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de Lima TM, Silva SF, Ribeiro RV, Sánchez-Vilas J, Pinheiro F. Salt tolerance in a neotropical orchid in the absence of local adaptation to salt spray. AMERICAN JOURNAL OF BOTANY 2024; 111:e16373. [PMID: 39010314 DOI: 10.1002/ajb2.16373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 07/17/2024]
Abstract
PREMISE Salt tolerance has rarely been investigated regionally in the neotropics and even more rarely in Orchidaceae, one of the largest families. Therefore, investigating local adaptation to salt spray and its physiological basis in Epidendrum fulgens, a neotropical orchid species, brings important new insights. METHODS We assessed the degree of salt tolerance in E. fulgens by testing whether coastal populations are more tolerant to salt, which could point to local adaptation. To understand the physiological basis of such salt tolerance, we exposed wild-collected individuals to salt spray for 60 days, then measured leaf expansion, osmotic potential, sodium leaf concentration, chlorophyll leaf index, chlorophyll fluorescence, relative growth rate, and pressure-volume curves. RESULTS There is no local adaptation to salt spray since both inland and coastal plants have a high tolerance to salt stress. This tolerance is explained by the ability to tolerate high concentrations of salt in leaf tissues, which is related to the high succulence displayed by this species. CONCLUSIONS We showed an unprecedented salt tolerance level for an orchid species, highlighting our limited knowledge of that trait beyond the traditional studied groups. Another interesting finding is that salt tolerance in E. fulgens is linked to succulence, is widespread, and is not the result of local adaptation. We suggest that E. fulgens and its allied species could be an interesting group to explore the evolution of important traits related to tolerance to salt stress, like succulence.
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Affiliation(s)
- Thales M de Lima
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Laboratório de Ecologia Evolutiva e Genômica de Plantas, Campinas, 13083-862, SP, Brazil
| | - Simone F Silva
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Laboratory of Crop Physiology (LCroP), Campinas, 13083-862, SP, Brazil
| | - Rafael V Ribeiro
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Laboratory of Crop Physiology (LCroP), Campinas, 13083-862, SP, Brazil
| | - Julia Sánchez-Vilas
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, CF10 3AX, UK
- Departamento de Bioloxía Funcional, Facultade de Bioloxía, Universidade de Santiago de Compostela, Lope Gomez de Marzoa s/n, Santiago de Compostela, 15782, Spain
| | - Fabio Pinheiro
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Laboratório de Ecologia Evolutiva e Genômica de Plantas, Campinas, 13083-862, SP, Brazil
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2
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Guedri MM, Krir N, Terol CC, Romdhane M, Boulila A, Guetat A. Phytochemical Analysis, Acetylcholinesterase Inhibition, Antidiabetic and Antioxidant Activities of Atriplex halimus L. (Amaranthaceae Juss.). Chem Biodivers 2024; 21:e202301941. [PMID: 38224199 DOI: 10.1002/cbdv.202301941] [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: 12/10/2023] [Revised: 01/13/2024] [Accepted: 01/14/2024] [Indexed: 01/16/2024]
Abstract
Mediterranean saltbush Atriplex halimus L. (Amaranthaceae) from different bioclimatic arid zones (ten wild populations) were studied. Phenols contents, flavonoids, flavonols, tannins and anthocyanins were determined and then tested for their antioxidants, antidiabetic and anti-acetylcholinesterase (AChE) activities. Levels of total polyphenols including flavonoids and flavonols, tannins and anthocyanins were high and varied significantly among analyzed populations. Nine phenolic acids and four flavonoids were identified for the first time in the methanolic fraction and quantified by liquid high-performance chromatography system HPLC (DAD). All extracts showed a substantial antioxidant activity, as assessed by DPPH assay (1,1-diphenyl-2-picrylhydrazyl free radical) (IC50DPPH=147.3for population of Seliena), Ferric Reducing Antioxidant Power (FRAP; IC50FRAP=3.2 for populations of Sousse and Kairouan), and Chelation Fer test (IC50FerCh=1.5 μg/mL for populations of El-hamma and Mednine). Atriplex halimus possessed a high inhibitory effect against α-amylase activity (up to 2.6 mg ACE/gE), a moderate activity for α-glucosidase (up to 91.0 mg ACE/gE) and AChE (up to 147.2 μg/mL) compared to standard. The analyzed populations were isolated and subdivided into three distinct groups, without any bioclimatic structuration. Enzymatic activities seem to be associated with the presence, in plant extracts, of other classes of compounds then phenols such as terpenes, sterols, saponins, coumarins and carotenoids.
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Affiliation(s)
- Mounira Mkaddem Guedri
- Laboratory of Energy, Water, Environment and Process, LR18ES35), National Engineering School of Gabes, University of Gabes, Zrig Eddakhlania, 6072, Gabes, Tunisia
- Omar elkhattab city-, ZRIG-6029, Gabes, Tunisia
| | - Nouha Krir
- Laboratory of Energy, Water, Environment and Process, LR18ES35), National Engineering School of Gabes, University of Gabes, Zrig Eddakhlania, 6072, Gabes, Tunisia
- Omar elkhattab city-, ZRIG-6029, Gabes, Tunisia
| | - Carolina Clausell Terol
- Départamento de Ingeniería Química, Instituto Universitario de Tecnología Cerámica, Universitat Jaume I, 12071, Castellón, Spain
| | - Mehrez Romdhane
- Laboratory of Energy, Water, Environment and Process, LR18ES35), National Engineering School of Gabes, University of Gabes, Zrig Eddakhlania, 6072, Gabes, Tunisia
- Omar elkhattab city-, ZRIG-6029, Gabes, Tunisia
| | - Abdennacer Boulila
- Laboratory of Natural Substances LR10INRAP02, National Institute of Research and Physico-Chemical Analyses, Biotechpole of Sidi Thabet, Ariana, Tunisia
| | - Arbi Guetat
- Northern Border University, College of Sciences, Department of Biological Sciences, Arar, Saudi Arabia
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3
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Wesselkamp M, Roberts DR, Dormann CF. Identifying potential provenances for climate-change adaptation using spatially variable coefficient models. BMC Ecol Evol 2024; 24:70. [PMID: 38807083 DOI: 10.1186/s12862-024-02260-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 05/22/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Selection of climate-change adapted ecotypes of commercially valuable species to date relies on DNA-assisted screening followed by growth trials. For trees, such trials can take decades, hence any approach that supports focussing on a likely set of candidates may save time and money. We use a non-stationary statistical analysis with spatially varying coefficients to identify ecotypes that indicate first regions of similarly adapted varieties of Douglas-fir (Pseudotsuga menziesii (Mirbel) Franco) in North America. For over 70,000 plot-level presence-absences, spatial differences in the survival response to climatic conditions are identified. RESULTS The spatially-variable coefficient model fits the data substantially better than a stationary, i.e. constant-effect analysis (as measured by AIC to account for differences in model complexity). Also, clustering the model terms identifies several potential ecotypes that could not be derived from clustering climatic conditions itself. Comparing these six identified ecotypes to known genetically diverging regions shows some congruence, as well as some mismatches. However, comparing ecotypes among each other, we find clear differences in their climate niches. CONCLUSION While our approach is data-demanding and computationally expensive, with the increasing availability of data on species distributions this may be a useful first screening step during the search for climate-change adapted varieties. With our unsupervised learning approach being explorative, finely resolved genotypic data would be helpful to improve its quantitative validation.
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Affiliation(s)
- Marieke Wesselkamp
- Department of Biometry and Environmental System Analysis, University of Freiburg, Tennenbacher Straße 4, Freiburg, 79106, Germany.
| | - David R Roberts
- Department of Biometry and Environmental System Analysis, University of Freiburg, Tennenbacher Straße 4, Freiburg, 79106, Germany
- InnoTech Alberta, 3608 - 33 Street NW, Calgary, AB, T2L 2A6, Canada
- Alberta Biodiversity Monitoring Institute, 1-107 Centennial Centre for Interdisciplinary Studies (CCIS), University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Carsten F Dormann
- Department of Biometry and Environmental System Analysis, University of Freiburg, Tennenbacher Straße 4, Freiburg, 79106, Germany
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McLaughlin CM, Li M, Perryman M, Heymans A, Schneider H, Lasky JR, Sawers RJH. Evidence that variation in root anatomy contributes to local adaptation in Mexican native maize. Evol Appl 2024; 17:e13673. [PMID: 38468714 PMCID: PMC10925829 DOI: 10.1111/eva.13673] [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: 12/07/2023] [Revised: 02/07/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Mexican native maize (Zea mays ssp. mays) is adapted to a wide range of climatic and edaphic conditions. Here, we focus specifically on the potential role of root anatomical variation in this adaptation. Given the investment required to characterize root anatomy, we present a machine-learning approach using environmental descriptors to project trait variation from a relatively small training panel onto a larger panel of genotyped and georeferenced Mexican maize accessions. The resulting models defined potential biologically relevant clines across a complex environment that we used subsequently for genotype-environment association. We found evidence of systematic variation in maize root anatomy across Mexico, notably a prevalence of trait combinations favoring a reduction in axial hydraulic conductance in varieties sourced from cooler, drier highland areas. We discuss our results in the context of previously described water-banking strategies and present candidate genes that are associated with both root anatomical and environmental variation. Our strategy is a refinement of standard environmental genome-wide association analysis that is applicable whenever a training set of georeferenced phenotypic data is available.
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Affiliation(s)
- Chloee M. McLaughlin
- Intercollege Graduate Degree Program in Plant BiologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Meng Li
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Melanie Perryman
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Adrien Heymans
- Umeå Plant Science Centre, Department of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeåSweden
- Earth and Life InstituteUC LouvainLouvain‐la‐NeuveBelgium
| | - Hannah Schneider
- Department of Physiology and Cell BiologyLeibniz Institute for Plant Genetics and Crop Plant Research (IPK)SeelandGermany
| | - Jesse R. Lasky
- Department of BiologyThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Ruairidh J. H. Sawers
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
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5
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Muniz AC, de Oliveira Buzatti RS, de Lemos-Filho JP, Heuertz M, Nazareno AG, Lovato MB. Genomic signatures of ecological divergence between savanna and forest populations of a Neotropical tree. ANNALS OF BOTANY 2023; 132:523-540. [PMID: 37642427 PMCID: PMC10667007 DOI: 10.1093/aob/mcad120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND AND AIMS In eastern Neotropical South America, the Cerrado, a large savanna vegetation, and the Atlantic Forest harbour high biodiversity levels, and their habitats are rather different from each other. The biomes have intrinsic evolutionary relationships, with high lineage exchange that can be attributed, in part, to a large contact zone between them. The genomic study of ecotypes, i.e. populations adapted to divergent habitats, can be a model to study the genomic signatures of ecological divergence. Here, we investigated two ecotypes of the tree Plathymenia reticulata, one from the Cerrado and the other from the Atlantic Forest, which have a hybrid zone in the ecotonal zone of Atlantic Forest-Cerrado. METHODS The ecotypes were sampled in the two biomes and their ecotone. The evolutionary history of the divergence of the species was analysed with double-digest restriction site-associated DNA sequencing. The genetic structure and the genotypic composition of the hybrid zone were determined. Genotype-association analyses were performed, and the loci under putative selection and their functions were investigated. KEY RESULTS High divergence between the two ecotypes was found, and only early-generation hybrids were found in the hybrid zone, suggesting a partial reproductive barrier. Ancient introgression between the Cerrado and Atlantic Forest was not detected. The soil and climate were associated with genetic divergence in Plathymenia ecotypes and outlier loci were found to be associated with the stress response, with stomatal and root development and with reproduction. CONCLUSIONS The high genomic, ecological and morphophysiological divergence between ecotypes, coupled with partial reproductive isolation, indicate that the ecotypes represent two species and should be managed as different evolutionary lineages. We advise that the forest species should be re-evaluated and restated as vulnerable. Our results provide insights into the genomic mechanisms underlying the diversification of species across savanna and forest habitats and the evolutionary forces acting in the species diversification in the Neotropics.
