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Shape asymmetry - what's new? Emerg Top Life Sci 2022; 6:285-294. [PMID: 35758318 DOI: 10.1042/etls20210273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022]
Abstract
Studies of shape asymmetry have become increasingly abundant as the methods of geometric morphometrics have gained widespread use. Most of these studies have focussed on fluctuating asymmetry and have largely obtained similar results as more traditional analyses of asymmetry in distance measurements, but several notable differences have also emerged. A key difference is that shape analyses provide information on the patterns, not just the amount of variation, and therefore tend to be more sensitive. Such analyses have shown that apparently symmetric structures in animals consistently show directional asymmetry for shape, but not for size. Furthermore, the long-standing prediction that phenotypic plasticity in response to environmental heterogeneity can contribute to fluctuating asymmetry has been confirmed for the first time for the shape of flower parts (but not for size). Finally, shape analyses in structures with complex symmetry, such as many flowers, can distinguish multiple types of directional asymmetry, generated by distinct direction-giving factors, which combine to the single component observable in bilaterally symmetric structures. While analyses of shape asymmetry are broadly compatible with traditional analyses of asymmetry, they incorporate more detailed morphological information, particularly for structures with complex symmetry, and therefore can reveal subtle biological effects that would otherwise not be apparent. This makes them a promising tool for a wide range of studies in the basic and applied life sciences.
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Budečević S, Manitašević Jovanović S, Vuleta A, Tucić B, Klingenberg CP. Directional asymmetry and direction-giving factors: Lessons from flowers with complex symmetry. Evol Dev 2022; 24:92-108. [PMID: 35708164 PMCID: PMC9542681 DOI: 10.1111/ede.12402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/06/2022] [Accepted: 04/22/2022] [Indexed: 11/28/2022]
Abstract
Directional asymmetry is a systematic difference between the left and right sides for structures with bilateral symmetry or a systematic differentiation among repeated parts for complex symmetry. This study explores factors that produce directional asymmetry in the flower of Iris pumila, a structure with complex symmetry that makes it possible to investigate multiple such factors simultaneously. The shapes and sizes of three types of floral organs, the falls, standards, and style branches, were quantified using the methods of geometric morphometrics. For each flower, this study recorded the compass orientations of floral organs as well as their anatomical orientations relative to the two spathes subtending each flower. To characterize directional asymmetry at the whole-flower level, differences in the average sizes and shapes according to compass orientation and relative orientation were computed, and the left-right asymmetry was also evaluated for each individual organ. No size or shape differences within flowers were found in relation to anatomical position; this may relate to the terminal position of flowers in Iris pumila, suggesting that there may be no adaxial-abaxial polarity, which is very prominent in many other taxa. There was clear directional asymmetry of shape in relation to compass orientation, presumably driven by a consistent environmental gradient such as solar irradiance. There was also clear directional asymmetry between left and right halves of every floral organ, most likely related to the arrangement of organs in the bud. These findings indicate that different factors are acting to produce directional asymmetry at different levels. In conventional analyses not recording flower orientations, these effects would be impossible to disentangle from each other and would probably be included as part of fluctuating asymmetry.
