistance between sites (isolation-by-resistance, IBR), likely due to a cold and dry mountain ridge between the northern and southern elevational transects that limits dispersal and separates two color morphs. Moreover, environmental differences among sites also explained genetic and phenotypic divergence, suggesting isolation-by-environment (IBE). When northern and southern transects were analyzed separately, genetic divergence was predicted either by distance (isolation-by-distance, IBD; northern) or environmental resistance between sites (IBR; southern). In contrast, phenotypic divergence was primarily explained by environmental differences among sites, supporting the IBE hypothesis. These results indicate that although distance and geographic barriers are important drivers of population divergence, environmental variation has a two-fold effect on population divergence. On the one hand, landscape resistance between sites reduces gene flow (IBR), while on the other hand, environmental differences among sites exert divergent selective pressures on phenotypic traits (IBE). Our work highlights the importance of studying both genetic and phenotypic divergence to better understand the processes of population divergence and speciation along ecological gradients.
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14
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Toczydlowski RH, Waller DM. Plastic and quantitative genetic divergence mirror environmental gradients among wild, fragmented populations of Impatiens capensis. AMERICAN JOURNAL OF BOTANY 2022; 109:99-114. [PMID: 34643270 DOI: 10.1002/ajb2.1782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Habitat fragmentation generates molecular genetic divergence among isolated populations, but few studies have assessed phenotypic divergence and fitness in populations where the genetic consequences of habitat fragmentation are known. Phenotypic divergence could reflect plasticity, local adaptation, and/or genetic drift. METHODS We examined patterns and potential drivers of phenotypic divergence among 12 populations of jewelweed (Impatiens capensis) that show strong molecular genetic signals of isolation and drift among fragmented habitats. We measured morphological and reproductive traits in both maternal plants within natural populations and their self-fertilized progeny grown together in a common garden. We also quantified environmental divergence between home sites and the common garden. RESULTS Populations with less molecular genetic variation expressed less maternal phenotypic variation. Progeny in the common garden converged in phenotypes relative to their wild mothers but retained among-population differences in morphology, survival, and reproduction. Among-population phenotypic variance was 3-10× greater in home sites than in the common garden for 6 of 7 morphological traits measured. Patterns of phenotypic divergence paralleled environmental gradients in ways suggestive of adaptation. Progeny resembled their mothers less as the environmental distance between their home site and the common garden increased. CONCLUSIONS Despite strong molecular signatures of isolation and drift, phenotypic differences among these Impatiens populations appear to reflect both adaptive quantitative genetic divergence and plasticity. Quantifying the extent of local adaptation and plasticity and how these covary with molecular and phenotypic variation help us predict when populations may lose their adaptive capacity.
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Affiliation(s)
- Rachel H Toczydlowski
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Donald M Waller
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
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15
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Faske TM, Agneray AC, Jahner JP, Sheta LM, Leger EA, Parchman TL. Genomic and common garden approaches yield complementary results for quantifying environmental drivers of local adaptation in rubber rabbitbrush, a foundational Great Basin shrub. Evol Appl 2021; 14:2881-2900. [PMID: 34950235 PMCID: PMC8674890 DOI: 10.1111/eva.13323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/17/2021] [Accepted: 11/03/2021] [Indexed: 01/21/2023] Open
Abstract
The spatial structure of genomic and phenotypic variation across populations reflects historical and demographic processes as well as evolution via natural selection. Characterizing such variation can provide an important perspective for understanding the evolutionary consequences of changing climate and for guiding ecological restoration. While evidence for local adaptation has been traditionally evaluated using phenotypic data, modern methods for generating and analyzing landscape genomic data can directly quantify local adaptation by associating allelic variation with environmental variation. Here, we analyze both genomic and phenotypic variation of rubber rabbitbrush (Ericameria nauseosa), a foundational shrub species of western North America. To quantify landscape genomic structure and provide perspective on patterns of local adaptation, we generated reduced representation sequencing data for 17 wild populations (222 individuals; 38,615 loci) spanning a range of environmental conditions. Population genetic analyses illustrated pronounced landscape genomic structure jointly shaped by geography and environment. Genetic-environment association (GEA) analyses using both redundancy analysis (RDA) and a machine-learning approach (Gradient Forest) indicated environmental variables (precipitation seasonality, slope, aspect, elevation, and annual precipitation) influenced spatial genomic structure and were correlated with allele frequency shifts indicative of local adaptation at a consistent set of genomic regions. We compared our GEA-based inference of local adaptation with phenotypic data collected by growing seeds from each population in a greenhouse common garden. Population differentiation in seed weight, emergence, and seedling traits was associated with environmental variables (e.g., precipitation seasonality) that were also implicated in GEA analyses, suggesting complementary conclusions about the drivers of local adaptation across different methods and data sources. Our results provide a baseline understanding of spatial genomic structure for E. nauseosa across the western Great Basin and illustrate the utility of GEA analyses for detecting the environmental causes and genetic signatures of local adaptation in a widely distributed plant species of restoration significance.
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Affiliation(s)
- Trevor M. Faske
- Department of BiologyUniversity of NevadaRenoNevadaUSA
- Ecology, Evolution, and Conservation Biology ProgramUniversity of NevadaRenoNevadaUSA
| | - Alison C. Agneray
- Department of BiologyUniversity of NevadaRenoNevadaUSA
- Ecology, Evolution, and Conservation Biology ProgramUniversity of NevadaRenoNevadaUSA
| | | | - Lana M. Sheta
- Department of BiologyUniversity of NevadaRenoNevadaUSA
| | - Elizabeth A. Leger
- Department of BiologyUniversity of NevadaRenoNevadaUSA
- Ecology, Evolution, and Conservation Biology ProgramUniversity of NevadaRenoNevadaUSA
| | - Thomas L. Parchman
- Department of BiologyUniversity of NevadaRenoNevadaUSA
- Ecology, Evolution, and Conservation Biology ProgramUniversity of NevadaRenoNevadaUSA
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16
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Hasan N, Choudhary S, Naaz N, Sharma N, Laskar RA. Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. J Genet Eng Biotechnol 2021; 19:128. [PMID: 34448979 PMCID: PMC8397809 DOI: 10.1186/s43141-021-00231-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 08/17/2021] [Indexed: 11/28/2022]
Abstract
Background DNA markers improved the productivity and accuracy of classical plant breeding by means of marker-assisted selection (MAS). The enormous number of quantitative trait loci (QTLs) mapping read for different plant species have given a plenitude of molecular marker-gene associations. Main body of the abstract In this review, we have discussed the positive aspects of molecular marker-assisted selection and its precise applications in plant breeding programmes. Molecular marker-assisted selection has considerably shortened the time for new crop varieties to be brought to the market. To explore the information about DNA markers, many reviews have been published in the last few decades; all these reviews were intended by plant breeders to obtain information on molecular genetics. In this review, we intended to be a synopsis of recent developments of DNA markers and their application in plant breeding programmes and devoted to early breeders with little or no knowledge about the DNA markers. The progress made in molecular plant breeding, plant genetics, genomics selection, and editing of genome contributed to the comprehensive understanding of DNA markers and provides several proofs on the genetic diversity available in crop plants and greatly complemented plant breeding devices. Short conclusion MAS has revolutionized the process of plant breeding with acceleration and accuracy, which is continuously empowering plant breeders around the world.
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Affiliation(s)
- Nazarul Hasan
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India.
| | - Sana Choudhary
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India
| | - Neha Naaz
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India
| | - Nidhi Sharma
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India
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17
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Liu N, Du Y, Warburton ML, Xiao Y, Yan J. Phenotypic Plasticity Contributes to Maize Adaptation and Heterosis. Mol Biol Evol 2021; 38:1262-1275. [PMID: 33212480 PMCID: PMC8480182 DOI: 10.1093/molbev/msaa283] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plant phenotypic plasticity describes altered phenotypic performance of an individual when grown in different environments. Exploring genetic architecture underlying plant plasticity variation may help mitigate the detrimental effects of a rapidly changing climate on agriculture, but little research has been done in this area to date. In the present study, we established a population of 976 maize F1 hybrids by crossing 488 diverse inbred lines with two elite testers. Genome-wide association study identified hundreds of quantitative trait loci associated with phenotypic plasticity variation across diverse F1 hybrids, the majority of which contributed very little variance, in accordance with the polygenic nature of these traits. We identified several quantitative trait locus regions that may have been selected during the tropical-temperate adaptation process. We also observed heterosis in terms of phenotypic plasticity, in addition to the traditional genetic value differences measured between hybrid and inbred lines, and the pattern of which was affected by genetic background. Our results demonstrate a landscape of phenotypic plasticity in maize, which will aid in the understanding of its genetic architecture, its contribution to adaptation and heterosis, and how it may be exploited for future maize breeding in a rapidly changing environment.