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Affiliation(s)
- André Carneiro Muniz
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP 486, Belo Horizonte, MG 31270-901, Brazil
| | | | - José Pires de Lemos-Filho
- Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Myriam Heuertz
- Biogeco, INRAE, Univ. Bordeaux, 69 route d’Arcachon, 33610 Cestas, France
| | - Alison Gonçalves Nazareno
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP 486, Belo Horizonte, MG 31270-901, Brazil
| | - Maria Bernadete Lovato
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP 486, Belo Horizonte, MG 31270-901, Brazil
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Gao L, Kantar MB, Moxley D, Ortiz-Barrientos D, Rieseberg LH. Crop adaptation to climate change: An evolutionary perspective. MOLECULAR PLANT 2023; 16:1518-1546. [PMID: 37515323 DOI: 10.1016/j.molp.2023.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023]
Abstract
The disciplines of evolutionary biology and plant and animal breeding have been intertwined throughout their development, with responses to artificial selection yielding insights into the action of natural selection and evolutionary biology providing statistical and conceptual guidance for modern breeding. Here we offer an evolutionary perspective on a grand challenge of the 21st century: feeding humanity in the face of climate change. We first highlight promising strategies currently under way to adapt crops to current and future climate change. These include methods to match crop varieties with current and predicted environments and to optimize breeding goals, management practices, and crop microbiomes to enhance yield and sustainable production. We also describe the promise of crop wild relatives and recent technological innovations such as speed breeding, genomic selection, and genome editing for improving environmental resilience of existing crop varieties or for developing new crops. Next, we discuss how methods and theory from evolutionary biology can enhance these existing strategies and suggest novel approaches. We focus initially on methods for reconstructing the evolutionary history of crops and their pests and symbionts, because such historical information provides an overall framework for crop-improvement efforts. We then describe how evolutionary approaches can be used to detect and mitigate the accumulation of deleterious mutations in crop genomes, identify alleles and mutations that underlie adaptation (and maladaptation) to agricultural environments, mitigate evolutionary trade-offs, and improve critical proteins. Continuing feedback between the evolution and crop biology communities will ensure optimal design of strategies for adapting crops to climate change.
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Affiliation(s)
- Lexuan Gao
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Michael B Kantar
- Department of Tropical Plant & Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Dylan Moxley
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences and Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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Bock DG, Cai Z, Elphinstone C, González-Segovia E, Hirabayashi K, Huang K, Keais GL, Kim A, Owens GL, Rieseberg LH. Genomics of plant speciation. PLANT COMMUNICATIONS 2023; 4:100599. [PMID: 37050879 PMCID: PMC10504567 DOI: 10.1016/j.xplc.2023.100599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Studies of plants have been instrumental for revealing how new species originate. For several decades, botanical research has complemented and, in some cases, challenged concepts on speciation developed via the study of other organisms while also revealing additional ways in which species can form. Now, the ability to sequence genomes at an unprecedented pace and scale has allowed biologists to settle decades-long debates and tackle other emerging challenges in speciation research. Here, we review these recent genome-enabled developments in plant speciation. We discuss complications related to identification of reproductive isolation (RI) loci using analyses of the landscape of genomic divergence and highlight the important role that structural variants have in speciation, as increasingly revealed by new sequencing technologies. Further, we review how genomics has advanced what we know of some routes to new species formation, like hybridization or whole-genome duplication, while casting doubt on others, like population bottlenecks and genetic drift. While genomics can fast-track identification of genes and mutations that confer RI, we emphasize that follow-up molecular and field experiments remain critical. Nonetheless, genomics has clarified the outsized role of ancient variants rather than new mutations, particularly early during speciation. We conclude by highlighting promising avenues of future study. These include expanding what we know so far about the role of epigenetic and structural changes during speciation, broadening the scope and taxonomic breadth of plant speciation genomics studies, and synthesizing information from extensive genomic data that have already been generated by the plant speciation community.
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Affiliation(s)
- Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Zhe Cai
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Cassandra Elphinstone
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Eric González-Segovia
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | | | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Graeme L Keais
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Amy Kim
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Gregory L Owens
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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Brandvain Y, Sianta S. A few genetic variants go a long way in differentiating Penstemon species. PLoS Biol 2023; 21:e3002322. [PMID: 37773919 PMCID: PMC10540943 DOI: 10.1371/journal.pbio.3002322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023] Open
Abstract
The integrity of hybridizing species is usually maintained by genome-wide selection or by selection on a few genomic regions. A study published in PLOS Biology finds a different pattern-60 SNPs spread across the genome differentiate a Penstemon species pair.
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Affiliation(s)
- Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Shelley Sianta
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
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Iozia LM, Varone L. Tackling local ecological homogeneity: Finding intraspecific trait variability in local populations of Mediterranean plants. Ecol Evol 2023; 13:e10550. [PMID: 37732284 PMCID: PMC10507572 DOI: 10.1002/ece3.10550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/26/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023] Open
Abstract
Local homogeneity, in ecology, is the often undisclosed assumption that variability within populations is negligible or mostly distributed evenly. In large areas, this can lead to the aggregation of different populations without regard for their unique needs and characteristics, such as drought sensitivity and functional trait distributions. Here, we discuss whether this assumption can be justified, and we hypothesize that discerning the source of variation between plasticity and adaptation could be a feasible approach to formulate an informed decision. We test this hypothesis on plants, resorting to a common garden experiment to determine the source of variation of several plant functional traits at a local scale (~60 km) of three wild species: Quercus ilex, Pistacia lentiscus, and Cistus salviifolius. Individuals of each species were sourced from three key sites chosen along a local aridity gradient. Our approach led to the rejection of the local homogeneity assumption for Q. ilex and C. salviifolius at this scale due to the adaptive divergence observed among neighboring populations. This case study provides evidence that addressing local homogeneity can highlight diverging populations in a relatively simple way. We conclude that gathering empirical evidence on intraspecific variability is a feasible approach that can provide researchers with solid bases to decide whether to adopt the local homogeneity assumption or not.
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Affiliation(s)
| | - Laura Varone
- Department of Environmental BiologySapienza University of RomeRomeItaly
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Muluneh B, Taye M, Dessie T, Wondim DS, Kebede D, Tenagne A. Morpho-biometric characterization of indigenous chicken ecotypes in north-western Ethiopia. PLoS One 2023; 18:e0286299. [PMID: 37267393 DOI: 10.1371/journal.pone.0286299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/13/2023] [Indexed: 06/04/2023] Open
Abstract
Morphological characterization of Animal Genetic Resources is the first step to documenting diversity and designing breed specific breeding programs. The current study characterized the morpho-biometric variation of indigenous chicken ecotypes prevailing in northwestern Ethiopia. A multi-stage purposive, stratified, and random sampling method was employed to select the study areas and chickens. A total of 1200 adult chickens were sampled and characterized for 12 qualitative and 11 quantitative traits. Univariate and multivariate data analysis methods were employed to analyze the data using SAS and R statistical software. Red plumage colour (33.2%), white and red earlobe colour (73.8%) and yellow shank colour (57.0%) were the most predominant colour trait categories. Sex, agro-ecology, location, and the interaction of sex and location had a highly significant (p<0.001) effect on all body measurements. Shank traits were found to have the highest discriminating power in both sexes. The overall classification rates for the female and male sample populations were 57.47% and 69.97%, respectively. The squared Mahalanobis distances between sites were significant (p<0.001) for both sexes. The longest distance was obtained between North Achefer and Banja (19.25) and between North Achefer and Dembecha (16.80) in female and male chickens, respectively. In female chickens, canonical variates 1 (CAN 1) and 2 (CAN 2) explained 82% of total variation and distinctly separated the sample populations of North Achefer and Jawi from others. In male chickens, 90% of the total variance is explained by CAN1, CAN2, and CAN3, which distinctly separate the sample populations of the North Achefer, Sinan, and Jawi, among others. Using cluster analysis, the indigenous chickens found in the study area could be classified into four ecotypes: ecotype 1 (Banja, Dembecha, and Aneded), ecotype 2 (North Achefer), ecotype 3 (Sinan), and ecotype 4 (Jawi).
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Affiliation(s)
- Bekalu Muluneh
- Department of Animal Science, College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Animal and Range Sciences, Dawuro Tarcha Campus, Wolaita Sodo University, Sodo, Ethiopia
| | - Mengistie Taye
- Department of Animal Science, College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Tadelle Dessie
- Department of Animal Science, College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Dessie Salilew Wondim
- Department of Animal Science, College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Animal Breeding and Husbandry, Institute of Animal Sciences, University of Bonn, Bonn, Germany
| | - Damitie Kebede
- Department of Animal Science, College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Andualem Tenagne
- Department of Animal Science, College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Animal Sciences, Assosa University, Assosa, Ethiopia
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Small ST, Costantini C, Sagnon N, Guelbeogo MW, Emrich SJ, Kern AD, Fontaine MC, Besansky NJ. Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria mosquito. Proc Natl Acad Sci U S A 2023; 120:e2219835120. [PMID: 36881629 PMCID: PMC10089221 DOI: 10.1073/pnas.2219835120] [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: 11/26/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
Species distributed across heterogeneous environments often evolve locally adapted ecotypes, but understanding of the genetic mechanisms involved in their formation and maintenance in the face of gene flow is incomplete. In Burkina Faso, the major African malaria mosquito Anopheles funestus comprises two strictly sympatric and morphologically indistinguishable yet karyotypically differentiated forms reported to differ in ecology and behavior. However, knowledge of the genetic basis and environmental determinants of An. funestus diversification was impeded by lack of modern genomic resources. Here, we applied deep whole-genome sequencing and analysis to test the hypothesis that these two forms are ecotypes differentially adapted to breeding in natural swamps versus irrigated rice fields. We demonstrate genome-wide differentiation despite extensive microsympatry, synchronicity, and ongoing hybridization. Demographic inference supports a split only ~1,300 y ago, closely following the massive expansion of domesticated African rice cultivation ~1,850 y ago. Regions of highest divergence, concentrated in chromosomal inversions, were under selection during lineage splitting, consistent with local adaptation. The origin of nearly all variations implicated in adaptation, including chromosomal inversions, substantially predates the ecotype split, suggesting that rapid adaptation was fueled mainly by standing genetic variation. Sharp inversion frequency differences likely facilitated adaptive divergence between ecotypes by suppressing recombination between opposing chromosomal orientations of the two ecotypes, while permitting free recombination within the structurally monomorphic rice ecotype. Our results align with growing evidence from diverse taxa that rapid ecological diversification can arise from evolutionarily old structural genetic variants that modify genetic recombination.