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Affiliation(s)
- Sanja Budečević
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković"-National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Sanja Manitašević Jovanović
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković"-National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Ana Vuleta
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković"-National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Branka Tucić
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković"-National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
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Soza VL, Kriebel R, Ramage E, Hall BD, Twyford AD. The symmetry spectrum in a hybridising, tropical group of rhododendrons. THE NEW PHYTOLOGIST 2022; 234:1491-1506. [PMID: 35274743 PMCID: PMC9313591 DOI: 10.1111/nph.18083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
Many diverse plant clades possess bilaterally symmetrical flowers and specialised pollination syndromes, suggesting that these traits may promote diversification. We examined the evolution of diverse floral morphologies in a species-rich tropical radiation of Rhododendron. We used restriction-site associated DNA sequencing on 114 taxa from Rhododendron sect. Schistanthe to reconstruct phylogenetic relationships and examine hybridisation. We then captured and quantified floral variation using geometric morphometric analyses, which we interpreted in a phylogenetic context. We uncovered phylogenetic conflict and uncertainty caused by introgression within and between clades. Morphometric analyses revealed flower symmetry to be a morphological continuum without clear transitions between radial and bilateral symmetry. Tropical Rhododendron species that began diversifying into New Guinea c. 6 million years ago expanded into novel floral morphological space. Our results showed that the evolution of tropical Rhododendron is characterised by recent speciation, recurrent hybridisation and the origin of floral novelty. Floral variation evolved via changes to multiple components of the corolla that are only recognised in geometric morphometrics with both front and side views of flowers.
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Affiliation(s)
- Valerie L. Soza
- Department of BiologyUniversity of WashingtonSeattleWA98115USA
| | - Ricardo Kriebel
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | | | | | - Alex D. Twyford
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghCharlotte Auerbach RoadEdinburghEH9 3FLUK
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghEH3 5LRUK
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Caiza Guamba JC, Corredor D, Galárraga C, Herdoiza JP, Santillán M, Segovia-Salcedo MC. Geometry morphometrics of plant structures as a phenotypic tool to differentiate Polylepis incana Kunth. and Polylepis racemosa Ruiz & Pav. reforested jointly in Ecuador. NEOTROPICAL BIODIVERSITY 2021. [DOI: 10.1080/23766808.2021.1906138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
| | - Daniel Corredor
- Department of Life Sciences and Agriculture, Universidad De Las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
| | - Cristina Galárraga
- Department of Life Sciences and Agriculture, Universidad De Las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
| | - Jean Pierre Herdoiza
- Department of Life Sciences and Agriculture, Universidad De Las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
| | - Michelle Santillán
- Department of Life Sciences and Agriculture, Universidad De Las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
| | - María C. Segovia-Salcedo
- Department of Life Sciences and Agriculture, Universidad De Las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
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Shepherd KA, Lepschi BJ, Johnson EA, Gardner AG, Sessa EB, Jabaily RS. The concluding chapter: recircumscription of Goodenia (Goodeniaceae) to include four allied genera with an updated infrageneric classification. PHYTOKEYS 2020; 152:27-104. [PMID: 32733134 PMCID: PMC7360637 DOI: 10.3897/phytokeys.152.49604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
Close scrutiny of Goodenia (Goodeniaceae) and allied genera in the 'Core Goodeniaceae' over recent years has clarified our understanding of this captivating group. While expanded sampling, sequencing of multiple regions, and a genome skimming reinforced backbone clearly supported Goodenia s.l. as monophyletic and distinct from Scaevola and Coopernookia, there appears to be no synapomorphic characters that uniquely characterise this morphologically diverse clade. Within Goodenia s.l., there is strong support from nuclear, chloroplast and mitochondrial data for three major clades (Goodenia Clades A, B and C) and various subclades, which lead to earlier suggestions for the possible recognition of these as distinct genera. Through ongoing work, it has become evident that this is impractical, as conflict remains within the most recently diverged Clade C, likely due to recent radiation and incomplete lineage sorting. In light of this, it is proposed that a combination of morphological characters is used to circumscribe an expanded Goodenia that now includes Velleia, Verreauxia, Selliera and Pentaptilon, and an updated infrageneric classification is proposed to accommodate monophyletic subclades. A total of twenty-five new combinations, three reinstatements, and seven new names are published herein including Goodenia subg. Monochila sect. Monochila subsect. Infracta K.A.Sheph. subsect. nov. Also, a type is designated for Goodenia subg. Porphyranthus sect. Ebracteolatae (K.Krause) K.A.Sheph. comb. et stat. nov., and lectotypes or secondstep lectotypes are designated for a further three names.