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Affiliation(s)
- Nannan Liu
- Horticulture Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuanhao Du
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Marilyn L Warburton
- United States Department of Agriculture-Agricultural Research Service: Corn Host Plant Resistance Research Unit, Mississippi State, MS
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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18
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Pennington LK, Slatyer RA, Ruiz-Ramos DV, Veloz SD, Sexton JP. How is adaptive potential distributed within species ranges? Evolution 2021; 75:2152-2166. [PMID: 34164814 DOI: 10.1111/evo.14292] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 05/20/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022]
Abstract
Quantitative genetic variation (QGV) represents a major component of adaptive potential and, if reduced toward range-edge populations, could prevent a species' expansion or adaptive response to rapid ecological change. It has been hypothesized that QGV will be lower at the range edge due to small populations-often the result of poor habitat quality-and potentially decreased gene flow. However, whether central populations are higher in QGV is unknown. We used a meta-analytic approach to test for a general QGV-range position relationship, including geographic and climatic distance from range centers. We identified 35 studies meeting our criteria, yielding nearly 1000 estimates of QGV (including broad-sense heritability, narrow-sense heritability, and evolvability) from 34 species. The relationship between QGV and distance from the geographic range or climatic niche center depended on the focal trait and how QGV was estimated. We found some evidence that QGV declines from geographic centers but that it increases toward niche edges; niche and geographic distances were uncorrelated. Nevertheless, few studies have compared QGV in both central and marginal regions or environments within the same species. We call for more research in this area and discuss potential research avenues related to adaptive potential in the context of global change.
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Affiliation(s)
- Lillie K Pennington
- Environmental Systems Graduate Group, University of California, Merced, California, 95343
| | - Rachel A Slatyer
- Department of Entomology, University of Wisconsin-Madison, Madison, Wisconsin, 53703.,Current Address: Research School of Biology, Australian National University, Acton, ACT, 2600, Australia
| | - Dannise V Ruiz-Ramos
- Life and Environmental Sciences Department, University of California, Merced, California, 95343.,Current Address: U.S. Geological Survey, Columbia Environmental Research Center, Columbia, Missouri, 65201
| | - Samuel D Veloz
- Point Blue Conservation Science, Petaluma, California, 94954
| | - Jason P Sexton
- Life and Environmental Sciences Department, University of California, Merced, California, 95343
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19
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Stacy EA, Sakishima T, Tharp H, Snow N. Isolation of Metrosideros ('Ohi'a) Taxa on O'ahu Increases with Elevation and Extreme Environments. J Hered 2021; 111:103-118. [PMID: 31844884 DOI: 10.1093/jhered/esz069] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 11/08/2019] [Indexed: 01/04/2023] Open
Abstract
Species radiations should be facilitated by short generation times and limited dispersal among discontinuous populations. Hawaii's hyper-diverse, landscape-dominant tree, Metrosideros, is unique among the islands' radiations for its massive populations that occur continuously over space and time within islands, its exceptional capacity for gene flow by both pollen and seed, and its extended life span (ca. >650 years). Metrosideros shows the greatest phenotypic and microsatellite DNA diversity on O'ahu, where taxa occur in tight sympatry or parapatry in mesic and montane wet forest on 2 volcanoes. We document the nonrandom distributions of 12 taxa (including unnamed morphotypes) along elevation gradients, measure phenotypes of ~6-year-old common-garden plants of 8 taxa to verify heritability of phenotypes, and examine genotypes of 476 wild adults at 9 microsatellite loci to compare the strengths of isolation across taxa, volcanoes, and distance. All 8 taxa retained their diagnostic phenotypes in the common garden. Populations were isolated by taxon to a range of degrees (pairwise FST between taxa: 0.004-0.267), and there was no pattern of isolation by distance or by elevation; however, significant isolation between volcanoes was observed within monotypic species, suggesting limited gene flow between volcanoes. Among the infraspecific taxa of Metrosideros polymorpha, genetic diversity and isolation significantly decreased and increased, respectively, with elevation. Overall, 5 of the 6 most isolated taxa were associated with highest elevations or otherwise extreme environments. These findings suggest a principal role for selection in the origin and maintenance of the exceptional diversity that occurs within continuous Metrosideros stands on O'ahu.
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Affiliation(s)
- Elizabeth A Stacy
- Department of Biology, University of Hawai'i Hilo, Hilo, HI.,Tropical Conservation Biology and Environmental Science Graduate Program, University of Hawai'i Hilo, Hilo, HI
| | - Tomoko Sakishima
- Department of Biology, University of Hawai'i Hilo, Hilo, HI.,Tropical Conservation Biology and Environmental Science Graduate Program, University of Hawai'i Hilo, Hilo, HI
| | - Heaven Tharp
- Department of Biology, University of Hawai'i Hilo, Hilo, HI
| | - Neil Snow
- Department of Biology, Pittsburg State University, Pittsburg, KS
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20
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Liu Y, El-Kassaby YA. Transcriptome-wide analysis of introgression-resistant regions reveals genetic divergence genes under positive selection in Populus trichocarpa. Heredity (Edinb) 2021; 126:442-462. [PMID: 33214679 PMCID: PMC8027638 DOI: 10.1038/s41437-020-00388-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 11/09/2022] Open
Abstract
Comparing gene expression patterns and genetic polymorphisms between populations is of central importance for understanding the origin and maintenance of biodiversity. Based on population-specific gene expression levels and allele frequency differences, we sought to identify population divergence (PD) genes across the introgression-resistant genomic regions of Populus trichocarpa. Genes containing highly diverged loci [i.e., genetic divergence (GD)] or showing expression divergence (ED) between populations were widely distributed in the genome and substantially enriched in functional categories related to stress responses, disease resistance, timing of flowering, cell cycle regulation, plant growth, and development. Nine genomic regions showing evidence of strong positive selection were overlapped with GD genes, which had significant differences between Oregon (a southernmost peripheral deme) and the other demes. However, we did not find evidence that genes under positive selection show an enrichment for ED. PD genes and genes under selection pertained to the same gene classes, such as SERINE/CYSTEINE PROTEASE, ABC TRANSPORTER, GLYCOSYLTRANSFERASE and other transferases. Our analysis also revealed that GD genes were polymorphic within the species (41.9 ± 3.66 biallelic variants per gene), as previously reported in herbaceous plants. By contrast, ED genes contained less genetic variants (10.73 ± 1.14) and were likely highly expressed. In addition, we found that trans- rather than cis-acting variants considerably contribute to the evolution of >90% PD genes. Overall, this study elucidates that cohorts of PD genes agree with the general attributes of known speciation genes and GD genes will provide substrates for positive selection to operate on.