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Affiliation(s)
- Scott T. Small
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR97403
| | - Carlo Costantini
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
- Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control (MIVEGEC), Université de Montpellier, CNRS 5290, Institute of Research for Development (IRD) 224, F-34394Montpellier, France
| | - N’Fale Sagnon
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
| | - Moussa W. Guelbeogo
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
| | - Scott J. Emrich
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN46556
| | - Andrew D. Kern
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR97403
| | - Michael C. Fontaine
- Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control (MIVEGEC), Université de Montpellier, CNRS 5290, Institute of Research for Development (IRD) 224, F-34394Montpellier, France
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AGGroningen, The Netherlands
| | - Nora J. Besansky
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
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12
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Vogt G. Environmental Adaptation of Genetically Uniform Organisms with the Help of Epigenetic Mechanisms-An Insightful Perspective on Ecoepigenetics. EPIGENOMES 2022; 7:1. [PMID: 36648862 PMCID: PMC9844400 DOI: 10.3390/epigenomes7010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022] Open
Abstract
Organisms adapt to different environments by selection of the most suitable phenotypes from the standing genetic variation or by phenotypic plasticity, the ability of single genotypes to produce different phenotypes in different environments. Because of near genetic identity, asexually reproducing populations are particularly suitable for the investigation of the potential and molecular underpinning of the latter alternative in depth. Recent analyses on the whole-genome scale of differently adapted clonal animals and plants demonstrated that epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs are among the molecular pathways supporting phenotypic plasticity and that epigenetic variation is used to stably adapt to different environments. Case studies revealed habitat-specific epigenetic fingerprints that were maintained over subsequent years pointing at the existence of epigenetic ecotypes. Environmentally induced epimutations and corresponding gene expression changes provide an ideal means for fast and directional adaptation to changing or new conditions, because they can synchronously alter phenotypes in many population members. Because microorganisms inclusive of human pathogens also exploit epigenetically mediated phenotypic variation for environmental adaptation, this phenomenon is considered a universal biological principle. The production of different phenotypes from the same DNA sequence in response to environmental cues by epigenetic mechanisms also provides a mechanistic explanation for the "general-purpose genotype hypothesis" and the "genetic paradox of invasions".
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Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
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13
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Razzaque S, Juenger TE. The ecology and quantitative genetics of seed and seedling traits in upland and lowland ecotypes of a perennial grass. Evol Lett 2022; 6:460-473. [PMID: 36579162 PMCID: PMC9783394 DOI: 10.1002/evl3.297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 09/19/2022] [Accepted: 09/29/2022] [Indexed: 11/23/2022] Open
Abstract
Plants have evolved diverse reproductive allocation strategies and seed traits to aid in dispersal, persistence in the seed bank, and establishment. In particular, seed size, dormancy, and early seedling vigor are thought to be key functional traits with important recruitment and fitness consequences across abiotic stress gradients. Selection for favored seed-trait combinations, or against maladaptive combinations, is likely an important driver shaping recruitment strategies. Here, we test for seed-trait plasticity and patterns of recruitment using two genotypes representative of contrasting upland and lowland ecotypes of Panicum hallii with field experiments in native versus foreign habitats. Furthermore, we test whether seed traits have been under directional selection in P. hallii using the v-test based on trait variance in a genetic cross. Finally, we evaluate the genetic architecture of ecotypic divergence for these traits with quantitative trait locus (QTL) mapping. Field experiments reveal little plasticity but support a hypothesis of adaptation divergence among ecotypes based on recruitment. Patterns of segregation within recombinant hybrids provides strong support for directional selection driving ecotypic divergence in seed traits. Genetic mapping revealed a polygenic architecture with evidence of genetic correlation between seed mass, dormancy, and seedling vigor. Our results suggest that the evolution of these traits may involve constraints that affect the direction of adaptive divergence. For example, seed size and germination percentage shared two colocalized QTL with antagonistic additive effects. This supports the hypothesis of a functional genetic relationship between these traits, resulting in either large seed/strong dormancy or small seed/weak dormancy trait combinations. Overall, our study provides insights into the factors facilitating and potentially constraining ecotypic differentiation in seed traits.
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Affiliation(s)
- Samsad Razzaque
- Department of Integrative BiologyUniversity of Texas at AustinAustinTexas78712,Current Address: Plant Molecular and Cellular Biology LaboratorySalk Institute for Biological StudiesLa JollaCalifornia92037
| | - Thomas E. Juenger
- Department of Integrative BiologyUniversity of Texas at AustinAustinTexas78712
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14
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Wadgymar SM, DeMarche ML, Josephs EB, Sheth SN, Anderson JT. Local adaptation: Causal agents of selection and adaptive trait divergence. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2022; 53:87-111. [PMID: 37790997 PMCID: PMC10544833 DOI: 10.1146/annurev-ecolsys-012722-035231] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Divergent selection across the landscape can favor the evolution of local adaptation in populations experiencing contrasting conditions. Local adaptation is widely observed in a diversity of taxa, yet we have a surprisingly limited understanding of the mechanisms that give rise to it. For instance, few have experimentally confirmed the biotic and abiotic variables that promote local adaptation, and fewer yet have identified the phenotypic targets of selection that mediate local adaptation. Here, we highlight critical gaps in our understanding of the process of local adaptation and discuss insights emerging from in-depth investigations of the agents of selection that drive local adaptation, the phenotypes they target, and the genetic basis of these phenotypes. We review historical and contemporary methods for assessing local adaptation, explore whether local adaptation manifests differently across life history, and evaluate constraints on local adaptation.
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Affiliation(s)
| | - Megan L DeMarche
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Seema N Sheth
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Jill T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, 30602
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15
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Dunning LT, Olofsson JK, Papadopulos AST, Hibdige SGS, Hidalgo O, Leitch IJ, Baleeiro PC, Ntshangase S, Barker N, Jobson RW. Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia. Mol Ecol 2022; 31:5846-5860. [PMID: 36089907 PMCID: PMC9828686 DOI: 10.1111/mec.16691] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 01/13/2023]
Abstract
Ecotypes are distinct populations within a species that are adapted to specific environmental conditions. Understanding how these ecotypes become established, and how they interact when reunited, is fundamental to elucidating how ecological adaptations are maintained. This study focuses on Themeda triandra, a dominant grassland species across Asia, Africa and Australia. It is the most widespread plant in Australia, where it has distinct ecotypes that are usually restricted to either wetter and cooler coastal regions or the drier and hotter interior. We generate a reference genome for T. triandra and use whole genome sequencing for over 80 Themeda accessions to reconstruct the evolutionary history of T. triandra and related taxa. Organelle phylogenies confirm that Australia was colonized by T. triandra twice, with the division between ecotypes predating their arrival in Australia. The nuclear genome provides evidence of differences in the dominant ploidal level and gene-flow among the ecotypes. In northern Queensland there appears to be a hybrid zone between ecotypes with admixed nuclear genomes and shared chloroplast haplotypes. Conversely, in the cracking claypans of Western Australia, there is cytonuclear discordance with individuals possessing the coastal chloroplast and interior clade nuclear genome. This chloroplast capture is potentially a result of adaptive introgression, with selection detected in the rpoC2 gene which is associated with water use efficiency. The reason that T. triandra is the most widespread plant in Australia appears to be a result of distinct ecotypic genetic variation and genome duplication, with the importance of each depending on the geographic scale considered.
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Affiliation(s)
- Luke T. Dunning
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldSheffieldUK
| | - Jill K. Olofsson
- Section for Forest, Nature and Biomass, Department of Geosciences and Natural Resource ManagementUniversity of CopenhagenFrederiksberg CDenmark
| | | | - Samuel G. S. Hibdige
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldSheffieldUK
| | - Oriane Hidalgo
- Royal Botanic GardensSurreyUK,Institut Botànic de Barcelona (IBB), CSIC‐Ajuntament de BarcelonaBarcelonaSpain
| | | | - Paulo C. Baleeiro
- Department of Biological ScienceThe University of QueenslandSt LuciaQueenslandAustralia
| | | | - Nigel Barker
- Department of Plant and Soil SciencesUniversity of PretoriaHatfieldSouth Africa
| | - Richard W. Jobson
- National Herbarium of New South Wales, Australian Institute of Botanical ScienceSydneyNew South WalesAustralia
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16
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Bertel C, Kaplenig D, Ralser M, Arc E, Kolář F, Wos G, Hülber K, Holzinger A, Kranner I, Neuner G. Parallel Differentiation and Plastic Adjustment of Leaf Anatomy in Alpine Arabidopsis arenosa Ecotypes. PLANTS (BASEL, SWITZERLAND) 2022; 11:2626. [PMID: 36235492 PMCID: PMC9573220 DOI: 10.3390/plants11192626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 09/29/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
Functional and structural adjustments of plants in response to environmental factors, including those occurring in alpine habitats, can result in transient acclimation, plastic phenotypic adjustments and/or heritable adaptation. To unravel repeatedly selected traits with potential adaptive advantage, we studied parallel (ecotypic) and non-parallel (regional) differentiation in leaf traits in alpine and foothill ecotypes of Arabidopsis arenosa. Leaves of plants from eight alpine and eight foothill populations, representing three independent alpine colonization events in different mountain ranges, were investigated by microscopy techniques after reciprocal transplantation. Most traits clearly differed between the foothill and the alpine ecotype, with plastic adjustments to the local environment. In alpine populations, leaves were thicker, with altered proportions of palisade and spongy parenchyma, and had fewer trichomes, and chloroplasts contained large starch grains with less stacked grana thylakoids compared to foothill populations. Geographical origin had no impact on most traits except for trichome and stomatal density on abaxial leaf surfaces. The strong parallel, heritable ecotypic differentiation in various leaf traits and the absence of regional effects suggests that most of the observed leaf traits are adaptive. These trait shifts may reflect general trends in the adaptation of leaf anatomy associated with the colonization of alpine habitats.
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Affiliation(s)
- Clara Bertel
- Department of Botany, University of Innsbruck, 6020 Innsbruck, Austria
| | - Dominik Kaplenig
- Department of Botany, University of Innsbruck, 6020 Innsbruck, Austria
| | - Maria Ralser
- Department of Botany, University of Innsbruck, 6020 Innsbruck, Austria
| | - Erwann Arc
- Department of Botany, University of Innsbruck, 6020 Innsbruck, Austria
| | - Filip Kolář
- Department of Botany, Charles University of Prague, 110 00 Prague, Czech Republic
| | - Guillaume Wos
- Institute of Nature Conservation, Polish Academy of Sciences, 00-901 Krakow, Poland
| | - Karl Hülber
- Department of Botany and Biodiversity Research, University of Vienna, 1010 Vienna, Austria
| | - Andreas Holzinger
- Department of Botany, University of Innsbruck, 6020 Innsbruck, Austria
| | - Ilse Kranner
- Department of Botany, University of Innsbruck, 6020 Innsbruck, Austria
| | - Gilbert Neuner
- Department of Botany, University of Innsbruck, 6020 Innsbruck, Austria
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17
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Christie K, Fraser LS, Lowry DB. The strength of reproductive isolating barriers in seed plants: Insights from studies quantifying premating and postmating reproductive barriers over the past 15 years. Evolution 2022; 76:2228-2243. [PMID: 35838076 PMCID: PMC9796645 DOI: 10.1111/evo.14565] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/23/2022] [Accepted: 06/30/2022] [Indexed: 01/22/2023]
Abstract
Speciation is driven by the evolution of reproductive isolating barriers that reduce, and ultimately prevent, substantial gene flow between lineages. Despite its central role in evolutionary biology, the process can be difficult to study because it proceeds differently among groups and may occur over long timescales. Due to this complexity, we typically rely on generalizations of empirical data to describe and understand the process. Previous reviews of reproductive isolation (RI) in flowering plants have suggested that prezygotic or extrinsic barriers generally have a stronger effect on reducing gene flow compared to postzygotic or intrinsic barriers. Past conclusions have rested on relatively few empirical estimates of RI; however, RI data have become increasingly abundant over the past 15 years. We analyzed data from recent studies quantifying multiple pre- and postmating barriers in plants and compared the strengths of isolating barriers across 89 taxa pairs using standardized RI metrics. Individual prezygotic barriers were on average stronger than individual postzygotic barriers, and the total strength of prezygotic RI was approximately twice that of postzygotic RI. These findings corroborate that ecological divergence and extrinsic factors, as opposed to solely the accumulation of genetic incompatibilities, are important to speciation and the maintenance of species boundaries in plants. Despite an emphasis in the literature on asymmetric postmating and postzygotic RI, we found that prezygotic barriers acted equally asymmetrically. Overall, substantial variability in the strengths of 12 isolating barriers highlights the great diversity of mechanisms that contribute to plant diversification.