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Affiliation(s)
- Kelly A. Shepherd
- Western Australian Herbarium, Department of Biodiversity, Conservation & Attractions, Kensington, WA 6151, AustraliaWestern Australian HerbariumKensingtonAustralia
| | - Brendan J. Lepschi
- Australian National Herbarium, Centre for Australian National Biodiversity Research, GPO Box 1700, Canberra, ACT, 2601, AustraliaAustralian National HerbariumCanberraAustralia
| | - Eden A. Johnson
- Department of Biology, University of Mississippi, Oxford, MS 38677, USAUniversity of MississippiOxfordUnited States of America
| | - Andrew G. Gardner
- Department of Biological Sciences, California State University, Stanislaus, Turlock, CA 95382, USACalifornia State UniversityTurlockUnited States of America
| | - Emily B. Sessa
- Department of Biology, University of Florida, Gainesville, FL 32607, USAUniversity of FloridaGainesvilleUnited States of America
| | - Rachel S. Jabaily
- Department of Organismal Biology & Ecology, Colorado College, Colorado Springs, CO 80903, USAColorado CollegeColorado SpringsUnited States of America
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Zhou T, Zhang W, Zhang D, El-Kassaby YA, Fan J, Jiang H, Wang G, Cao F. A Binary-Based Matrix Model for Malus Corolla Symmetry and Its Variational Significance. FRONTIERS IN PLANT SCIENCE 2020; 11:416. [PMID: 32457766 PMCID: PMC7198884 DOI: 10.3389/fpls.2020.00416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
Floral symmetry (corolla symmetry) has important biological significance in plant genetics and evolution. However, it is often multi-dimensional and difficult to quantify. Here, we constructed a multi-dimensional data matrix [X Y Z] by extracting three qualitative variables with binary properties (X: corolla regularity of interval and coplanarity; Y: petal regularity of shape and size; Z: petal local regularity of curling and wrinkle) from different dimensions of petals (overall to individual, and then to the local): all petals (corolla), individual petals, and local areas of petals. To quantitatively express the degree of Malus corolla symmetry, these variables were then combined with weight assignments (X: 22 > Y: 21 > Z: 20) based on their contributions to the corolla symmetry and the algorithm rule of converting binary to decimal values, which facilitated the unification of qualitative and quantitative analyses. Our results revealed significant reduction in degrees of Malus corolla symmetry along the direction of local to overall. Species showed higher degree of corolla symmetry than cultivars; however, taxa with stronger corolla symmetry might not necessarily be species. These findings provide new insights into the circumscription of Malus controversial species. The matrix model should be reference for future evaluation of angiosperm flower symmetry (lack of corolla fusion).
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Affiliation(s)
- Ting Zhou
- College of Forestry, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Department of Horticulture, University of Georgia, Athens, GA, United States
| | - Wangxiang Zhang
- College of Forestry, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Yangzhou Crabapple Horticulture Company Limited, Yangzhou, China
| | - Donglin Zhang
- Department of Horticulture, University of Georgia, Athens, GA, United States
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Junjun Fan
- College of Horticulture Jinling Institute of Technology, Nanjing, China
| | - Hao Jiang
- College of Forestry, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Guibin Wang
- College of Forestry, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Fuliang Cao
- College of Forestry, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Jabaily RS, Shepherd KA, Michener PS, Bush CJ, Rivero R, Gardner AG, Sessa EB. Employing hypothesis testing and data from multiple genomic compartments to resolve recalcitrant backbone nodes in Goodenia s.l. (Goodeniaceae). Mol Phylogenet Evol 2018; 127:502-512. [PMID: 29758275 DOI: 10.1016/j.ympev.2018.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/22/2018] [Accepted: 05/07/2018] [Indexed: 11/30/2022]
Abstract
Goodeniaceae is a primarily Australian flowering plant family with a complex taxonomy and evolutionary history. Previous phylogenetic analyses have successfully resolved the backbone topology of the largest clade in the family, Goodenia s.l., but have failed to clarify relationships within the species-rich and enigmatic Goodenia clade C, a prerequisite for taxonomic revision of the group. We used genome skimming to retrieve sequences for chloroplast, mitochondrial, and nuclear markers for 24 taxa representing Goodenia s.l., with a particular focus on Goodenia clade C. We performed extensive hypothesis tests to explore incongruence in clade C and evaluate statistical support for clades within this group, using datasets from all three genomic compartments. The mitochondrial dataset is comparable to the chloroplast dataset in providing resolution within Goodenia clade C, though backbone support values within this clade remain low. The hypothesis tests provided an additional, complementary means of evaluating support for clades. We propose that the major subclades of Goodenia clade C (C1-C3 + Verreauxia) are the result of a rapid radiation, and each represents a distinct lineage.