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Affiliation(s)
- Yang Liu
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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21
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do Amaral TS, Dos Santos JS, Rosa FF, Pessôa MB, Chaves LJ, Ribeiro MC, Collevatti RG. Agricultural Landscape Heterogeneity Matter: Responses of Neutral Genetic Diversity and Adaptive Traits in a Neotropical Savanna Tree. Front Genet 2021; 11:606222. [PMID: 33613620 PMCID: PMC7890196 DOI: 10.3389/fgene.2020.606222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/31/2020] [Indexed: 11/27/2022] Open
Abstract
Plants are one of the most vulnerable groups to fragmentation and habitat loss, that may affect community richness, abundance, functional traits, and genetic diversity. Here, we address the effects of landscape features on adaptive quantitative traits and evolutionary potential, and on neutral genetic diversity in populations of the Neotropical savanna tree Caryocar brasiliense. We sampled adults and juveniles in 10 savanna remnants within five landscapes. To obtain neutral genetic variation, we genotyped all individuals from each site using nine microsatellite loci. For adaptive traits we measured seed size and mass and grown seeds in nursery in completely randomized experimental design. We obtained mean, additive genetic variance (Va) and coefficient of variation (CVa%), which measures evolvability, for 17 traits in seedlings. We found that landscapes with higher compositional heterogeneity (SHDI) had lower evolutionary potential (CVa%) in leaf length (LL) and lower aboveground dry mass (ADM) genetic differentiation (QST). We also found that landscapes with higher SHDI had higher genetic diversity (He) and allelic richness (AR) in adults, and lower genetic differentiation (FST). In juveniles, SHDI was also positively related to AR. These results are most likely due to longer dispersal distance of pollen in landscapes with lower density of flowering individuals. Agricultural landscapes with low quality mosaic may be more stressful for plant species, due to the lower habitat cover (%), higher cover of monocropping (%) and other land covers, and edge effects. However, in landscapes with higher SHDI with high quality mosaic, forest nearby savanna habitat and the other environments may facilitate the movement or provide additional habitat and resources for seed disperses and pollinators, increasing gene flow and genetic diversity. Finally, despite the very recent agriculture expansion in Central Brazil, we found no time lag in response to habitat loss, because both adults and juveniles were affected by landscape changes.
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Affiliation(s)
- Tatiana Souza do Amaral
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Juliana Silveira Dos Santos
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil.,Laboratório de Ecologia Espacial e Conservação (LEEC), Departamento de Biodiversidade, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Fernanda Fraga Rosa
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Marcelo Bruno Pessôa
- Laboratório de Metacomunidades e Paisagem, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Lázaro José Chaves
- Escola de Agronomia, Universidade Federal de Goiás (UFG), Goiânia, Brazil
| | - Milton Cezar Ribeiro
- Laboratório de Ecologia Espacial e Conservação (LEEC), Departamento de Biodiversidade, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Rosane Garcia Collevatti
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás (UFG), Goiânia, Brazil
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22
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Perrin A, Khimoun A, Faivre B, Ollivier A, de Pracontal N, Théron F, Loubon M, Leblond G, Duron O, Garnier S. Habitat fragmentation differentially shapes neutral and immune gene variation in a tropical bird species. Heredity (Edinb) 2021; 126:148-162. [PMID: 32934360 PMCID: PMC7853120 DOI: 10.1038/s41437-020-00366-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/30/2020] [Accepted: 08/30/2020] [Indexed: 01/11/2023] Open
Abstract
Habitat fragmentation is a major cause of biodiversity loss, responsible for an alteration of intraspecific patterns of neutral genetic diversity and structure. Although neutral genetic variation can be informative for demographic inferences, it may be a poor predictor of adaptive genetic diversity and thus of the consequences of habitat fragmentation on selective evolutionary processes. In this context, we contrasted patterns of genetic diversity and structure of neutral loci (microsatellites) and immune genes (i.e., toll-like receptors) in an understorey bird species, the wedge-billed woodcreeper Glyphorynchus spirurus. The objectives were (1) to investigate forest fragmentation effects on population genetic diversity, (2) to disentangle the relative role of demography (genetic drift and migration) and selection, and (3) to assess whether immunogenetic patterns could be associated with variation of ectoparasite (i.e., ticks) pressures. Our results revealed an erosion of neutral genetic diversity and a substantial genetic differentiation among fragmented populations, resulting from a decrease in landscape connectivity and leading to the divergence of distinct genetic pools at a small spatial scale. Patterns of genetic diversity observed for TLR4 and TLR5 were concordant with neutral genetic patterns, whereas those observed for TLR3 and TLR21 were discordant. This result underlines that the dominant evolutionary force shaping immunogenetic diversity (genetic drift vs. selection) may be different depending on loci considered. Finally, tick prevalence was higher in fragmented environments. We discussed the hypothesis that pathogen selective pressures may contribute to maintain adaptive genetic diversity despite the negative demographic effect of habitat fragmentation on neutral genetic diversity.
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Affiliation(s)
- Antoine Perrin
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France.
| | - Aurélie Khimoun
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Bruno Faivre
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Anthony Ollivier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Nyls de Pracontal
- Groupe d'Etude et de Protection des Oiseaux en Guyane, 431 route d'Attila Cabassou, 97354, Rémire-Montjoly, France
| | - Franck Théron
- Groupe d'Etude et de Protection des Oiseaux en Guyane, 431 route d'Attila Cabassou, 97354, Rémire-Montjoly, France
| | - Maxime Loubon
- Groupe d'Etude et de Protection des Oiseaux en Guyane, 431 route d'Attila Cabassou, 97354, Rémire-Montjoly, France
| | - Gilles Leblond
- SARL BIOS, Route de Davidon, Duzer, 97115, Sainte-Rose, France
| | - Olivier Duron
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS), Institut pour la Recherche et le Développement (IRD), Université de Montpellier (UM), Montpellier, France
| | - Stéphane Garnier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
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23
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Melo WA, Vieira LD, Novaes E, Bacon CD, Collevatti RG. Selective Sweeps Lead to Evolutionary Success in an Amazonian Hyperdominant Palm. Front Genet 2020; 11:596662. [PMID: 33424928 PMCID: PMC7786001 DOI: 10.3389/fgene.2020.596662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/18/2020] [Indexed: 01/21/2023] Open
Abstract
Despite the global importance of tropical ecosystems, few studies have identified how natural selection has shaped their megadiversity. Here, we test for the role of adaptation in the evolutionary success of the widespread, highly abundant Neotropical palm Mauritia flexuosa. We used a genome scan framework, sampling 16,262 single-nucleotide polymorphisms (SNPs) with target sequence capture in 264 individuals from 22 populations in rainforest and savanna ecosystems. We identified outlier loci as well as signal of adaptation using Bayesian correlations of allele frequency with environmental variables and detected both selective sweeps and genetic hitchhiking events. Functional annotation of SNPs with selection footprints identified loci affecting genes related to adaptation to environmental stress, plant development, and primary metabolic processes. The strong differences in climatic and soil variables between ecosystems matched the high differentiation and low admixture in population Bayesian clustering. Further, we found only small differences in allele frequency distribution in loci putatively under selection among widespread populations from different ecosystems, with fixation of a single allele in most populations. Taken together, our results indicate that adaptive selective sweeps related to environmental stress shaped the spatial pattern of genetic diversity in M. flexuosa, leading to high similarity in allele frequency among populations from different ecosystems.
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Affiliation(s)
- Warita A Melo
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Lucas D Vieira
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Evandro Novaes
- Departamento de Biologia, Universidade Federal de Lavras, Lavras, Brazil
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Rosane G Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
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24
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Zhang H, Mitchell-Olds T, Mujacic I, Song BH. De novo Genome Assembly, Annotation, and SNP Identification of an Endangered Rockcress, Boechera fecunda. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.550936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Wani GA, Shah MA, Tekeu H, Reshi ZA, Atangana AR, Khasa DP. Phenotypic Variability and Genetic Diversity of Phragmites australis in Quebec and Kashmir Reveal Contrasting Population Structure. PLANTS 2020; 9:plants9101392. [PMID: 33092113 PMCID: PMC7589717 DOI: 10.3390/plants9101392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 11/23/2022]
Abstract
The origin of differences in traits influencing competitive success between invasive and native wild populations of alien species is subject of debate. Herbarium-based information sources from 2005 onwards about nativity and distributional range of Phragmites australis were used to survey putative native populations of the species in Quebec, and chloroplast DNA (cpDNA) PCR-RFLP analyses identified only one native population, whereas the same analyses revealed that the Kashmir populations are invasive. We compared the native population of P. australis in Quebec (QN), ten populations invasive to Quebec (QE), and five populations invasive in Kashmir, India (KE) using morphometric traits. Using nine cpDNA microsatellite loci, we also compared nine KE populations, ten QE populations, and the QN population. Phenotypic variation was observed among and within populations. Only dry mass of flowers varied across regions. Characterization of morphotypes defined three distinct haplotypes. A bimodal distribution of stem diameter (SD), internode length (IL), leaf length (LL), and leaf width (LW) suggests that a major gene may control growth traits or occurrence of co-selection. High genetic differentiation was observed between populations (RST = 0.353) and haplotypes (RST = 0.133 to 0.418), indicating limited gene flow and probable local adaptation. Principal coordinates analysis and the neighbor-joining phylogenetic tree clearly distinguished the three haplotypes. Among-populations phenotypic difference (PST) was lower than overall RST for plant height, SD, and fresh and dry mass of flowers and seeds, whereas PST estimates for LL and LW exceeded among-populations RST, suggesting divergent selection, while local adaptation might have occurred in IL, LL, and flower masses. Genetic drift probably influenced among-populations IL differences.
