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Petrizzelli M, Coton C, de Vienne D. Formalizing the law of diminishing returns in metabolic networks using an electrical analogy. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240165. [PMID: 39359456 PMCID: PMC11444769 DOI: 10.1098/rsos.240165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/04/2024] [Accepted: 07/04/2024] [Indexed: 10/04/2024]
Abstract
The way biological systems respond to changes in parameter values caused by mutations is a key issue in evolution and quantitative genetics, as it affects fundamental aspects such as adaptation, selective neutrality, robustness, optimality, evolutionary equilibria, etc. We address this question using the enzyme-flux relationship in a metabolic network as a model of the genotype-phenotype relationship. The lack of a suitable mathematical tool from biochemical theory to investigate this relationship led us to use an analogy between electrical circuits and metabolic networks with uni-uni reactions. We show that a behaviour of diminishing returns, which is commonly observed at various phenotypic levels, is inevitable, irrespective of the complexity of the system. We also present a possible generalization to metabolic networks with both uni-uni and bi-bi reactions.
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Schneemann H, De Sanctis B, Welch JJ. Fisher's Geometric Model as a Tool to Study Speciation. Cold Spring Harb Perspect Biol 2024; 16:a041442. [PMID: 38253415 PMCID: PMC11216183 DOI: 10.1101/cshperspect.a041442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Interactions between alleles and across environments play an important role in the fitness of hybrids and are at the heart of the speciation process. Fitness landscapes capture these interactions and can be used to model hybrid fitness, helping us to interpret empirical observations and clarify verbal models. Here, we review recent progress in understanding hybridization outcomes through Fisher's geometric model, an intuitive and analytically tractable fitness landscape that captures many fitness patterns observed across taxa. We use case studies to show how the model parameters can be estimated from different types of data and discuss how these estimates can be used to make inferences about the divergence history and genetic architecture. We also highlight some areas where the model's predictions differ from alternative incompatibility-based models, such as the snowball effect and outlier patterns in genome scans.
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Affiliation(s)
- Hilde Schneemann
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Bianca De Sanctis
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
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3
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de Vienne D, Coton C, Dillmann C. The genotype-phenotype relationship and evolutionary genetics in the light of the Metabolic Control Analysis. Biosystems 2023; 232:105000. [PMID: 37586656 DOI: 10.1016/j.biosystems.2023.105000] [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: 05/10/2023] [Revised: 08/05/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023]
Abstract
Metabolic control analysis has long been used as a systemic model of the genotype-phenotype (GP) relationship. By considering kinetic parameters and enzyme concentrations as reflecting the genotype level and metabolic fluxes or pools as phenotypes related to fitness, MCA has given a biological basis to the relationship between these two levels. The non-linear and concave relationship between enzymes and fluxes can account for common genetic effects that reductionist approaches have been powerless to explain, such as the dominance of active alleles over less active alleles, the various types of epistasis and heterosis, and reveals the structural links between these genetic effects. The summation property of the flux control coefficients accounts for the L-shaped distribution of Quantitative Trait Locus (QTL) effects, irrespective of other possible causes. Metabolic models of response to selection results in evolutionary scenarios that are markedly different from those derived from the classical infinitesimal model of quantitative genetics. In particular, evolution towards selective neutrality appears to be a consequence of the diminishing return of the flux-enzyme relationship. In this paper, we survey the historical and recent achievements of MCA in genetics, quantitative genetics and evolution, focusing on epistasis and the evolution of flux in relation to enzyme concentrations.
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Affiliation(s)
- D de Vienne
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech. GQE-Le Moulon, IDEEV, 12, route 128, Gif-sur-Yvette, 91190, France.
| | - C Coton
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech. GQE-Le Moulon, IDEEV, 12, route 128, Gif-sur-Yvette, 91190, France.
| | - C Dillmann
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech. GQE-Le Moulon, IDEEV, 12, route 128, Gif-sur-Yvette, 91190, France.