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Affiliation(s)
- Rachel S Jabaily
- Department of Organismal Biology & Ecology, Colorado College, Colorado Springs, CO 80903, USA; Department of Biology, Rhodes College, Memphis, TN 38112, USA.
| | - Kelly A Shepherd
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Kensington, WA 6151, Australia.
| | | | - Caroline J Bush
- Department of Biology, Rhodes College, Memphis, TN 38112, USA.
| | - Rodrigo Rivero
- Department of Biology, University of Florida, Gainesville, FL 32607, USA; Department of Natural Resources and Environmental Management, University of Hawaii- Mānoa, Honolulu, HI 96822, USA.
| | - Andrew G Gardner
- Department of Biological Sciences, California State University, Stanislaus, One University Circle, Turlock, CA 95382, USA.
| | - Emily B Sessa
- Department of Biology, University of Florida, Gainesville, FL 32607, USA; Genetics Institute, University of Florida, Gainesville, FL 32607, USA.
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Rozov SM, Deineko EV, Deyneko IV. FlowerMorphology: fully automatic flower morphometry software. PLANTA 2018; 247:1163-1173. [PMID: 29392396 DOI: 10.1007/s00425-018-2856-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 01/24/2018] [Indexed: 06/07/2023]
Abstract
MAIN CONCLUSION The software FlowerMorphology is designed for automatic morphometry of actinomorphic flowers. The novel complex parameters of flowers calculated by FlowerMorphology allowed us to quantitatively characterize a polyploid series of tobacco. Morphological differences of plants representing closely related lineages or mutants are mostly quantitative. Very often, there are only very fine variations in plant morphology. Therefore, accurate and high-throughput methods are needed for their quantification. In addition, new characteristics are necessary for reliable detection of subtle changes in morphology. FlowerMorphology is an all-in-one software package to automatically image and analyze five-petal actinomorphic flowers of the dicotyledonous plants. Sixteen directly measured parameters and ten calculated complex parameters of a flower allow us to characterize variations with high accuracy. The program was developed for the needs of automatic characterization of Nicotiana tabacum flowers, but is applicable to many other plants with five-petal actinomorphic flowers and can be adopted for flowers of other merosity. A genetically similar polyploid series of N. tabacum plants was used to investigate differences in flower morphology. For the first time, we could quantify the dependence between ploidy and size and form of the tobacco flowers. We found that the radius of inner petal incisions shows a persistent positive correlation with the chromosome number. In contrast, a commonly used parameter-radius of outer corolla-does not discriminate 2n and 4n plants. Other parameters show that polyploidy leads to significant aberrations in flower symmetry and are also positively correlated with chromosome number. Executables of FlowerMorphology, source code, documentation, and examples are available at the program website: https://github.com/Deyneko/FlowerMorphology .
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Affiliation(s)
- Sergey M Rozov
- Laboratory of Bioengineering of Plants, Institute of Cytology and Genetics SD RAS, Novosibirsk, Russia.
| | - Elena V Deineko
- Laboratory of Bioengineering of Plants, Institute of Cytology and Genetics SD RAS, Novosibirsk, Russia
- Tomsk State University, Tomsk, Russia
| | - Igor V Deyneko
- Biomarkers in Infection and Immunity, Helmholtz Centre for Infection Research, Brunswick, Germany.