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Affiliation(s)
- Gowher A. Wani
- Department of Botany, University of Kashmir, Srinagar 190006, Jammu & Kashmir, India; (M.A.S.); (Z.A.R.)
- Centre for Forest Research (CEF) and Institute for Integrative and Systems Biology (IBIS), Université Laval, Québec, QC G1V0A6, Canada; (H.T.); or (A.R.A.); (D.P.K.)
- Correspondence: ; Tel.: +91-700-601-1834
| | - Manzoor A. Shah
- Department of Botany, University of Kashmir, Srinagar 190006, Jammu & Kashmir, India; (M.A.S.); (Z.A.R.)
| | - Honoré Tekeu
- Centre for Forest Research (CEF) and Institute for Integrative and Systems Biology (IBIS), Université Laval, Québec, QC G1V0A6, Canada; (H.T.); or (A.R.A.); (D.P.K.)
- Department of Plant Biology, Faculty of Science, University of Yaoundé, IPO Box 812 Yaoundé, Cameroon
| | - Zafar A. Reshi
- Department of Botany, University of Kashmir, Srinagar 190006, Jammu & Kashmir, India; (M.A.S.); (Z.A.R.)
| | - Alain R. Atangana
- Centre for Forest Research (CEF) and Institute for Integrative and Systems Biology (IBIS), Université Laval, Québec, QC G1V0A6, Canada; (H.T.); or (A.R.A.); (D.P.K.)
- World Agroforestry, West and Central Africa Region, Cocody, Angré 7ème Tranche B.P. 2823, Abidjan 08 BP 2823, Cote D’Ivoire
| | - Damase P. Khasa
- Centre for Forest Research (CEF) and Institute for Integrative and Systems Biology (IBIS), Université Laval, Québec, QC G1V0A6, Canada; (H.T.); or (A.R.A.); (D.P.K.)
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Chapuis E, Ali N, Noûs C, Besnard G. Adaptive response to olive cultivation in a generalist parasitic nematode (Meloidogyne javanica). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractCultivated plants usually differ from their wild progenitors in several morphological and/or physiological traits. Their microbe communities might also differ because of adaptation to new conditions related to cultivation. To test this hypothesis, we investigated morphological traits in a parthenogenetic root-knot nematode (Meloidogyne javanica) from natural and agricultural environments. Seventeen populations of M. javanica were sampled on cultivated and wild olives in Morocco, then maintained in controlled conditions for a ‘common garden’ experiment. We estimated the genetic variation based on three traits (stylet size, neck width and body width) by a quantitative genetic design (ten families per population and nine individuals per family were measured), and molecular variation was investigated with a mitochondrial marker to identify the genetic lineages of nematode isolates sampled from wild and cultivated olives. Significant morphological differences were detected between individuals from wild vs. cultivated hosts for the three traits, whereas no phylogenetic clustering was observed among isolates collected on those two hosts. Our results thus suggest an adaptive response of the asexual parasite, possibly related to the deep modification of soil nematode communities between natural olive stands and orchards.
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Affiliation(s)
- Elodie Chapuis
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Nadeen Ali
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | | | - Guillaume Besnard
- CNRS, UPS, IRD, UMR5174, EDB, Université Toulouse III Paul Sabatier, Toulouse Cedex, France
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27
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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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28
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Gauzere J, Klein EK, Brendel O, Davi H, Oddou-Muratorio S. Microgeographic adaptation and the effect of pollen flow on the adaptive potential of a temperate tree species. THE NEW PHYTOLOGIST 2020; 227:641-653. [PMID: 32167572 DOI: 10.1111/nph.16537] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/29/2020] [Indexed: 06/10/2023]
Abstract
In species with long-distance dispersal capacities and inhabiting a large ecological niche, local selection and gene flow are expected to be major evolutionary forces affecting the genetic adaptation of natural populations. Yet, in species such as trees, evidence of microgeographic adaptation and the quantitative assessment of the impact of gene flow on adaptive genetic variation are still limited. Here, we used extensive genetic and phenotypic data from European beech seedlings collected along an elevation gradient, and grown in a common garden, to study the signature of selection on the divergence of eleven potentially adaptive traits, and to assess the role of gene flow in resupplying adaptive genetic variation. We found a significant signal of adaptive differentiation among plots separated by < 1 km, with selection acting on growth and phenological traits. Consistent with theoretical expectations, our results suggest that pollen dispersal contributes to increase genetic diversity for these locally differentiated traits. Our results thus highlight that local selection is an important evolutionary force in natural tree populations and suggest that management interventions to facilitate movement of gametes along short ecological gradients would boost genetic diversity of individual tree populations, and enhance their adaptive potential to rapidly changing environments.
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Affiliation(s)
- Julie Gauzere
- INRAE, URFM, Avignon, 84000, France
- INRAE, BioSP, Avignon, 84000, France
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, UK
| | | | - Oliver Brendel
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, Nancy, 54000, France
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29
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Collevatti RG, dos Santos JS, Rosa FF, Amaral TS, Chaves LJ, Ribeiro MC. Multi-Scale Landscape Influences on Genetic Diversity and Adaptive Traits in a Neotropical Savanna Tree. Front Genet 2020; 11:259. [PMID: 32269588 PMCID: PMC7109282 DOI: 10.3389/fgene.2020.00259] [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: 10/30/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
Changes in landscape structure can affect essential population ecological features, such as dispersal and recruitment, and thus genetic processes. Here, we analyze the effects of landscape metrics on adaptive quantitative traits variation, evolutionary potential, and on neutral genetic diversity in populations of the Neotropical savanna tree Tabebuia aurea. Using a multi-scale approach, we sampled five landscapes with two sites of savanna in each. To obtain neutral genetic variation, we genotyped 60 adult individuals from each site using 10 microsatellite loci. We measured seed size and mass. Seeds were grown in nursery in completely randomized experimental design and 17 traits were measured in seedlings to obtain the average, additive genetic variance (V a ) and coefficient of variation (CV a %), which measures evolvability, for each trait. We found that habitat loss increased genetic diversity (He) and allelic richness (AR), and decreased genetic differentiation among populations (F ST ), most likely due to longer dispersal distance of pollen in landscapes with lower density of flowering individuals. Habitat amount positively influenced seed size. Seeds of T. aurea are wind-dispersed and larger seeds may be dispersed to short distance, increasing genetic differentiation and decreasing genetic diversity and allelic richness. Evolvability (CV a %) in root length decreased with habitat amount. Savanna trees have higher root than shoot growth rate in the initial stages, allowing seedlings to obtain water from water tables. Landscapes with lower habitat amount may be more stressful for plant species, due to the lower plant density, edge effects and the negative impacts of agroecosystems. In these landscapes, larger roots may provide higher ability to obtain water, increasing survival and avoiding dying back because of fire. Despite the very recent agriculture expansion in Central Brazil, landscape changes are affecting neutral and adaptive variation in T. aurea. Several populations have low additive genetic variation for some traits and thus, may have limited evolvability, which may jeopardize species long-term persistence. The effect of habitat loss on highly variable neutral loci may only be detected after a certain threshold of population size is attained, that could become dangerously small masking important losses of heterozygosity endangering species conservation.