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Affiliation(s)
- Kyle Christie
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan48824,Department of Biological SciencesNorthern Arizona UniversityFlagstaffArizona86011
| | - Linnea S. Fraser
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan48824
| | - David B. Lowry
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan48824
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18
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Kaplenig D, Bertel C, Arc E, Villscheider R, Ralser M, Kolář F, Wos G, Hülber K, Kranner I, Neuner G. Repeated colonization of alpine habitats by Arabidopsis arenosa viewed through freezing resistance and ice management strategies. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:939-949. [PMID: 35833328 PMCID: PMC9804731 DOI: 10.1111/plb.13454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 06/15/2022] [Indexed: 05/17/2023]
Abstract
Success or failure of plants to cope with freezing temperatures can critically influence plant distribution and adaptation to new habitats. Especially in alpine environments, frost is a likely major selective force driving adaptation. In Arabidopsis arenosa (L.) Lawalrée, alpine populations have evolved independently in different mountain ranges, enabling studying mechanisms of acclimation and adaptation to alpine environments. We tested for heritable, parallel differentiation in freezing resistance, cold acclimation potential and ice management strategies using eight alpine and eight foothill populations. Plants from three European mountain ranges (Niedere Tauern, Făgăraș and Tatra Mountains) were grown from seeds of tetraploid populations in four common gardens, together with diploid populations from the Tatra Mountains. Freezing resistance was assessed using controlled freezing treatments and measuring effective quantum yield of photosystem II, and ice management strategies by infrared video thermography and cryomicroscopy. The alpine ecotype had a higher cold acclimation potential than the foothill ecotype, whereby this differentiation was more pronounced in tetraploid than diploid populations. However, no ecotypic differentiation was found in one region (Făgăraș), where the ancient lineage had a different evolutionary history. Upon freezing, an ice lens within a lacuna between the palisade and spongy parenchyma tissues was formed by separation of leaf tissues, a mechanism not previously reported for herbaceous species. The dynamic adjustment of freezing resistance to temperature conditions may be particularly important in alpine environments characterized by large temperature fluctuations. Furthermore, the formation of an extracellular ice lens may be a useful strategy to avoid tissue damage during freezing.
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Affiliation(s)
- D. Kaplenig
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
| | - C. Bertel
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
| | - E. Arc
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
| | | | - M. Ralser
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
| | - F. Kolář
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
- Department of BotanyCharles University of PraguePragueCzech Republic
| | - G. Wos
- Department of BotanyCharles University of PraguePragueCzech Republic
| | - K. Hülber
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - I. Kranner
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
| | - G. Neuner
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
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19
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Vallejo-Trujillo A, Kebede A, Lozano-Jaramillo M, Dessie T, Smith J, Hanotte O, Gheyas AA. Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.866587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In evolutionary ecology, an “ecotype” is a population that is genetically adapted to specific environmental conditions. Environmental and genetic characterisation of livestock ecotypes can play a crucial role in conservation and breeding improvement, particularly to achieve climate resilience. However, livestock ecotypes are often arbitrarily defined without a detailed characterisation of their agro-ecologies. In this study, we employ a novel integrated approach, combining ecological niche modelling (ENM) with genomics, to delineate ecotypes based on environmental characterisation of population habitats and unravel the signatures of adaptive selection in the ecotype genomes. The method was applied on 25 Ethiopian village chicken populations representing diverse agro-climatic conditions. ENM identified six key environmental drivers of adaptation and delineated 12 ecotypes. Within-ecotype selection signature analyses (using Hp and iHS methods) identified 1,056 candidate sweep regions (SRs) associated with diverse biological processes. While most SRs are ecotype-specific, the biological pathways perturbed by overlapping genes are largely shared among ecotypes. A few biological pathways were shared amongst most ecotypes and the genes involved showed functions important for scavenging chickens, e.g., neuronal development/processes, immune response, vision development, and learning. Genotype-environment association using redundancy analysis (RDA) allowed for correlating ∼33% of the SRs with major environmental drivers. Inspection of some strong candidate genes from selection signature analysis and RDA showed highly relevant functions in relation to the major environmental drivers of corresponding ecotypes. This integrated approach offers a powerful tool to gain insight into the complex processes of adaptive evolution including the genotype × environment (G × E) interactions.
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20
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Hager ER, Harringmeyer OS, Wooldridge TB, Theingi S, Gable JT, McFadden S, Neugeboren B, Turner KM, Jensen JD, Hoekstra HE. A chromosomal inversion contributes to divergence in multiple traits between deer mouse ecotypes. Science 2022; 377:399-405. [PMID: 35862520 DOI: 10.1126/science.abg0718] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
How locally adapted ecotypes are established and maintained within a species is a long-standing question in evolutionary biology. Using forest and prairie ecotypes of deer mice (Peromyscus maniculatus), we characterized the genetic basis of variation in two defining traits-tail length and coat color-and discovered a 41-megabase chromosomal inversion linked to both. The inversion frequency is 90% in the dark, long-tailed forest ecotype; decreases across a habitat transition; and is absent from the light, short-tailed prairie ecotype. We implicate divergent selection in maintaining the inversion at frequencies observed in the wild, despite high levels of gene flow, and explore fitness benefits that arise from suppressed recombination within the inversion. We uncover a key role for a large, previously uncharacterized inversion in the evolution and maintenance of classic mammalian ecotypes.
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Affiliation(s)
- Emily R Hager
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Olivia S Harringmeyer
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - T Brock Wooldridge
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Shunn Theingi
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Jacob T Gable
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Sade McFadden
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Beverly Neugeboren
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Kyle M Turner
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Hopi E Hoekstra
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
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21
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African trypanosome strategies for conquering new hosts and territories: the end of monophyly? Trends Parasitol 2022; 38:724-736. [DOI: 10.1016/j.pt.2022.05.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 11/22/2022]
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22
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VanWallendael A, Lowry DB, Hamilton JA. One hundred years into the study of ecotypes, new advances are being made through large-scale field experiments in perennial plant systems. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102152. [PMID: 35065527 DOI: 10.1016/j.pbi.2021.102152] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/31/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
A hundred years after Turesson first clearly described how locally adaptive variation is distributed within species, plant biologists are making major breakthroughs in our understanding of mechanisms underlying adaptation from local populations to the scale of continents. Although the genetics of local adaptation has typically been studied in smaller reciprocal transplant experiments, it is now being evaluated with whole genomes in large-scale networks of common garden experiments with perennial switchgrass and poplar trees. These studies support the hypothesis that a complex combination of loci, both with and without adaptive trade-offs, underlies local adaptation and that hybridization and adaptive introgression play a key role in the evolution of these species. Future studies incorporating high-throughput phenotyping, gene expression, and modeling will be used to predict responses of these species to climate change.
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Affiliation(s)
- Acer VanWallendael
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA; Program in Ecology, Evolution, and Behaviour, Michigan State University, East Lansing, MI, 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA; Program in Ecology, Evolution, and Behaviour, Michigan State University, East Lansing, MI, 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA.
| | - Jill A Hamilton
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16801, USA
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23
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Population diversification in the frog Mantidactylus bellyi on an isolated massif in northern Madagascar based on genetic, morphological, bioacoustic and ecological evidence. PLoS One 2022; 17:e0263764. [PMID: 35358210 PMCID: PMC8970393 DOI: 10.1371/journal.pone.0263764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 01/26/2022] [Indexed: 11/19/2022] Open
Abstract
In the processes that give rise to new species, changes first occur at the population level. But with the continuous nature of the divergence process, change in biological properties delimiting the shift from “individuals of divergent populations” towards “individuals of distinct species”, as well as abiotic factors driving the change, remain largely ambivalent. Here we study diversification processes at the population level in a semi-aquatic frog, Mantidactylus (Brygoomantis) bellyi, across the diverse vegetation types of Montagne d’Ambre National Park (MANP), Madagascar. Genetic diversity was assessed with seven newly developed microsatellite markers as well as mitochondrial DNA sequences and concordance with patterns of ecological, morphological, and bioacoustic divergence evaluated. We found M. bellyi lacking mitochondrial differentiation within MANP, while microsatellite datasets partitioned them into three highly differentiated, geographically separated subpopulations (with indications for up to five subpopulations). The molecular grouping–primarily clustering individuals by geographic proximity–was coincident with differences in mean depth and width of waters, suggesting a possible role of fluvial characteristics in genetic exchange in this stream-breeding species. Genetic clustering not consistent with differences in call properties, except for dominant call frequencies under the two-subpopulations model. Morphological divergence was mostly consistent with the genetic clustering; subpopulations strongly differed by their snout-vent length, with individuals from high-elevation subpopulations smaller than those from populations below 1000 m above sea level. These results exemplify how mountains and environmental conditions might primarily shape genetic and morphological divergence in frog populations, without strongly affecting their calls.
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24
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Khan Z, Khan MS, Bawazeer S, Bawazeer N, Suleman, Irfan M, Rauf A, Su XH, Xing LX. A comprehensive review on the documented characteristics of four Reticulitermes termites (Rhinotermitidae, Blattodea) of China. BRAZ J BIOL 2022; 84:e256354. [PMID: 35319619 DOI: 10.1590/1519-6984.256354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/11/2022] [Indexed: 11/22/2022] Open
Abstract
Termites are known as social insects worldwide. Presently in China 473 species, 44 genera and 4 families of termites have been reported. Of them, 111 Reticulitermes species are widely spread in different zones of China. The dispersion flight season of these Chinese Reticulitermes species are usually started from February to June, but in some regions different species are distributed, sharing their boundaries and having overlapping flight seasons. These reasons become important sources of hybridization between two different heterospecific populations of termites. It was confirmed that the fertilized eggs and unfertilized eggs of some Reticulitermes termites have the capacity of cleavage. While the unfertilized eggs of R. aculabialis, R. chinensis and R. labralis cleaved normally and the only R. aculabialis unfertilized eggs develop in embryos. While, the R. flaviceps and R. chinensis were observed with their abnormal embryonic development, and not hatching of eggs parthenogenetically. They were reported more threatening to Chinese resources as they propagate with parthenogenesis, hybridization and sexual reproduction. Eggshell and macrophiles of eggs play important roles in species identification and control. Although, they are severe pests and cause a wide range of damages to wooden structures and products in homes, buildings, building materials, trees, crops, and forests in China's Mainland.