- Institute of Microbiology and Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Brunswick, Germany.
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Strelin MM, Benitez-Vieyra S, Fornoni J, Klingenberg CP, Cocucci A. The evolution of floral ontogenetic allometry in the Andean genus Caiophora (Loasaceae, subfam. Loasoideae). Evol Dev 2017; 20:29-39. [PMID: 29243890 DOI: 10.1111/ede.12246] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The astounding variety of angiosperm flower morphologies has evolved in response to many selective forces. Flower development is highly coordinated and involves developmental associations between size and shape, ontogenetic allometry, which in turn affect the morphology of mature flowers. Although ontogenetic allometries can act as a developmental constraint and may influence adaptive evolution, allometries can evolve themselves and may change rapidly in response to selection. We explored the evolution of ontogenetic allometry in the flowers of 11 species of Loasoideae. Seven species belong to Caiophora, which radiated recently in the central Andes, and contains species that are pollinated by bees, hummingbirds, and small rodents. According to a previous study, the diversification of Caiophora involved departures from simple allometric scaling, but the changes to allometry that enabled flower diversification have not been explored yet. We characterized the ontogenetic allometry of each species with the methods of geometric morphometrics. We studied the evolution of allometries by constructing allometric spaces, in which the allometry of each species is represented by a point and the arrangement of points indicates the relations among allometric trajectories. To examine the history of changes of ontogenetic allometries, we projected the phylogeny into the allometric spaces. Inspection of allometric spaces suggests that ontogenetic variation is limited to a few dominant features. The allometries of the two main functional flower parts under study differ in their evolutionary labilities, and patterns of variation reflect pollination systems, differences in structural organization, and abiotic environmental factors.
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Affiliation(s)
- Marina Micaela Strelin
- Laboratorio Ecotono, INIBIOMA (Universidad Nacional del Comahue-CONICET), Bariloche, Rio Negro, Argentina
| | - Santiago Benitez-Vieyra
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Córdoba, Argentina.,CONICET, Instituto Multidisciplinario de Biología Vegetal (IMBIV), Córdoba, Argentina
| | - Juan Fornoni
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Córdoba, Argentina.,Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Andrea Cocucci
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Córdoba, Argentina.,CONICET, Instituto Multidisciplinario de Biología Vegetal (IMBIV), Córdoba, Argentina
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10
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Tucić B, Budečević S, Manitašević Jovanović S, Vuleta A, Klingenberg CP. Phenotypic plasticity in response to environmental heterogeneity contributes to fluctuating asymmetry in plants: first empirical evidence. J Evol Biol 2017; 31:197-210. [PMID: 29134739 DOI: 10.1111/jeb.13207] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/06/2017] [Indexed: 11/28/2022]
Abstract
Fluctuating asymmetry (FA) is widely used to quantify developmental instability (DI) in ecological and evolutionary studies. It has long been recognized that FA may not exclusively originate from DI for sessile organisms such as plants, because phenotypic plasticity in response to heterogeneities in the environment might also produce FA. This study provides the first empirical evidence for this hypothesis. We reasoned that solar irradiance, which is greater on the southern side than on the northern side of plants growing in the temperate zone of the Northern Hemisphere, would cause systematic morphological differences and asymmetry associated with the orientation of plant parts. We used geometric morphometrics to characterize the size and shape of flower parts in Iris pumila grown in a common garden. The size of floral organs was not significantly affected by orientation. Shape and particularly its asymmetric component differed significantly according to orientation for three different floral parts. Orientation accounted for 10.4% of the total shape asymmetry within flowers in the falls, for 11.4% in the standards and for 2.2% in the style branches. This indicates that phenotypic plasticity in response to a directed environmental factor, most likely solar irradiance, contributes to FA of flowers under natural conditions. That FA partly results from phenotypic plasticity and not just from DI needs to be considered by studies of FA in plants and other sessile organisms.