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Affiliation(s)
| | - Juliana Silveira dos Santos
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás, Goiânia, Brazil
- Laboratório de Ecologia Espacial e Conservação (LEEC), Departamento de Biodiversidade, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, Brazil
| | - Fernanda Fraga Rosa
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás, Goiânia, Brazil
| | - Tatiana S. Amaral
- Laboratório de Genética & Biodiversidade, ICB, Universidade Federal de Goiás, Goiânia, Brazil
| | | | - Milton Cezar Ribeiro
- Laboratório de Ecologia Espacial e Conservação (LEEC), Departamento de Biodiversidade, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, Brazil
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30
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Price N, Lopez L, Platts AE, Lasky JR. In the presence of population structure: From genomics to candidate genes underlying local adaptation. Ecol Evol 2020; 10:1889-1904. [PMID: 32128123 DOI: 10.1101/642306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 05/26/2023] Open
Abstract
Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. To identify loci underlying local adaptation, models that combine allelic and environmental variation while controlling for the effects of population structure have emerged as the method of choice. Despite being evaluated in simulation studies, there has not been a thorough investigation of empirical evidence supporting local adaptation across these alleles. To evaluate these methods, we use 875 Arabidopsis thaliana Eurasian accessions and two mixed models (GEMMA and LFMM) to identify candidate SNPs underlying local adaptation to climate. Subsequently, to assess evidence of local adaptation and function among significant SNPs, we examine allele frequency differentiation and recent selection across Eurasian populations, in addition to their distribution along quantitative trait loci (QTL) explaining fitness variation between Italy and Sweden populations and cis-regulatory/nonsynonymous sites showing significant selective constraint. Our results indicate that significant LFMM/GEMMA SNPs show low allele frequency differentiation and linkage disequilibrium across locally adapted Italy and Sweden populations, in addition to a poor association with fitness QTL peaks (highest logarithm of odds score). Furthermore, when examining derived allele frequencies across the Eurasian range, we find that these SNPs are enriched in low-frequency variants that show very large climatic differentiation but low levels of linkage disequilibrium. These results suggest that their enrichment along putative functional sites most likely represents deleterious variation that is independent of local adaptation. Among all the genomic signatures examined, only SNPs showing high absolute allele frequency differentiation (AFD) and linkage disequilibrium (LD) between Italy and Sweden populations showed a strong association with fitness QTL peaks and were enriched along selectively constrained cis-regulatory/nonsynonymous sites. Using these SNPs, we find strong evidence linking flowering time, freezing tolerance, and the abscisic-acid pathway to local adaptation.
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Affiliation(s)
- Nicholas Price
- Department of Bioagricultural Sciences & Pest Management Colorado State University Fort Collins CO USA
- Department of Biological Sciences University of Cyprus Nicosia Cyprus
| | - Lua Lopez
- Department of Biology Binghamton University (State University of New York) Binghamton NY USA
| | - Adrian E Platts
- Simons Center for Quantitative Biology Cold Spring Harbor Laboratory Cold Spring Harbor NY USA
- Department of Biology Center for Genomics and Systems Biology New York University New York NY USA
| | - Jesse R Lasky
- Department of Biology Pennsylvania State University University Park PA USA
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31
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Liu Y, El-Kassaby YA. Phenotypic plasticity of natural Populus trichocarpa populations in response to temporally environmental change in a common garden. BMC Evol Biol 2019; 19:231. [PMID: 31878866 PMCID: PMC6933736 DOI: 10.1186/s12862-019-1553-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 12/05/2019] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Natural selection on fitness-related traits can be temporally heterogeneous among populations. As climate changes, understanding population-level responses is of scientific and practical importance. We examined 18 phenotypic traits associated with phenology, biomass, and ecophysiology in 403 individuals of natural Populus trichocarpa populations, growing in a common garden. RESULTS Compared with tree origin settings, propagules likely underwent drought exposures in the common garden due to significantly low rainfall during the years of measurement. All study traits showed population differentiation reflecting adaptive responses due to local genetic adaptation. Phenology and biomass traits were strongly under selection and showed plastic responses between years, co-varying with latitude. While phenological events (e.g., bud set and growth period) and biomass were under positive directional selection, post-bud set period, particularly from final bud set to the onset of leaf drop, was selected against. With one exception to water-use efficiency, ecophysiology traits were under negative directional selection. Moreover, extended phenological events jointly evolved with source niches under increased temperature and decreased rainfall exposures. High biomass coevolved with climatic niches of high temperature; low rainfall promoted high photosynthetic rates evolution. CONCLUSIONS This work underpins that P. trichocarpa is likely to experience increased fitness (height gain) by evolving toward extended bud set and growth period, abbreviated post-bud set period, and increased drought resistance, potentially constituting a powerful mechanism for long-lived tree species in surviving unpredictably environmental extremes (e.g., drought).
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Affiliation(s)
- Yang Liu
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, V6T 1Z4, Canada.
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, V6T 1Z4, Canada
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32
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García-Zubia LC, Hernández-Velasco J, Hernández-Díaz JC, Simental-Rodríguez SL, López-Sánchez CA, Quiñones-Pérez CZ, Carrillo-Parra A, Wehenkel C. Spatial genetic structure in Pinus cembroides Zucc. at population and landscape levels in central and northern Mexico. PeerJ 2019; 7:e8002. [PMID: 31844562 PMCID: PMC6910111 DOI: 10.7717/peerj.8002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/07/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Spatial genetic structure (SGS) analysis is a powerful approach to quantifying gene flow between trees, thus clarifying the functional connectivity of trees at population and landscape scales. The findings of SGS analysis may be useful for conservation and management of natural populations and plantations. Pinus cembroides is a widely distributed tree species, covering an area of about 2.5 million hectares in Mexico. The aim of this study was to examine five natural seed stands of P. cembroides in the Sierra Madre Occidental to determine the SGS at population (within the seed stand) and landscape (among seed stands) levels in order to establish guidelines for the conservation and management of the species. We hypothesized that P. cembroides, in which the seeds are dispersed by birds and mammals, creates weaker SGS than species with wind-dispersed seeds. METHODS DNA fingerprinting was performed using the amplified fragment length polymorphism (AFLP) technique. In order to estimate the SGS at population and landscape levels, we measured the geographical (spatial) distance as the Euclidean distance. We also estimated the genetic distances between individuals using the pairwise kinship coefficient. RESULTS The results showed non-significant autocorrelation in four out of five seed stands studied (i.e., a mainly random distribution in the space of the genetic variants of P. cembroides at population level). DISCUSSION SGS was detected at the landscape scale, supporting the theory of isolation by distance as a consequence of restricted pollen and seed dispersal. However, the SGS may also have been generated by our sampling strategy. We recommended establishing a close network of seed stands of P. cembroides to prevent greater loss of local genetic variants and alteration of SGS. We recommend seed stands of P. cembroides of a minimum width of 225 m.
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Affiliation(s)
- Luis C. García-Zubia
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, México
| | - Javier Hernández-Velasco
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, México
| | - José C. Hernández-Díaz
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, México
| | | | - Carlos A. López-Sánchez
- Department of Biology of Organisms and Systems, Mieres Polytechnic School, University of Oviedo, Campus Universitario de Mieres, C/Gonzalo Gutiérrez Quirós S/N, Mieres, Spain
| | | | - Artemio Carrillo-Parra
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, México
| | - Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, México
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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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34
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Heuring C, Barber D, Rains N, Erxleben D, Martin C, Williams D, McElroy EJ. Genetics, morphology and diet of introduced populations of the ant-eating Texas Horned Lizard (Phrynosoma cornutum). Sci Rep 2019; 9:11470. [PMID: 31391496 PMCID: PMC6685972 DOI: 10.1038/s41598-019-47856-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/24/2019] [Indexed: 11/09/2022] Open
Abstract
Introduced species can diverge from their source population when they become established in a new ecosystem. The Texas Horned Lizard (Phrynosoma cornutum) is native to the western United States (US) and was historically introduced to several locations in the southeastern US. We studied three introduced populations in South Carolina, US to determine if they exhibit dietary, morphological and genetic divergence from the native western US populations. We expected little divergence from western populations because P. cornutum is a specialist whose biology is largely shaped by its diet of Pogonomyrmex harvester ants. We show that the introduced populations have mixed ancestry between south Texas and more northern areas and experienced founder effects and genetic bottlenecks resulting in decreased genetic diversity. South Carolina lizards primarily consume ants (94%), but surprisingly, they did not eat harvester ants. Introduced lizards primarily eat Dorymyrmex ants, but each introduced population complements Dorymyrmex with significantly different amounts of other species of ants, insects and plant matter. Introduced populations have smaller body size and have different limb and head shapes compared to western populations. This study demonstrates successful persistence of an introduced vertebrate that may be attributed to phenotypic change, even in the face of reduced genetic diversity.