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Affiliation(s)
- Z Khan
- Northwest University, College of Life Sciences, Xi'an, China.,University of Swabi, Zoology Department, Khyber Pakhtunkhwa, Pakistan
| | - M S Khan
- University of Swabi, Zoology Department, Khyber Pakhtunkhwa, Pakistan
| | - S Bawazeer
- Umm Al-Qura University, Faculty of Pharmacy, Department of Pharmacognosy, Makkah, Kingdom of Saudi Arabia
| | - N Bawazeer
- Minister of Interior General Directorate of Prison's Health, Pharmacy Department, Kingdom of Saudi Arabia
| | - Suleman
- University of Swabi, Zoology Department, Khyber Pakhtunkhwa, Pakistan
| | - M Irfan
- Abdul Wali Khan University, Department of Botany, Mardan, Pakistan.,University of Swabi, Department of Botany, Swabi, Pakistan.,Missouri Botanical Garden, St. Louis, MO, U.S.A
| | - A Rauf
- University of Swabi, Department of Chemistry, Anbar, Khyber Pakhtunkhwa, Pakistan
| | - X-H Su
- Northwest University, College of Life Sciences, Xi'an, China.,Northwest University, Shaanxi Key Laboratory for Animal Conservation, Xi'an, China.,Northwest University, Key Laboratory of Resource Biology and Biotechnology, Xi'an, China
| | - L-X Xing
- Northwest University, College of Life Sciences, Xi'an, China.,Northwest University, Shaanxi Key Laboratory for Animal Conservation, Xi'an, China.,Northwest University, Key Laboratory of Resource Biology and Biotechnology, Xi'an, China
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25
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Distinct Cold Acclimation of Productivity Traits in Arabidopsis thaliana Ecotypes. Int J Mol Sci 2022; 23:ijms23042129. [PMID: 35216246 PMCID: PMC8879503 DOI: 10.3390/ijms23042129] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 12/10/2022] Open
Abstract
Improvement of crop climate resilience will require an understanding of whole-plant adaptation to specific local environments. This review places features of plant form and function related to photosynthetic productivity, as well as associated gene-expression patterns, into the context of the adaptation of Arabidopsis thaliana ecotypes to local environments with different climates in Sweden and Italy. The growth of plants under common cool conditions resulted in a proportionally greater emphasis on the maintenance of photosynthetic activity in the Swedish ecotype. This is compared to a greater emphasis on downregulation of light-harvesting antenna size and upregulation of a host of antioxidant enzymes in the Italian ecotype under these conditions. This differential response is discussed in the context of the climatic patterns of the ecotypes’ native habitats with substantial opportunity for photosynthetic productivity under mild temperatures in Italy but not in Sweden. The Swedish ecotype’s response is likened to pushing forward at full speed with productivity under low temperature versus the Italian ecotype’s response of staying safe from harm (maintaining redox homeostasis) while letting productivity decline when temperatures are transiently cold. It is concluded that either strategy can offer directions for the development of climate-resilient crops for specific locations of cultivation.
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26
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Stronen AV, Norman AJ, Vander Wal E, Paquet PC. The relevance of genetic structure in ecotype designation and conservation management. Evol Appl 2022; 15:185-202. [PMID: 35233242 PMCID: PMC8867706 DOI: 10.1111/eva.13339] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/02/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022] Open
Abstract
The concept of ecotypes is complex, partly because of its interdisciplinary nature, but the idea is intrinsically valuable for evolutionary biology and applied conservation. The complex nature of ecotypes has spurred some confusion and inconsistencies in the literature, thereby limiting broader theoretical development and practical application. We provide suggestions for how incorporating genetic analyses can ease confusion and help define ecotypes. We approach this by systematically reviewing 112 publications across taxa that simultaneously mention the terms ecotype, conservation and management, to examine the current use of the term in the context of conservation and management. We found that most ecotype studies involve fish, mammals and plants with a focus on habitat use, which at 60% was the most common criterion used for categorization of ecotypes. Only 53% of the studies incorporated genetic analyses, and major discrepancies in available genomic resources among taxa could have contributed to confusion about the role of genetic structure in delineating ecotypes. Our results show that the rapid advances in genetic methods, also for nonmodel organisms, can help clarify the spatiotemporal distribution of adaptive and neutral genetic variation and their relevance to ecotype designations. Genetic analyses can offer empirical support for the ecotype concept and provide a timely measure of evolutionary potential, especially in changing environmental conditions. Genetic variation that is often difficult to detect, including polygenic traits influenced by small contributions from several genes, can be vital for adaptation to rapidly changing environments. Emerging ecotypes may signal speciation in progress, and findings from genome‐enabled organisms can help clarify important selective factors driving ecotype development and persistence, and thereby improve preservation of interspecific genetic diversity. Incorporation of genetic analyses in ecotype studies will help connect evolutionary biology and applied conservation, including that of problematic groups such as natural hybrid organisms and urban or anthropogenic ecotypes.
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Affiliation(s)
- Astrid V. Stronen
- Department of Biology Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
- Department of Biotechnology and Life Sciences Insubria University Varese Italy
- Department of Chemistry and Bioscience Aalborg University Aalborg Denmark
| | - Anita J. Norman
- Department of Fish, Wildlife and Environmental Studies Swedish University of Agricultural Sciences Umeå Sweden
| | - Eric Vander Wal
- Department of Biology Memorial University of Newfoundland St. John’s NL Canada
| | - Paul C. Paquet
- Department of Geography University of Victoria Victoria BC Canada
- Raincoast Conservation Foundation Sidney BC Canada
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27
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Jamal A, Wen J, Ma ZY, Ahmed I, Abdullah, Chen LQ, Nie ZL, Liu XQ. Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic Genus Chimonanthus (Calycanthaceae) With Implications For Its Phylogeny and Diversification. Front Genet 2021; 12:709996. [PMID: 34917123 PMCID: PMC8670589 DOI: 10.3389/fgene.2021.709996] [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: 05/14/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Chimonanthus of Calycanthaceae is a small endemic genus in China, with unusual winter-blooming sweet flowers widely cultivated for ornamentals and medicinal uses. The evolution of Chimonanthus plastomes and its phylogenetic relationships remain unresolved due to limited availability of genetic resources. Here, we report fully assembled and annotated chloroplast genomes of five Chimonanthus species. The chloroplast genomes of the genus (size range 153,010 – 153,299 bp) reveal high similarities in gene content, gene order, GC content, codon usage, amino acid frequency, simple sequence repeats, oligonucleotide repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions. Signatures of positive selection are detected in atpF and rpoB genes in C. campanulatus. The correlations among substitutions, InDels, and oligonucleotide repeats reveal weak to strong correlations in distantly related species at the intergeneric levels, and very weak to weak correlations among closely related Chimonanthus species. Chloroplast genomes are used to reconstruct a well-resolved phylogenetic tree, which supports the monophyly of Chimonanthus. Within Chimonanthus, C. praecox and C. campanulatus form one clade, while C. grammatus, C. salicifolius, C. zhejiangensis, and C. nitens constitute another clade. Chimonanthus nitens appears paraphyletic and is closely related to C. salicifolius and C. zhejiangensis, suggesting the need to reevaluate the species delimitation of C. nitens. Chimonanthus and Calycanthus diverged in mid-Oligocene; the radiation of extant Chimonanthus species was dated to the mid-Miocene, while C. grammatus diverged from other Chimonanthus species in the late Miocene. C. salicifolius, C. nitens(a), and C. zhejiangensis are inferred to have diverged in the Pleistocene of the Quaternary period, suggesting recent speciation of a relict lineage in the subtropical forest regions in eastern China. This study provides important insights into the chloroplast genome features and evolutionary history of Chimonanthus and family Calycanthaceae.
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Affiliation(s)
- Abbas Jamal
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC, United States
| | - Zhi-Yao Ma
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC, United States
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
| | - Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Long-Qing Chen
- Southwest Engineering Technology and Research Center of Landscape Architecture, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Xiu-Qun Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
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28
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de Aranzamendi MC, Martínez JJ, Held C, Sahade R. Parallel shape divergence between ecotypes of the limpet Nacella concinna along the Antarctic Peninsula: a new model species for parallel evolution? ZOOLOGY 2021; 150:125983. [PMID: 34915245 DOI: 10.1016/j.zool.2021.125983] [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: 06/01/2021] [Revised: 09/23/2021] [Accepted: 11/23/2021] [Indexed: 10/19/2022]
Abstract
Parallel phenotypic divergence is the independent differentiation between phenotypes of the same lineage or species occupying ecologically similar environments in different populations. We tested in the Antarctic limpet Nacella concinna the extent of parallel morphological divergence in littoral and sublittoral ecotypes throughout its distribution range. These ecotypes differ in morphological, behavioural and physiological characteristics. We studied the lateral and dorsal outlines of shells and the genetic variation of the mitochondrial gene Cytochrome Oxidase subunit I from both ecotypes in 17 sample sites along more than 2,000 km. The genetic data indicate that both ecotypes belong to a single evolutionary lineage. The magnitude and direction of phenotypic variation differ between ecotypes across sample sites; completely parallel ecotype-pairs (i.e., they diverge in the same magnitude and in the same direction) were detected in 84.85% of lateral and 65.15% in dorsal view comparisons. Besides, specific traits (relative shell height, position of shell apex, and elliptical/pear-shape outline variation) showed high parallelism. We observed weak morphological covariation between the two shape shell views, indicating that distinct evolutionary forces and environmental pressures could be acting on this limpet shell shape. Our results demonstrate there is a strong parallel morphological divergence pattern in N. concinna along its distribution, making this Antarctic species a suitable model for the study of different evolutionary forces shaping the shell evolution of this limpet.
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Affiliation(s)
- María Carla de Aranzamendi
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Cátedra de Ecología Marina, Av. Vélez Sarsfield 299, X5000JJC, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Ecosistemas Marinos y Polares (ECOMARES), Av. Vélez Sarsfield 299, X5000JJC, Córdoba, Argentina.
| | - Juan José Martínez
- Laboratorio de Ecología Evolutiva y Biogeografía, Instituto de Ecorregiones Andinas (INECOA), CONICET and Universidad Nacional de Jujuy, C. Gorriti 237, San Salvador de Jujuy, 4600, Argentina.
| | - Christoph Held
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, D-27570 Bremerhaven, Germany.
| | - Ricardo Sahade
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Cátedra de Ecología Marina, Av. Vélez Sarsfield 299, X5000JJC, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Ecosistemas Marinos y Polares (ECOMARES), Av. Vélez Sarsfield 299, X5000JJC, Córdoba, Argentina.
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29
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Jónsson EP, Campana SE, Sólmundsson J, Jakobsdóttir KB, Bárðarson H. The effect of growth rate on otolith-based discrimination of cod (Gadus morhua) ecotypes. PLoS One 2021; 16:e0247630. [PMID: 34587180 PMCID: PMC8480848 DOI: 10.1371/journal.pone.0247630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/09/2021] [Indexed: 01/10/2023] Open
Abstract
Otolith shape has previously been used to identify ecotypes within the Icelandic cod (Gadus morhua) stock, using DST profiles to validate the results. Fish otolith shape variation has repeatedly been found to be largely determined by growth rate. To examine the effect of growth rate on the relationship between otolith shape and cod ecotypes (using the Pan I genotype as a proxy for ecotype), 826 archived sagittal otoliths collected over a 58 year sampling period were retrieved, the individual growth rate calculated, and otolith shape described using both Normalized Elliptic Fourier transform and Discrete Wavelet transform. Discriminant functions of otolith shape successfully classified ecotype, whether using Fourier or Wavelet descriptors, but only when excluding a heterozygous genotype from the analysis. The otolith shape variability of this genotype lowered the classification success, while otolith shape, in turn, was significantly affected by growth rate and cohort. Growth rate differences previously reported for the ecotypes were present, but were less marked than expected and indeed, growth rate variance attributable to ecotype identity was dwarfed by cohort- and location-related variance in growth. Such a strong effect of growth rate suggests that cod ecotype discrimination based on otolith shape is sensitive to both temporal and spatial variations in growth, which can mask the effect of ecotype-related growth rate differences on otolith shape.