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Affiliation(s)
- Branka Tucić
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade, Serbia
| | - Sanja Budečević
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade, Serbia
| | - Sanja Manitašević Jovanović
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade, Serbia
| | - Ana Vuleta
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade, Serbia
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Berger BA, Han J, Sessa EB, Gardner AG, Shepherd KA, Ricigliano VA, Jabaily RS, Howarth DG. The unexpected depths of genome-skimming data: A case study examining Goodeniaceae floral symmetry genes. APPLICATIONS IN PLANT SCIENCES 2017; 5:apps.1700042. [PMID: 29109919 PMCID: PMC5664964 DOI: 10.3732/apps.1700042] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 09/07/2017] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae. METHODS Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes. De novo assemblies were generated using multiple assemblers, and BLAST searches were performed for CYC1, CYC2, and CYC3 genes. RESULTS Overall Trinity, SOAPdenovo-Trans, and SOAPdenovo implementing lower k-mer values uncovered the most data, although no assembler consistently outperformed the others. Using SOAPdenovo-Trans across all 24 data sets, we recovered four CYC-like gene groups (CYC1, CYC2, CYC3A, and CYC3B) from a majority of the species. Alignments of the fragments included the entire coding sequence as well as upstream and downstream regions. DISCUSSION Genome-skimming data sets can provide a significant source of low-copy nuclear gene sequence data that may be used for multiple downstream applications.
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Affiliation(s)
- Brent A. Berger
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, New York 11439 USA
| | - Jiahong Han
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, New York 11439 USA
| | - Emily B. Sessa
- Department of Biology, University of Florida, Box 118525, Gainesville, Florida 32611 USA
| | - Andrew G. Gardner
- Department of Biological Sciences, California State University, Stanislaus, One University Circle, Turlock, California 95382 USA
| | - Kelly A. Shepherd
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington 6151, Western Australia, Australia
| | - Vincent A. Ricigliano
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Road, Tucson, Arizona 85719 USA
| | - Rachel S. Jabaily
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee 38112 USA
| | - Dianella G. Howarth
- Department of Biological Sciences, St. John’s University, 8000 Utopia Parkway, Queens, New York 11439 USA
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12
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Berger BA, Han J, Sessa EB, Gardner AG, Shepherd KA, Ricigliano VA, Jabaily RS, Howarth DG. The unexpected depths of genome-skimming data: A case study examining Goodeniaceae floral symmetry genes. APPLICATIONS IN PLANT SCIENCES 2017. [PMID: 29109919 DOI: 10.5061/dryad.0500c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae. METHODS Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes. De novo assemblies were generated using multiple assemblers, and BLAST searches were performed for CYC1, CYC2, and CYC3 genes. RESULTS Overall Trinity, SOAPdenovo-Trans, and SOAPdenovo implementing lower k-mer values uncovered the most data, although no assembler consistently outperformed the others. Using SOAPdenovo-Trans across all 24 data sets, we recovered four CYC-like gene groups (CYC1, CYC2, CYC3A, and CYC3B) from a majority of the species. Alignments of the fragments included the entire coding sequence as well as upstream and downstream regions. DISCUSSION Genome-skimming data sets can provide a significant source of low-copy nuclear gene sequence data that may be used for multiple downstream applications.