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Affiliation(s)
- Courtney Heuring
- Department of Biology, College of Charleston, Charleston, South Carolina, 29412, USA
| | | | - Nathan Rains
- Texas Parks and Wildlife Department, Austin, Texas, 78744, USA
| | - Devin Erxleben
- Texas Parks and Wildlife Department, Austin, Texas, 78744, USA
| | - Cameron Martin
- Texas Parks and Wildlife Department, Austin, Texas, 78744, USA
| | - Dean Williams
- Department of Biology, Texas Christian University, Fort Worth, Texas, 76129, USA
| | - Eric J McElroy
- Department of Biology, College of Charleston, Charleston, South Carolina, 29412, USA.
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35
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Cai Z, Zhou L, Ren NN, Xu X, Liu R, Huang L, Zheng XM, Meng QL, Du YS, Wang MX, Geng MF, Chen WL, Jing CY, Zou XH, Guo J, Chen CB, Zeng HZ, Liang YT, Wei XH, Guo YL, Zhou HF, Zhang FM, Ge S. Parallel Speciation of Wild Rice Associated with Habitat Shifts. Mol Biol Evol 2019; 36:875-889. [PMID: 30861529 PMCID: PMC6501882 DOI: 10.1093/molbev/msz029] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The occurrence of parallel speciation strongly implies the action of natural selection. However, it is unclear how general a phenomena parallel speciation is since it was only shown in a small number of animal species. In particular, the adaptive process and mechanisms underlying the process of parallel speciation remain elusive. Here, we used an integrative approach incorporating population genomics, common garden, and crossing experiments to investigate parallel speciation of the wild rice species Oryza nivara from O. rufipogon. We demonstrated that O. nivara originated multiple times from different O. rufipogon populations and revealed that different O. nivara populations have evolved similar phenotypes under divergent selection, a reflection of recurrent local adaptation of ancient O. rufipogon populations to dry habitats. Almost completed premating isolation was detected between O. nivara and O. rufipogon in the absence of any postmating barriers between and within these species. These results suggest that flowering time is a “magic” trait that contributes to both local adaptation and reproductive isolation in the origin of wild rice species. Our study thus demonstrates a convincing case of parallel ecological speciation as a consequence of adaptation to new environments.
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Affiliation(s)
- Zhe Cai
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lian Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ning-Ning Ren
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xun Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Rong Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Lei Huang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Ming Zheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Qing-Lin Meng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Su Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Xia Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mu-Fan Geng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Li Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Chun-Yan Jing
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Hui Zou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jie Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Cheng-Bin Chen
- Guangxi Academy Agricultural Sciences, Nanning, Guangxi, China
| | - Hua-Zhong Zeng
- Guangxi Academy Agricultural Sciences, Nanning, Guangxi, China
| | - Yun-Tao Liang
- Guangxi Academy Agricultural Sciences, Nanning, Guangxi, China
| | - Xing-Hua Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hai-Fei Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Fu-Min Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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Shen Y, Wang L, Fu J, Xu X, Yue GH, Li J. Population structure, demographic history and local adaptation of the grass carp. BMC Genomics 2019; 20:467. [PMID: 31174480 PMCID: PMC6555922 DOI: 10.1186/s12864-019-5872-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/31/2019] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Genetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation. Grass carp is the most important freshwater foodfish species for food and water weed control. However, there is as yet no overall picture on genetic variations and population structure of this species, which is important for its aquaculture. RESULTS We used 43,310 SNPs to infer the population structure, evidence of local adaptation and sources of introduction. The overall genetic differentiation of this species was low. The native populations were differentiated into three genetic clusters, corresponding to the Yangtze, Pearl and Heilongjiang River Systems, respectively. The populations in Malaysia, India and Nepal were introduced from both the Yangtze and Pearl River Systems. Loci and genes involved in putative local selection for native locations were identified. Evidence of both positive and balancing selection was found in the introduced locations. Genes associated with loci under putative selection were involved in many biological functions. Outlier loci were grouped into clusters as genomic islands within some specific genomic regions, which likely agrees with the divergence hitchhiking scenario of divergence-with-gene-flow. CONCLUSIONS This study, for the first time, sheds novel insights on the population differentiation of the grass carp, genetics of its strong ability in adaption to diverse environments and sources of some introduced grass carp populations. Our data also suggests that the natural populations of the grass carp have been affected by the aquaculture besides neutral and adaptive forces.
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Affiliation(s)
- Yubang Shen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China.,Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
| | - Le Wang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
| | - Jianjun Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Gen Hua Yue
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore. .,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Republic of Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, 201306, China. .,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China.
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37
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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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38
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Míguez-Soto B, Fernández-Cruz J, Fernández-López J. Mediterranean and Northern Iberian gene pools of wild Castanea sativa Mill. are two differentiated ecotypes originated under natural divergent selection. PLoS One 2019; 14:e0211315. [PMID: 30753199 PMCID: PMC6372156 DOI: 10.1371/journal.pone.0211315] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/13/2019] [Indexed: 11/18/2022] Open
Abstract
Nine wild Iberian provenances of Castanea sativa Mill. grouped in two gene pools, North Iberian Peninsula and Mediterranean, were evaluated for several adaptive traits in two provenance-progeny trials with the aim of evaluating the role of natural selection in shaping adaptive variation and increasing our understanding of the genetic structure of this species, as well as reporting complete information on the genetic variation among and within the studied populations. An annual growth rhythm experiment was evaluated during the first 3 years after establishment for phenology, growth, stem form and survival, and a periodic drought-stress experiment was evaluated for dry weight, growth, survival and other related drought traits in both well-watered and drought-stress treatments. The high genetic variability reported in both trials is largely due to the genetic variation among populations. The significant differences reported between quantitative genetic and neutral marker differentiation indicated the local adaptation of these populations through directional selection, mainly for phenology, growth and biomass allocation. A clinal variation among populations was determined through correlations of phenology with latitude and xerothermic index of the provenances, showing that central and southern Mediterranean populations had earlier phenology than northern populations and that drought played a relevant role in this differentiation. The significant correlation between phenological traits and the ancestry values in the Mediterranean gene pool supported the different pattern of behavior between both gene pools and also indicated the existence of two ecotypes: xeric and mesophytic ecotypes, corresponding to Mediterranean and North Iberian gene pools, respectively. The results obtained in the drought-stress experiment confirmed that, in general terms, xeric populations showed a greater adaptability to drought, with more developed root systems and higher survival than northern populations. Moreover, the genetic variability observed within populations indicated the potential response capacity of Iberian C. sativa populations to undergo fast adaptive evolution.