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Affiliation(s)
- Einar Pétur Jónsson
- School of Engineering and Natural Sciences, University of Iceland, Askja, Reykjavík, Iceland
- Marine and Freshwater Research Institute, Hafnarfjörður, Iceland
| | - Steven E. Campana
- School of Engineering and Natural Sciences, University of Iceland, Askja, Reykjavík, Iceland
| | - Jón Sólmundsson
- Marine and Freshwater Research Institute, Hafnarfjörður, Iceland
| | | | - Hlynur Bárðarson
- Marine and Freshwater Research Institute, Hafnarfjörður, Iceland
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30
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Genetic Divergence between Two Sympatric Ecotypes of Phalaenopsis pulcherrima on Hainan Island. DIVERSITY 2021. [DOI: 10.3390/d13090446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Ecotypes are the result of ecological differentiation at the early stages of speciation. Adaptation to soil conditions offers arguably the best examples of local adaptation in plants. Two sympatric ecotypes, with either a red or green abaxial leaf surface, were found without clear geographical isolation in Phalaenopsis pulcherrima, a Southeast Asia endemic and endangered orchid. The soil of the red leaf ecotype has a higher water content and nutrient content than the green ecotype. What is the genetic structure of the two ecotypes? Is there complete or partial reproductive isolation between the two ecotypes? In this work, leaf reflection of the two ecotypes in P. pulcherrima were compared, to illustrate their difference in leaf color. The genetic differentiation between two ecotypes was examined, using ISSR and SRAP markers to determine the genetic structure of the populations. Our results showed that the green ecotype had reflectance spectrum peaks at 530 nm and 620 nm, while in the red ecotype, the peak at 530 nm was absent. A total of 165 ISSR and SRAP loci showed a high level of genetic diversity within the green ecotype, and analyses of the population structure revealed two genetic clusters that corresponded to the red and green ecotypes. The percentage of variation between the two ecotypes (24.55%) was greater than the percentage of variation among the populations (16.54%)—indicating partial reproductive isolation, high genetic differentiation, and that ecological differentiation has been more important than geographical barriers among populations within ecotypes. Most pairwise FST values between the populations within either ecotype on Hainan Island were less than 0.15; however, the FST between both the Thai and Malaysian populations and the Hainan Island population was greater than 0.25, due to South China sea isolation. Ecotypic differentiation is an important part of speciation; therefore, we must take into account the axes along which lineages sort, when formulating protection strategies.
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31
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Zhang JX, Wang M, Fan J, Guo ZP, Guan Y, Qu G, Zhang CJ, Guo YX, Yan X. Non-linear genetic diversity and notable population differentiation caused by low gene flow of bermudagrass [ Cynodon dactylon (L.) Pers.] along longitude gradients. PeerJ 2021; 9:e11953. [PMID: 34458022 PMCID: PMC8378333 DOI: 10.7717/peerj.11953] [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: 11/27/2020] [Accepted: 07/21/2021] [Indexed: 11/20/2022] Open
Abstract
Background Environmental variation related to ecological habitat is the main driver of plant adaptive divergence. Longitude plays an important role in the formation of plant population structure, indicating that environmental differentiation can significantly shape population structure. Methods Genetic diversity and population genetic structure were estimated using 105 expressed sequence tag-derived simple sequence repeat (EST-SSR) loci. A total of 249 C. dactylon (L.) Pers. (common bermudagrass) individuals were sampled from 13 geographic sites along the longitude (105°57′34″–119°27′06″E). Results There was no obvious linear trend of intra-population genetic diversity along longitude and the intra-population genetic diversity was not related to climate in this study. Low gene flow (Nm = 0.7701) meant a rich genetic differentiation among populations of C. dactylon along longitude gradients. Significantly positive Mantel correlation (r = 0.438, P = 0.001) was found between genetic distance and geographical interval while no significant partial Mantel correlation after controlling the effect of mean annual precipitation, which indicated geographic distance correlated with mean annual precipitation affect genetic distance. The genetic diversity of C. dactylon with higher ploidy level was higher than that with lower ploidy level and groups of individuals with higher ploidy level were separated further away by genetic distance from the lower ploidy levels. Understanding the different genetic bases of local adaptation comparatively between latitude and longitude is one of the core findings in the adaptive evolution of plants.
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Affiliation(s)
- Jing-Xue Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China.,College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Miaoli Wang
- College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jibiao Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhi-Peng Guo
- College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yongzhuo Guan
- College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Gen Qu
- College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Chuan-Jie Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yu-Xia Guo
- College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xuebing Yan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
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32
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Bemmels JB, Bramwell AC, Anderson SAS, Luzuriaga-Aveiga VE, Mikkelsen EK, Weir JT. Geographic contact drives increased reproductive isolation in two cryptic Empidonax flycatchers. Mol Ecol 2021; 30:4833-4844. [PMID: 34347907 DOI: 10.1111/mec.16105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/05/2021] [Accepted: 07/28/2021] [Indexed: 01/02/2023]
Abstract
Geographic contact between sister lineages often occurs near the final stages of speciation, but its role in speciation's completion remains debated. Reproductive isolation may be essentially complete prior to secondary contact. Alternatively, costly interactions between partially reproductively isolated species - such as maladaptive hybridization or competition for resources - may select for divergence, increasing reproductive isolation and driving speciation toward completion. Here, we use coalescent demographic modelling and whole-genome data sets to show that a period of contact and elevated hybridization between sympatric eastern North American populations of two cryptic bird species preceded a major increase in reproductive isolation between these populations within the last 10,000 years. In contrast, substantial introgression continues to the present in a western contact zone where geographic overlap is much narrower and probably of more recent origin. In the sympatric eastern region where reproductive isolation has increased, it is not accompanied by character displacement in key morphometric traits, plumage coloration, or ecological traits. While the precise trait and underlying mechanism driving increased reproductive isolation remains unknown, we discuss several possibilities and outline avenues for future research. Overall, our results highlight how demographic models can reveal the geographic context in which reproductive isolation was completed, and demonstrate how contact can accelerate the final stages of speciation.
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Affiliation(s)
- Jordan B Bemmels
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Ashley C Bramwell
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Sean A S Anderson
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Vanessa E Luzuriaga-Aveiga
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Else K Mikkelsen
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Jason T Weir
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
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33
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Stankowski S, Ravinet M. Defining the speciation continuum. Evolution 2021; 75:1256-1273. [PMID: 33754340 DOI: 10.1111/evo.14215] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 03/01/2021] [Accepted: 03/13/2021] [Indexed: 02/06/2023]
Abstract
A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present-day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us.
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Affiliation(s)
- Sean Stankowski
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom.,Current Address: Sean Stankowski, IST Austria, Klosterneuburg, 3400, Austria
| | - Mark Ravinet
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, 0316, Norway.,School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
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34
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High genomic diversity maintained by populations of Carex scirpoidea subsp. convoluta, a paraphyletic Great Lakes ecotype. CONSERV GENET 2021. [DOI: 10.1007/s10592-020-01326-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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35
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Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190528. [PMID: 32654637 PMCID: PMC7423269 DOI: 10.1098/rstb.2019.0528] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2020] [Indexed: 12/12/2022] Open
Abstract
Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Jonna Kulmuni
- Organismal and Evolutionary Biology, University of Helsinki, Finland
| | - Roger K. Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
- Department of Marine Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Vincent Savolainen
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
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36
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Haase M, Meng S, Horsák M. Tracking parallel adaptation of shell morphology through geological times in the land snail genus Pupilla (Gastropoda: Stylommatophora: Pupillidae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Abstract
Changing environmental conditions force species either to disperse or to adapt locally either genetically or via phenotypic plasticity. Although limits of plasticity can be experimentally tested, the predictability of genetic adaptation is restricted due to its stochastic nature. Nevertheless, our understanding of evolutionary adaptation has been improving in particular through studies of parallel adaptation. Based on molecular phylogenetic inferences and morphological investigations of both recent and fossil shells we tracked the morphological changes in three land snails, Pupilla alpicola, Pupilla loessica and Pupilla muscorum. These species differ in habitat requirements as well as historical and extant distributions with P. alpicola and P. loessica being more similar to each other than to P. muscorum. Therefore, we hypothesized, that the three species reacted independently and individually to the conditions changing throughout the Pleistocene, but expected that changes within P. alpicola and P. loessica would be more similar compared to P. muscorum. Indeed, intraspecific shell shape differences across time were similar in P. alpicola and P. loessica, suggesting that similar niche shifts have led to similar transformations in parallel. In contrast, extant P. muscorum populations were practically identical in shape to their ancestors. They have probably tracked their ecological niches through time.
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Affiliation(s)
- Martin Haase
- AG Vogelwarte, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Stefan Meng
- Institute of Geography and Geology, University of Greifswald, Greifswald, Germany
| | - Michal Horsák
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
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Sakaguchi S, Nagano AJ, Yasugi M, Kudoh H, Ishikawa N, Ito M. Genetic consequences of being a dwarf: do evolutionary changes in life-history traits influence gene flow patterns in populations of the world's smallest goldenrod? ANNALS OF BOTANY 2020; 126:163-177. [PMID: 32249287 PMCID: PMC7304467 DOI: 10.1093/aob/mcaa062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND AIMS Contrasting life-history traits can evolve through generations of dwarf plant ecotypes, yet such phenotypic changes often involve decreased plant size and reproductive allocation, which can configure seed dispersal patterns and, subsequently, population demography. Therefore, evolutionary transitions to dwarfism can represent good study systems to test the roles of life-history traits in population demography by comparing genetic structure between related but phenotypically divergent ecotypes. METHODS In this study, we examined an ecotypic taxon pair of the world's smallest goldenrod (stem height 2.6 cm) in alpine habitats and its closely related lowland taxon (30-40 cm) found on Yakushima Island, Japan. Genetic variation in chloroplast DNA sequences, nuclear microsatellites and genome-wide single-nucleotide polymorphisms were used to investigate 197 samples from 16 populations, to infer the population genetic demography and compare local genetic structure of the ecotypes. KEY RESULTS We found a pronounced level of genetic differentiation among alpine dwarf populations, which were much less geographically isolated than their lowland counterparts. In particular, several neighbouring dwarf populations (located ~500 m apart) harboured completely different sets of chloroplast haplotypes and nuclear genetic clusters. Demographic modelling revealed that the dwarf populations have not exchanged genes at significant levels after population divergence. CONCLUSIONS These lines of evidence suggest that substantial effects of genetic drift have operated on these dwarf populations. The low-growing stature and reduced fecundity (only 3.1 heads per plant) of the dwarf plants may have reduced gene flow and rare long-distance seed dispersal among habitat patches, although the effects of life-history traits require further evaluation using ecological approaches.