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Affiliation(s)
- Brent A Berger
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, New York 11439 USA
| | - Jiahong Han
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, New York 11439 USA
| | - Emily B Sessa
- Department of Biology, University of Florida, Box 118525, Gainesville, Florida 32611 USA
| | - Andrew G Gardner
- Department of Biological Sciences, California State University, Stanislaus, One University Circle, Turlock, California 95382 USA
| | - Kelly A Shepherd
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Avenue, Kensington 6151, Western Australia, Australia
| | - Vincent A Ricigliano
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Road, Tucson, Arizona 85719 USA
| | - Rachel S Jabaily
- Department of Biology, Rhodes College, 2000 N. Parkway, Memphis, Tennessee 38112 USA
| | - Dianella G Howarth
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, New York 11439 USA
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Outomuro D, Johansson F. A potential pitfall in studies of biological shape: Does size matter? J Anim Ecol 2017; 86:1447-1457. [PMID: 28699246 DOI: 10.1111/1365-2656.12732] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/21/2017] [Indexed: 01/26/2023]
Abstract
The number of published studies using geometric morphometrics (GM) for analysing biological shape has increased steadily since the beginning of the 1990s, covering multiple research areas such as ecology, evolution, development, taxonomy and palaeontology. Unfortunately, we have observed that many published studies using GM do not evaluate the potential allometric effects of size on shape, which normally require consideration or assessment. This might lead to misinterpretations and flawed conclusions in certain cases, especially when size effects explain a large part of the shape variation. We assessed, for the first time and in a systematic manner, how often published studies that have applied GM consider the potential effects of allometry on shape. We reviewed the 300 most recent published papers that used GM for studying biological shape. We also estimated how much of the shape variation was explained by allometric effects in the reviewed papers. More than one-third (38%) of the reviewed studies did not consider the allometric component of shape variation. In studies where the allometric component was taken into account, it was significant in 88% of the cases, explaining up to 87.3% of total shape variation. We believe that one reason that may cause the observed results is a misunderstanding of the process that superimposes landmark configurations, i.e. the Generalized Procrustes Analysis, which removes isometric effects of size on shape, but not allometric effects. Allometry can be a crucial component of shape variation. We urge authors to address, and report, size effects in studies of biological shape. However, we do not propose to always remove size effects, but rather to evaluate the research question with and without the allometric component of shape variation. This approach can certainly provide a thorough understanding of how much size contributes to the observed shaped variation.
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Affiliation(s)
- David Outomuro
- Section for Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Frank Johansson
- Section for Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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Miller ND, Haase NJ, Lee J, Kaeppler SM, de Leon N, Spalding EP. A robust, high-throughput method for computing maize ear, cob, and kernel attributes automatically from images. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:169-178. [PMID: 27585732 DOI: 10.1111/tpj.13320] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 08/24/2016] [Indexed: 05/09/2023]
Abstract
Grain yield of the maize plant depends on the sizes, shapes, and numbers of ears and the kernels they bear. An automated pipeline that can measure these components of yield from easily-obtained digital images is needed to advance our understanding of this globally important crop. Here we present three custom algorithms designed to compute such yield components automatically from digital images acquired by a low-cost platform. One algorithm determines the average space each kernel occupies along the cob axis using a sliding-window Fourier transform analysis of image intensity features. A second counts individual kernels removed from ears, including those in clusters. A third measures each kernel's major and minor axis after a Bayesian analysis of contour points identifies the kernel tip. Dimensionless ear and kernel shape traits that may interrelate yield components are measured by principal components analysis of contour point sets. Increased objectivity and speed compared to typical manual methods are achieved without loss of accuracy as evidenced by high correlations with ground truth measurements and simulated data. Millimeter-scale differences among ear, cob, and kernel traits that ranged more than 2.5-fold across a diverse group of inbred maize lines were resolved. This system for measuring maize ear, cob, and kernel attributes is being used by multiple research groups as an automated Web service running on community high-throughput computing and distributed data storage infrastructure. Users may create their own workflow using the source code that is staged for download on a public repository.
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Affiliation(s)
- Nathan D Miller
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Nicholas J Haase
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Jonghyun Lee
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, 445 Henry Mall, Madison, WI, 53706, USA
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, 445 Henry Mall, Madison, WI, 53706, USA
| | - Edgar P Spalding
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
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