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Affiliation(s)
- B. Míguez-Soto
- Department of Forest Breeding, Forestry Research Centre of Lourizán, Pontevedra, Spain
| | - J. Fernández-Cruz
- Department of Forest Breeding, Forestry Research Centre of Lourizán, Pontevedra, Spain
| | - J. Fernández-López
- Department of Forest Breeding, Forestry Research Centre of Lourizán, Pontevedra, Spain
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39
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Mable BK. Conservation of adaptive potential and functional diversity: integrating old and new approaches. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1129-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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40
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Collevatti RG, Rodrigues EE, Vitorino LC, Lima-Ribeiro MS, Chaves LJ, Telles MPC. Unravelling the genetic differentiation among varieties of the Neotropical savanna tree Hancornia speciosa Gomes. ANNALS OF BOTANY 2018; 122:973-984. [PMID: 29897397 PMCID: PMC6266125 DOI: 10.1093/aob/mcy060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 04/04/2018] [Indexed: 06/08/2023]
Abstract
Background and Aims Spatial distribution of species genetic diversity is often driven by geographical distance (isolation by distance) or environmental conditions (isolation by environment), especially under climate change scenarios such as Quaternary glaciations. Here, we used coalescent analyses coupled with ecological niche modelling (ENM), spatially explicit quantile regression analyses and the multiple matrix regression with randomization (MMRR) approach to unravel the patterns of genetic differentiation in the widely distributed Neotropical savanna tree, Hancornia speciosa (Apocynaceae). Due to its high morphological differentiation, the species was originally classified into six botanical varieties by Monachino, and has recently been recognized as only two varieties by Flora do Brasil 2020. Thus, H. speciosa is a good biological model for learning about evolution of phenotypic plasticity under genetic and ecological effects, and predicting their responses to changing environmental conditions. Methods We sampled 28 populations (777 individuals) of Monachino's four varieties of H. speciosa and used seven microsatellite loci to genotype them. Key Results Bayesian clustering showed five distinct genetic groups (K = 5) with high admixture among Monachino's varieties, mainly among populations in the central area of the species geographical range. Genetic differentiation among Monachino's varieties was lower than the genetic differentiation among populations within varieties, with higher within-population inbreeding. A high historical connectivity among populations of the central Cerrado shown by coalescent analyses may explain the high admixture among varieties. In addition, areas of higher climatic suitability also presented higher genetic diversity in such a way that the wide historical refugium across central Brazil might have promoted the long-term connectivity among populations. Yet, FST was significantly related to geographic distances, but not to environmental distances, and coalescent analyses and ENM predicted a demographical scenario of quasi-stability through time. Conclusions Our findings show that demographical history and isolation by distance, but not isolation by environment, drove genetic differentiation of populations. Finally, the genetic clusters do not support the two recently recognized botanical varieties of H. speciosa, but partially support Monachino's classification at least for the four sampled varieties, similar to morphological variation.
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Affiliation(s)
- Rosane G Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | - Eduardo E Rodrigues
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | | | - Matheus S Lima-Ribeiro
- Laboratório de Macroecologia, Instituto de Biociências, Universidade Federal de Goiás (UFG), Regional Jataí, Jataí, GO, Brasil
| | - Lázaro J Chaves
- Escola de Agronomia, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | - Mariana P C Telles
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brasil
- Escola de Ciências Agrárias e Biológicas, Pontifícia Universidade Católica de Goiás, Goiânia, GO, Brasil
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41
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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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42
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Schäfer MA, Berger D, Rohner PT, Kjaersgaard A, Bauerfeind SS, Guillaume F, Fox CW, Blanckenhorn WU. Geographic clines in wing morphology relate to colonization history in New World but not Old World populations of yellow dung flies. Evolution 2018; 72:1629-1644. [PMID: 29911337 DOI: 10.1111/evo.13517] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/23/2018] [Indexed: 01/05/2023]
Abstract
Geographic clines offer insights about putative targets and agents of natural selection as well as tempo and mode of adaptation. However, demographic processes can lead to clines that are indistinguishable from adaptive divergence. Using the widespread yellow dung fly Scathophaga stercoraria (Diptera: Scathophagidae), we examine quantitative genetic differentiation (QST ) of wing shape across North America, Europe, and Japan, and compare this differentiation with that of ten microsatellites (FST ). Morphometric analyses of 28 populations reared at three temperatures revealed significant thermal plasticity, sexual dimorphism, and geographic differentiation in wing shape. In North America morphological differentiation followed the decline in microsatellite variability along the presumed route of recent colonization from the southeast to the northwest. Across Europe, where S. stercoraria presumably existed for much longer time and where no molecular pattern of isolation by distance was evident, clinal variation was less pronounced despite significant morphological differentiation (QST >FST ). Shape vector comparisons further indicate that thermal plasticity (hot-to-cold) does not mirror patterns of latitudinal divergence (south-to-north), as might have been expected under a scenario with temperature as the major agent of selection. Our findings illustrate the importance of detailed phylogeographic information when interpreting geographic clines of dispersal traits in an adaptive evolutionary framework.
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Affiliation(s)
- Martin A Schäfer
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - David Berger
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
- Animal Ecology at Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18d, SE-75236 Uppsala, Sweden
| | - Patrick T Rohner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Anders Kjaersgaard
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Stephanie S Bauerfeind
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Charles W Fox
- Department of Entomology, University of Kentucky, Lexington, Kentucky 40506
| | - Wolf U Blanckenhorn
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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Stojanova B, Šurinová M, Klápště J, Koláříková V, Hadincová V, Münzbergová Z. Adaptive differentiation of Festuca rubra along a climate gradient revealed by molecular markers and quantitative traits. PLoS One 2018; 13:e0194670. [PMID: 29617461 PMCID: PMC5884518 DOI: 10.1371/journal.pone.0194670] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/07/2018] [Indexed: 12/02/2022] Open
Abstract
Species response to climate change is influenced by predictable (selective) and unpredictable (random) evolutionary processes. To understand how climate change will affect present-day species, it is necessary to assess their adaptive potential and distinguish it from the effects of random processes. This will allow predicting how different genotypes will respond to forecasted environmental change. Space for time substitution experiments are an elegant way to test the response of present day populations to climate variation in real time. Here we assess neutral and putatively adaptive variation in 11 populations of Festuca rubra situated along crossed gradients of temperature and moisture using molecular markers and phenotypic measurements, respectively. By comparing population differentiation in putatively neutral molecular markers and phenotypic traits (QST-FST comparisons), we show the existence of adaptive differentiation in phenotypic traits and their plasticity across the climatic gradient. The observed patterns of differentiation are due to the high genotypic and phenotypic differentiation of the populations from the coldest (and wettest) environment. Finally, we observe statistically significant covariation between markers and phenotypic traits, which is likely caused by isolation by adaptation. These results contribute to a better understanding of the current adaptation and evolutionary potential to face climate change of a widespread species. They can also be extrapolated to understand how the studied populations will adjust to upcoming climate change without going through the lengthy process of phenotyping.
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Affiliation(s)
- Bojana Stojanova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Mária Šurinová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
| | - Jaroslav Klápště
- Scion (New Zealand Forest Research Institute Ltd.), Whakarewarewa, Rotorua, New Zealand
| | - Veronika Koláříková
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Věroslava Hadincová
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
| | - Zuzana Münzbergová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
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44
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Phenotypic divergence despite low genetic differentiation in house sparrow populations. Sci Rep 2018; 8:394. [PMID: 29321524 PMCID: PMC5762629 DOI: 10.1038/s41598-017-18718-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 12/17/2017] [Indexed: 11/09/2022] Open
Abstract
Studying patterns of phenotypic variation among populations can shed light on the drivers of evolutionary processes. The house sparrow (Passer domesticus) is one of the world's most ubiquitous bird species, as well as a successful invader. We investigated phenotypic variation in house sparrow populations across a climatic gradient and in relation to a possible scenario of an invasion. We measured variation in morphological, coloration, and behavioral traits (exploratory behavior and neophobia) and compared it to the neutral genetic variation. We found that sparrows were larger and darker in northern latitudes, in accordance with Bergmann's and Gloger's biogeographic rules. Morphology and behavior mostly differed between the southernmost populations and the other regions, supporting the possibility of an invasion. Genetic differentiation was low and diversity levels were similar across populations, indicating high gene flow. Nevertheless, the southernmost and northern populations differed genetically to some extent. Furthermore, genetic differentiation (F ST) was lower in comparison to phenotypic variation (P ST), indicating that the phenotypic variation is shaped by directional selection or by phenotypic plasticity. This study expands our knowledge on evolutionary mechanisms and biological invasions.