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Affiliation(s)
- Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, Japan
| | | | - Masaki Yasugi
- National Institute for Basic Biology, Myodaiji, Okazaki, Aichi, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Naoko Ishikawa
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Motomi Ito
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
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Hardion L, Perrier A, Martinez M, Navrot N, Gaquerel E, Tournay F, Nguefack J, Combroux I. Integrative revision of Dianthus superbus subspecies reveals different degrees of differentiation, from plasticity to species distinction. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1737979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Laurent Hardion
- Laboratoire Image Ville Environnement (LIVE), University of Strasbourg, CNRS, Strasbourg, France
| | - Antoine Perrier
- Laboratoire Image Ville Environnement (LIVE), University of Strasbourg, CNRS, Strasbourg, France
- Department of Environmental Sciences, University of Basel, Basel, 4056, Switzerland
| | - Marion Martinez
- Faculty of Life Sciences, Herbarium of the University of Strasbourg (STR), Strasbourg, France
| | - Nicolas Navrot
- Institut de Biologie Moléculaire des Plantes (IBMP), University of Strasbourg, CNRS, Strasbourg, France
| | - Emmanuel Gaquerel
- Institut de Biologie Moléculaire des Plantes (IBMP), University of Strasbourg, CNRS, Strasbourg, France
| | - Frédéric Tournay
- Faculty of Life Sciences, Botanical Garden of the University of Strasbourg, Strasbourg, France
| | | | - Isabelle Combroux
- Laboratoire Image Ville Environnement (LIVE), University of Strasbourg, CNRS, Strasbourg, France
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Walter GM, Abbott RJ, Brennan AC, Bridle JR, Chapman M, Clark J, Filatov D, Nevado B, Ortiz-Barrientos D, Hiscock SJ. Senecio as a model system for integrating studies of genotype, phenotype and fitness. THE NEW PHYTOLOGIST 2020; 226:326-344. [PMID: 31951018 DOI: 10.1111/nph.16434] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/17/2019] [Indexed: 05/24/2023]
Abstract
Two major developments have made it possible to use examples of ecological radiations as model systems to understand evolution and ecology. First, the integration of quantitative genetics with ecological experiments allows detailed connections to be made between genotype, phenotype, and fitness in the field. Second, dramatic advances in molecular genetics have created new possibilities for integrating field and laboratory experiments with detailed genetic sequencing. Combining these approaches allows evolutionary biologists to better study the interplay between genotype, phenotype, and fitness to explore a wide range of evolutionary processes. Here, we present the genus Senecio (Asteraceae) as an excellent system to integrate these developments, and to address fundamental questions in ecology and evolution. Senecio is one of the largest and most phenotypically diverse genera of flowering plants, containing species ranging from woody perennials to herbaceous annuals. These Senecio species exhibit many growth habits, life histories, and morphologies, and they occupy a multitude of environments. Common within the genus are species that have hybridized naturally, undergone polyploidization, and colonized diverse environments, often through rapid phenotypic divergence and adaptive radiation. These diverse experimental attributes make Senecio an attractive model system in which to address a broad range of questions in evolution and ecology.
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Affiliation(s)
- Greg M Walter
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Richard J Abbott
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK
| | - Adrian C Brennan
- School of Biological and Biomedical Sciences, University of Durham, Durham, DH1 3LE, UK
| | - Jon R Bridle
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Mark Chapman
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - James Clark
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Dmitry Filatov
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | | | - Simon J Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
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Popovic D, Lowry DB. Contrasting environmental factors drive local adaptation at opposite ends of an environmental gradient in the yellow monkeyflower (Mimulus guttatus). AMERICAN JOURNAL OF BOTANY 2020; 107:298-307. [PMID: 31989586 DOI: 10.1002/ajb2.1419] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/13/2019] [Indexed: 05/22/2023]
Abstract
PREMISE Identifying the environmental factors responsible for natural selection across different habitats is crucial for understanding the process of local adaptation in plants. Despite its importance, few studies have successfully isolated the environmental factors driving local adaptation in nature. In this study, we evaluated the agents of selection responsible for local adaptation of the monkeyflower Mimulus guttatus to California's coastal and inland habitats. METHODS We implemented a manipulative reciprocal transplant experiment at coastal and inland sites, where we excluded aboveground stressors in an effort to elucidate their role in the evolution of local adaptation. RESULTS Excluding aboveground stressors, most likely a combination of salt spray and herbivory, completely rescued inland annual plant fitness when transplanted to coastal habitat. The exclosures in inland habitat provided a benefit to the performance of coastal perennial plants. However, the exclosures are unlikely to provide much fitness benefit to the coastal plants at the inland site because of their general inability to flower in time to escape from the summer drought. CONCLUSIONS Our study demonstrates that a distinct set of selective agents (aboveground vs. belowground) are responsible for local adaptation at opposite ends of an environmental gradient.
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Affiliation(s)
- Damian Popovic
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
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Abstract
One of the main aims of the University of Pavia mycology laboratory was to collect wood decay fungal (WDF) strains in order to deepen taxonomic studies, species distribution, officinal properties or to investigate potential applications such as biocomposite material production based on fungi. The Italian Alps, Apennines and wood plains were investigated to collect Basidiomycota basidiomata from living or dead trees. The purpose of this study was to investigate the wood decay strains of the Mediterranean area, selecting sampling sites in North and Central Italy, including forests near the Ligurian and Adriatic seas, or near the Lombardy lakes. The isolation of mycelia in pure culture was performed according to the current methodology and the identity of the strains was confirmed by molecular analyses. The strains are maintained in the Research Culture Collection MicUNIPV of Pavia University (Italy). Among the 500 WDF strains in the collection, the most interesting isolates from the Mediterranean area are: Dichomitus squalens (basidioma collected from Pinus pinea), Hericium erinaceus (medicinal mushroom), Inocutis tamaricis (white-rot agent on Tamarix trees), Perenniporia meridionalis (wood degrader through Mn peroxidase) and P. ochroleuca. In addition, strains of species related to the Mediterranean climate (e.g., Fomitiporia mediterranea and Cellulariella warnieri) were obtained from sites with a continental-temperate climate.
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Costa APB, Fruet PF, Secchi ER, Daura-Jorge FG, Simões-Lopes PC, Di Tullio JC, Rosel PE. Ecological divergence and speciation in common bottlenose dolphins in the western South Atlantic. J Evol Biol 2019; 34:16-32. [PMID: 31808214 DOI: 10.1111/jeb.13575] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 11/01/2019] [Accepted: 11/28/2019] [Indexed: 01/02/2023]
Abstract
Coastal and offshore ecotypes of common bottlenose dolphins have been recognized in the western South Atlantic, and it is possible that trophic niche divergence associated with social interactions is leading them to genetic and phenotypic differentiation. The significant morphological differentiation observed between these ecotypes suggests they represent two different subspecies. However, there is still a need to investigate whether there is congruence between morphological and genetic data to rule out the possibility of ecophenotypic variation accompanied by gene flow. Mitochondrial DNA (mtDNA) control region sequence data and 10 microsatellite loci collected from stranded and biopsied dolphins sampled in coastal and offshore waters of Brazil as well as 106 skulls for morphological analyses were used to determine whether the morphological differentiation was supported by genetic differentiation. There was congruence among the data sets, reinforcing the presence of two distinct ecotypes. The divergence may be relatively recent, however, given the moderate values of mtDNA nucleotide divergence (dA = 0.008), presence of one shared mtDNA haplotype and possibly low levels of gene flow (around 1% of migrants per generation). Results suggest the ecotypes may be in the process of speciation and reinforce they are best described as two different subspecies until the degree of nuclear genetic divergence is thoroughly evaluated: Tursiops truncatus gephyreus (coastal ecotype) and T. t. truncatus (offshore ecotype). The endemic distribution of T. t. gephyreus in the western South Atlantic and number of anthropogenic threats in the area reinforces the importance of protecting this ecotype and its habitat.
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Affiliation(s)
- Ana P B Costa
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Pedro F Fruet
- Museu Oceanográfico 'Prof. Eliézer C. Rios', Universidade Federal do Rio Grande, Rio Grande, Brazil.,Laboratório de Ecologia e Conservação da Megafauna Marinha (EcoMega), Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil.,Kaosa, Rio Grande, Brazil.,Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos - ICMBio/CMA, Santos, Brazil
| | - Eduardo R Secchi
- Laboratório de Ecologia e Conservação da Megafauna Marinha (EcoMega), Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Fábio G Daura-Jorge
- Laboratório de Mamíferos Aquáticos (LAMAQ), Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Paulo C Simões-Lopes
- Laboratório de Mamíferos Aquáticos (LAMAQ), Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Juliana C Di Tullio
- Museu Oceanográfico 'Prof. Eliézer C. Rios', Universidade Federal do Rio Grande, Rio Grande, Brazil.,Laboratório de Ecologia e Conservação da Megafauna Marinha (EcoMega), Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil.,Kaosa, Rio Grande, Brazil
| | - Patricia E Rosel
- National Marine Fisheries Service, Southeast Fisheries Science Center, Lafayette, LA, USA
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Christie K, Strauss SY. Reproductive isolation and the maintenance of species boundaries in two serpentine endemic Jewelflowers. Evolution 2019; 73:1375-1391. [PMID: 31152435 DOI: 10.1111/evo.13767] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/28/2019] [Accepted: 05/03/2019] [Indexed: 12/30/2022]
Abstract
Speciation occurs when reproductive barriers substantially reduce gene flow between lineages. Understanding how specific barriers contribute to reproductive isolation offers insight into the initial forces driving divergence and the evolutionary and ecological processes responsible for maintaining diversity. Here, we quantified multiple pre- and post-pollination isolating barriers in a pair of closely related California Jewelflowers (Streptanthus, Brassicaceae) living in an area of sympatry. S. breweri and S. hesperidis are restricted to similar serpentine habitats; however, populations are spatially isolated at fine-scales and rarely co-occur in intermixed stands. Several intrinsic postzygotic barriers were among the strongest we quantified, yet, postzygotic barriers currently contribute little to overall reproductive isolation due to the cumulative strength of earlier-acting extrinsic barriers, including spatial isolation, and flowering time and pollinator differences. Data from multiple years suggest that pre-pollination barriers may have different strengths depending on annual environmental conditions. Similarly, crossing data suggest that the strength of intrinsic isolation may vary among different population pairs. Estimates of total reproductive isolation in S. breweri and S. hesperidis are robust to uncertainty and variability in individual barrier strength estimates, demonstrating how multiple barriers can act redundantly to prevent gene flow between close relatives living in sympatry.
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Affiliation(s)
- Kyle Christie
- UC Davis Department of Evolution and Ecology, and Center for Population Biology, University of California, One Shields Avenue, Davis, California, 95616
| | - Sharon Y Strauss
- UC Davis Department of Evolution and Ecology, and Center for Population Biology, University of California, One Shields Avenue, Davis, California, 95616
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Richards TJ, Ortiz‐Barrientos D, McGuigan K. Natural selection drives leaf divergence in experimental populations of Senecio lautus under natural conditions. Ecol Evol 2019; 9:6959-6967. [PMID: 31380026 PMCID: PMC6662321 DOI: 10.1002/ece3.5263] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 04/21/2019] [Accepted: 04/23/2019] [Indexed: 11/11/2022] Open
Abstract
Leaf morphology is highly variable both within and between plant species. This study employs a combination of common garden and reciprocal transplant experiments to determine whether differences in leaf shape between Senecio lautus ecotypes has evolved as an adaptive response to divergent ecological conditions.We created a synthetic population of hybrid genotypes to segregate morphological variation between three ecotypes and performed reciprocal transplants where this hybrid population was transplanted into the three adjacent native environments. We measured nine leaf morphology traits across the experimental and natural populations at these sites.We found significant divergence in multivariate leaf morphology toward the native character in each environment, suggesting environmental conditions at each site exert selective pressure that results in a phenotypic shift toward the local phenotype of the wild populations.These associations suggest that differences in leaf morphology between S. lautus ecotypes have arisen as a result of divergent selection on leaf shape or associated traits that confer an adaptive advantage in each environment, which has led to the formation of morphologically distinct ecotypes.
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Affiliation(s)
- Thomas J. Richards
- School of Biological Sciences St LuciaUniversity of QueenslandSt LuciaQueenslandAustralia
- Department of Plant BiologySwedish University of Agricultural SciencesLinnean Center for Plant BiologyUppsalaSweden
| | | | - Katrina McGuigan
- School of Biological Sciences St LuciaUniversity of QueenslandSt LuciaQueenslandAustralia
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Hirao AS, Shimono Y, Narita K, Wada N, Kudo G. Ecotypic divergences of the alpine herb Potentilla matsumurae adapted to fellfield-snowbed habitats across a series of mountain sky islands. AMERICAN JOURNAL OF BOTANY 2019; 106:772-787. [PMID: 31124143 DOI: 10.1002/ajb2.1290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/21/2019] [Indexed: 06/09/2023]
Abstract
PREMISE Divergent selection due to environmental heterogeneity can lead to local adaptation. However, the ecological and evolutionary processes of local adaptation that occurs across multiple regions are often unknown. Our previous studies reported on the ecotypic divergence within a local area of variation of Potentilla matsumurae, an alpine herb adapted to the fellfield-snowbed environment. Here we investigated large-scale geographic patterns of ecotypic differentiation in this species to infer local adaptation and selective forces across multiple regions. METHODS We compiled information on the overall distributions of fellfield and snowbed habitats on the mountains in Japan across the distribution of the species. Next, we conducted common garden experiments to test the adaptive divergence of the fellfield-snowbed plants derived from multiple regions. Finally, we evaluated phylogeographic structures based on cpDNA and allozyme variations and inferred the evolutionary history of ecotype differentiation. RESULTS The mosaic distribution of the fellfield-snowbed ecotypes across isolated mountaintops constitutes indirect evidence for habitat-specific natural selection. The significant difference in survivorship between the ecotypes observed in a controlled snow environment provides more substantial evidence of local selection. Phylogeographic structures support the hypothesis that ecotypic divergence events from fellfield to snowbed populations occurred independently in at least two distinct regions. CONCLUSIONS Ecotypic divergence of P. matsumurae has occurred across a series of mountain sky islands. Local selection in snowy environments is a driving force that maintains the divergent ecotypes across multiple mountain regions and can contribute to the diversification of plants in heavy-snow regions.
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Affiliation(s)
- Akira S Hirao
- Graduate School of Environmental Earth Science, Hokkaido University, Sapporo, 060-0810, Japan
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Ueda, 386-2204, Japan
| | - Yoshiko Shimono
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kenji Narita
- Faculty of Education and Human Studies, Akita University, Akita, 010-8502, Japan
| | - Naoya Wada
- Center for Far Eastern Studies, University of Toyama, Toyama, 930-8555, Japan
| | - Gaku Kudo
- Graduate School of Environmental Earth Science, Hokkaido University, Sapporo, 060-0810, Japan
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González V, Santamaría RI, Bustos P, Pérez-Carrascal OM, Vinuesa P, Juárez S, Martínez-Flores I, Cevallos MÁ, Brom S, Martínez-Romero E, Romero D. Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters. Front Microbiol 2019; 10:910. [PMID: 31114559 PMCID: PMC6503217 DOI: 10.3389/fmicb.2019.00910] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/10/2019] [Indexed: 01/07/2023] Open
Abstract
The bacterial genus Rhizobium comprises diverse symbiotic nitrogen-fixing species associated with the roots of plants in the Leguminosae family. Multiple genomic clusters defined by whole genome comparisons occur within Rhizobium, but their equivalence to species is controversial. In this study we investigated such genomic clusters to ascertain their significance in a species phylogeny context. Phylogenomic inferences based on complete sets of ribosomal proteins and stringent core genome markers revealed the main lineages of Rhizobium. The clades corresponding to R. etli and R. leguminosarum species show several genomic clusters with average genomic nucleotide identities (ANI > 95%), and a continuum of divergent strains, respectively. They were found to be inversely correlated with the genetic distance estimated from concatenated ribosomal proteins. We uncovered evidence of a Rhizobium pangenome that was greatly expanded, both in its chromosomes and plasmids. Despite the variability of extra-chromosomal elements, our genomic comparisons revealed only a few chromid and plasmid families. The presence/absence profile of genes in the complete Rhizobium genomes agreed with the phylogenomic pattern of species divergence. Symbiotic genes were distributed according to the principal phylogenomic Rhizobium clades but did not resolve genome clusters within the clades. We distinguished some types of symbiotic plasmids within Rhizobium that displayed different rates of synonymous nucleotide substitutions in comparison to chromosomal genes. Symbiotic plasmids may have been repeatedly transferred horizontally between strains and species, in the process displacing and substituting pre-existing symbiotic plasmids. In summary, the results indicate that Rhizobium genomic clusters, as defined by whole genomic identities, might be part of a continuous process of evolutionary divergence that includes the core and the extrachromosomal elements leading to species formation.
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Affiliation(s)
- Víctor González
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Rosa Isela Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Patricia Bustos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Soledad Juárez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Irma Martínez-Flores
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Miguel Ángel Cevallos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Susana Brom
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - David Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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VanWallendael A, Soltani A, Emery NC, Peixoto MM, Olsen J, Lowry DB. A Molecular View of Plant Local Adaptation: Incorporating Stress-Response Networks. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:559-583. [PMID: 30786237 DOI: 10.1146/annurev-arplant-050718-100114] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Ecological specialization in plants occurs primarily through local adaptation to different environments. Local adaptation is widely thought to result in costly fitness trade-offs that result in maladaptation to alternative environments. However, recent studies suggest that such trade-offs are not universal. Further, there is currently a limited understanding of the molecular mechanisms responsible for fitness trade-offs associated with adaptation. Here, we review the literature on stress responses in plants to identify potential mechanisms underlying local adaptation and ecological specialization. We focus on drought, high and low temperature, flooding, herbivore, and pathogen stresses. We then synthesize our findings with recent advances in the local adaptation and plant molecular biology literature. In the process, we identify mechanisms that could cause fitness trade-offs and outline scenarios where trade-offs are not a necessary consequence of adaptation. Future studies should aim to explicitly integrate molecular mechanisms into studies of local adaptation.
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Affiliation(s)
- Acer VanWallendael
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA;
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824, USA
| | - Ali Soltani
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA;
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan 48824, USA
| | - Nathan C Emery
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA;
| | - Murilo M Peixoto
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA;
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824, USA
| | - Jason Olsen
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA;
- Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan 48824, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA;
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824, USA
- Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan 48824, USA
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48
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Khasanova A, Lovell JT, Bonnette J, Weng X, Jenkins J, Yoshinaga Y, Schmutz J, Juenger TE. The Genetic Architecture of Shoot and Root Trait Divergence Between Mesic and Xeric Ecotypes of a Perennial Grass. FRONTIERS IN PLANT SCIENCE 2019; 10:366. [PMID: 31019518 PMCID: PMC6458277 DOI: 10.3389/fpls.2019.00366] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/08/2019] [Indexed: 05/16/2023]
Abstract
Environmental heterogeneity can drive patterns of functional trait variation and lead to the formation of locally adapted ecotypes. Plant ecotypes are often differentiated by suites of correlated root and shoot traits that share common genetic, developmental, and physiological relationships. For instance, although plant water loss is largely governed by shoot systems, root systems determine water access and constrain shoot water status. To evaluate the genetic basis of root and shoot trait divergence, we developed a recombinant inbred population derived from mesic and xeric ecotypes of the perennial grass Panicum hallii. Our study sheds light on the genetic architecture underlying the relationships between root and shoot traits. We identified several genomic "hotspots" which control suites of correlated root and shoot traits, thus indicating genetic coordination between plant organ systems in the process of ecotypic divergence. Genomic regions of colocalized quantitative trait locus (QTL) for the majority of shoot and root growth related traits were independent of colocalized QTL for shoot and root resource acquisition traits. The allelic effects of individual QTL underscore ecological specialization for drought adaptation between ecotypes and reveal possible hybrid breakdown through epistatic interactions. These results have implications for understanding the factors constraining or facilitating local adaptation in plants.
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Affiliation(s)
- Albina Khasanova
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - John T. Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Jason Bonnette
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - Xiaoyu Weng
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Yuko Yoshinaga
- United States Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Thomas E. Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
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49
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Lowry DB, Popovic D, Brennan DJ, Holeski LM. Mechanisms of a locally adaptive shift in allocation among growth, reproduction, and herbivore resistance in
Mimulus guttatus
*. Evolution 2019; 73:1168-1181. [DOI: 10.1111/evo.13699] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/21/2019] [Accepted: 01/31/2019] [Indexed: 12/24/2022]
Affiliation(s)
- David B. Lowry
- Department of Plant BiologyMichigan State University East Lansing Michigan 48824
- Program in Ecology, Evolutionary Biology, and BehaviorMichigan State University East Lansing Michigan 48824
- Plant Resilience Institute,Michigan State University East Lansing Michigan 48824
| | - Damian Popovic
- Department of Plant BiologyMichigan State University East Lansing Michigan 48824
- Program in Ecology, Evolutionary Biology, and BehaviorMichigan State University East Lansing Michigan 48824
| | - Darlene J. Brennan
- Department of Plant BiologyMichigan State University East Lansing Michigan 48824
| | - Liza M. Holeski
- Department of Biological SciencesNorthern Arizona University Flagstaff Arizona 86011
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Parallel colonization of subalpine habitats in the central European mountains by Primula elatior. Sci Rep 2019; 9:3294. [PMID: 30824749 PMCID: PMC6397301 DOI: 10.1038/s41598-019-39669-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/30/2019] [Indexed: 12/15/2022] Open
Abstract
The island-like distribution of subalpine habitats across mountain ranges can trigger the parallel evolution of locally adapted ecotypes. Such naturally replicated scenarios allow testing hypotheses on how elevational differentiation structures genetic diversity within species. Nevertheless, the parallel colonization of subalpine habitats across different mountain ranges has only rarely been documented with molecular data. We chose Primula elatior (Primulaceae), naturally spanning entire elevation range in multiple mountain regions of central Europe, to test for the origin of its scattered subalpine populations. Nuclear microsatellite variation revealed three genetic groups corresponding with the distinct study regions. We found that genetic differentiation between foothill and subalpine populations within each region was relatively low, suggesting that the colonization of subalpine habitats occurred independently within each mountain range. Furthermore, the strongest differentiation was usually found between the subalpine populations suggesting that mountain ridges may act as migration barriers that can reduce gene flow more strongly than elevational differences between foothill and subalpine populations. Finally, we found that subalpine colonization did not result in a loss of genetic diversity relative to foothill populations in agreement with the high migration rates that we document here between the subalpine and the foothill populations. In summary, our study shows subalpine Primula elatior populations are genetically diverse and distinct results of parallel colonization events from multiple foothill gene pools.
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