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45
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Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_61] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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46
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Abbott JM, Grosberg RK, Williams SL, Stachowicz JJ. Multiple dimensions of intraspecific diversity affect biomass of eelgrass and its associated community. Ecology 2017; 98:3152-3164. [PMID: 28983913 DOI: 10.1002/ecy.2037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 09/04/2017] [Accepted: 09/18/2017] [Indexed: 11/09/2022]
Abstract
Genetic diversity within key species can play an important role in the functioning of entire communities. However, the extent to which different dimensions of diversity (e.g., the number of genotypes vs. the extent of genetic differentiation among those genotypes) best predicts functioning is unknown and may yield clues into the different mechanisms underlying diversity effects. We explicitly test the relative influence of genotypic richness and genetic relatedness on eelgrass productivity, biomass, and the diversity of associated invertebrate grazers in a factorial field experiment using the seagrass species, Zostera marina (eelgrass). Genotypic richness had the strongest effect on eelgrass biomass accumulation, such that plots with more genotypes at the end of the experiment attained a higher biomass. Genotypic diversity (richness + evenness) was a stronger predictor of biomass than richness alone, and both genotype richness and diversity were positively correlated with trait diversity. The relatedness of genotypes in a plot reduced eelgrass biomass independently of richness. Plots containing eelgrass with greater trait diversity also had a higher abundance of invertebrate grazers, while the diversity and relatedness of eelgrass genotypes had little effect on invertebrate abundance or richness. Our work extends previous findings by explicitly relating genotypic diversity to trait diversity, thus mechanistically connecting genotypic diversity to plot-level yields. We also show that other dimensions of diversity, namely relatedness, influence eelgrass performance independent of trait differentiation. Ultimately, richness and relatedness captured fundamentally different components of intraspecific variation and should be treated as complementary rather than competing dimensions of biodiversity affecting ecosystem functioning.
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Affiliation(s)
- Jessica M Abbott
- Center for Population Biology, University of California, One Shields Avenue, Davis, California, 95616, USA.,Department of Evolution and Ecology, University of California, One Shields Avenue, Davis, California, 95616, USA
| | - Richard K Grosberg
- Center for Population Biology, University of California, One Shields Avenue, Davis, California, 95616, USA.,Department of Evolution and Ecology, University of California, One Shields Avenue, Davis, California, 95616, USA
| | - Susan L Williams
- Department of Evolution and Ecology, University of California, One Shields Avenue, Davis, California, 95616, USA.,Bodega Marine Laboratory, Bodega Bay, California, 94923, USA
| | - John J Stachowicz
- Center for Population Biology, University of California, One Shields Avenue, Davis, California, 95616, USA.,Department of Evolution and Ecology, University of California, One Shields Avenue, Davis, California, 95616, USA
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47
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Listl D, Poschlod P, Reisch C. Do seed transfer zones for ecological restoration reflect the spatial genetic variation of the common grassland species Lathyrus pratensis
? Restor Ecol 2017. [DOI: 10.1111/rec.12613] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniela Listl
- Institute of Plant Sciences; University of Regensburg; 93040 Regensburg Germany
| | - Peter Poschlod
- Institute of Plant Sciences; University of Regensburg; 93040 Regensburg Germany
| | - Christoph Reisch
- Institute of Plant Sciences; University of Regensburg; 93040 Regensburg Germany
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48
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Wang L, Bai B, Huang S, Liu P, Wan ZY, Ye B, Wu J, Yue GH. QTL Mapping for Resistance to Iridovirus in Asian Seabass Using Genotyping-by-Sequencing. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:517-527. [PMID: 28758171 DOI: 10.1007/s10126-017-9770-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 07/12/2017] [Indexed: 06/07/2023]
Abstract
Identifying quantitative trait loci (QTL) for viral disease resistance is of particular importance in selective breeding programs of fish species. Genetic markers linked to QTL can be useful in marker-assisted selection (MAS) for elites resistant to specific pathogens. Here, we conducted a genome scan for QTL associated with Singapore grouper iridovirus (SGIV) resistance in an Asian seabass (Lates calcarifer) family, using a high-density linkage map generated with genotyping-by-sequencing. One genome-wide significant and three suggestive QTL were detected at LG21, LG6, LG13, and LG15, respectively. The phenotypic variation explained (PVE) by the four QTL ranged from 7.5 to 15.6%. The position of the most significant QTL at LG21 was located between 31.88 and 36.81 cM. The SNP marker (SNP130416) nearest to the peak of this QTL was significantly associated with SGIV resistance in an unrelated multifamily population. One candidate gene, MECOM, close to the peak of this QTL region, was predicted. Evidence of alternative splicing was observed for MECOM and one specific category of splicing variants was differentially expressed at 5 days post-SGIV infection. The QTL detected in this study are valuable resources and can be used in the selective breeding programs of Asian seabass with regard to resistance to SGIV.
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Affiliation(s)
- Le Wang
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Bin Bai
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Shuqing Huang
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Peng Liu
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Zi Yi Wan
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Baoqing Ye
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Jinlu Wu
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
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Takahashi Y. Genome-wide population genetic analysis identifies evolutionary forces establishing continuous population divergence. Ecol Res 2017. [DOI: 10.1007/s11284-017-1459-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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50
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Faria J, Martins GM, Pita A, Ribeiro PA, Hawkins SJ, Presa P, Neto AI. Disentangling the genetic and morphological structure of Patella candei complex in Macaronesia (NE Atlantic). Ecol Evol 2017; 7:6125-6140. [PMID: 28861219 PMCID: PMC5574786 DOI: 10.1002/ece3.3121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 02/28/2017] [Accepted: 04/27/2017] [Indexed: 11/24/2022] Open
Abstract
The uptake of natural living resources for human consumption has triggered serious changes in the balance of ecosystems. In the archipelagos of Macaronesia (NE Atlantic), limpets have been extensively exploited probably since islands were first colonized. This has led to profound consequences in the dynamics of rocky shore communities. The Patella candei complex includes various subspecies of limpets that are ascribed to a particular archipelago and has been the focus of several taxonomic surveys without much agreement. Under a conservational perspective, we apply morphometric and genetic analyses to test subspecies boundaries in P. candei and to evaluate its current population connectivity throughout Macaronesia (Azores, Madeira, and Canaries). A highly significant genetic break between archipelagos following isolation by distance was detected (FST = 0.369, p < .001). Contrastingly, significant genetic differentiation among islands (i.e., Azores) was absent possibly indicating ongoing gene flow via larval exchange between populations. Significant shell‐shape differences among archipelagos were also detected using both distance‐based and geometric morphometric analyses. Adaptive processes associated with niche differentiation and strong barriers to gene flow among archipelagos may be the mechanisms underlying P. candei diversification in Macaronesia. Under the very probable assumption that populations of P. candei from each archipelago are geographically and/or ecologically isolated populations, the various subspecies within the P. candei complex may be best thought of as true species using the denomination: P. candei in Selvagens, Patella gomesii in Azores, Patella ordinaria in Madeira, and Patella crenata for Canaries. This would be in agreement with stock delimitation and units of conservation of P. candei sensu latu along Macaronesia.
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Affiliation(s)
- Joao Faria
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group Department of Biology University of Azores Ponta Delgada São Miguel, Azores Portugal
| | - Gustavo M Martins
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group Department of Biology University of Azores Ponta Delgada São Miguel, Azores Portugal
| | - Alfonso Pita
- Faculty of Marine Sciences - ECIMAT Laboratory of Marine Genetic Resources University of Vigo Vigo Spain.,Ocean and Earth Science, National Oceanography Centre Southampton Waterfront Campus University of Southampton Southampton UK
| | - Pedro A Ribeiro
- MARE - Marine and Environmental Sciences Centre and IMAR - Institute of Marine Research Department of Oceanography and Fisheries University of the Azores Horta Portugal
| | - Stephen J Hawkins
- Ocean and Earth Science, National Oceanography Centre Southampton Waterfront Campus University of Southampton Southampton UK.,The Laboratory Marine Biological Association of UK Plymouth UK
| | - Pablo Presa
- Faculty of Marine Sciences - ECIMAT Laboratory of Marine Genetic Resources University of Vigo Vigo Spain
| | - Ana I Neto
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group Department of Biology University of Azores Ponta Delgada São Miguel, Azores Portugal
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