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Vedder D, Lens L, Martin CA, Pellikka P, Adhikari H, Heiskanen J, Engler JO, Sarmento Cabral J. Hybridization may aid evolutionary rescue of an endangered East African passerine. Evol Appl 2022; 15:1177-1188. [PMID: 35899253 PMCID: PMC9309464 DOI: 10.1111/eva.13440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/26/2022] [Accepted: 06/08/2022] [Indexed: 11/29/2022] Open
Abstract
Introgressive hybridization is a process that enables gene flow across species barriers through the backcrossing of hybrids into a parent population. This may make genetic material, potentially including relevant environmental adaptations, rapidly available in a gene pool. Consequently, it has been postulated to be an important mechanism for enabling evolutionary rescue, that is the recovery of threatened populations through rapid evolutionary adaptation to novel environments. However, predicting the likelihood of such evolutionary rescue for individual species remains challenging. Here, we use the example of Zosterops silvanus, an endangered East African highland bird species suffering from severe habitat loss and fragmentation, to investigate whether hybridization with its congener Zosterops flavilateralis might enable evolutionary rescue of its Taita Hills population. To do so, we employ an empirically parameterized individual-based model to simulate the species' behaviour, physiology and genetics. We test the population's response to different assumptions of mating behaviour and multiple scenarios of habitat change. We show that as long as hybridization does take place, evolutionary rescue of Z. silvanus is likely. Intermediate hybridization rates enable the greatest long-term population growth, due to trade-offs between adaptive and maladaptive introgressed alleles. Habitat change did not have a strong effect on population growth rates, as Z. silvanus is a strong disperser and landscape configuration is therefore not the limiting factor for hybridization. Our results show that targeted gene flow may be a promising avenue to help accelerate the adaptation of endangered species to novel environments, and demonstrate how to combine empirical research and mechanistic modelling to deliver species-specific predictions for conservation planning.
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Affiliation(s)
- Daniel Vedder
- Ecosystem Modelling Group, Center for Computational and Theoretical BiologyUniversity of WürzburgWürzburgGermany
- Department of Ecosystem ServicesHelmholtz Centre for Environmental Research – UFZLeipzigGermany
- Institute of BiodiversityFriedrich Schiller University JenaJenaGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Luc Lens
- Terrestrial Ecology Unit, Biology DepartmentGhent UniversityGhentBelgium
| | - Claudia A. Martin
- Terrestrial Ecology Unit, Biology DepartmentGhent UniversityGhentBelgium
| | - Petri Pellikka
- Department of Geosciences and GeographyUniversity of HelsinkiHelsinkiFinland
- State Key Laboratory for Information Engineering in Surveying, Mapping and Remote SensingWuhan UniversityWuhanChina
| | - Hari Adhikari
- Department of Geosciences and GeographyUniversity of HelsinkiHelsinkiFinland
| | - Janne Heiskanen
- Department of Geosciences and GeographyUniversity of HelsinkiHelsinkiFinland
| | - Jan O. Engler
- Terrestrial Ecology Unit, Biology DepartmentGhent UniversityGhentBelgium
- Landscape Research, Department of GeographyGhent UniversityGhentBelgium
- Computational Landscape EcologyTechnische Universität DresdenDresdenGermany
| | - Juliano Sarmento Cabral
- Ecosystem Modelling Group, Center for Computational and Theoretical BiologyUniversity of WürzburgWürzburgGermany
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5
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Thompson KA, Schluter D. Heterosis counteracts hybrid breakdown to forestall speciation by parallel natural selection. Proc Biol Sci 2022; 289:20220422. [PMID: 35506223 PMCID: PMC9065978 DOI: 10.1098/rspb.2022.0422] [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: 03/04/2022] [Accepted: 03/30/2022] [Indexed: 01/04/2023] Open
Abstract
In contrast to ecological speciation, where reproductive isolation evolves as a consequence of divergent natural selection, speciation by parallel natural selection has been less thoroughly studied. To test whether parallel evolution drives speciation, we leveraged the repeated evolution of benthic and limnetic ecotypes of threespine stickleback fish and estimated fitness for pure crosses and within-ecotype hybrids in semi-natural ponds and in laboratory aquaria. In ponds, we detected hybrid breakdown in both ecotypes but this was counterbalanced by heterosis and the strength of post-zygotic isolation was nil. In aquaria, we detected heterosis in limnetic crosses and breakdown in benthic crosses, which is suggestive of process- and ecotype-specific environment-dependence. In ponds, heterosis and breakdown were three times greater in limnetic crosses than in benthic crosses, contrasting the prediction that the fitness consequences of hybridization should be greater in crosses among more derived ecotypes. Consistent with a primary role for stochastic processes, patterns differed among crosses between populations from different lakes. Yet, the observation of qualitatively similar patterns of heterosis and hybrid breakdown for both ecotypes when averaging the lake pairs indicates that the outcome of hybridization is repeatable in a general sense.
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Affiliation(s)
- Ken A. Thompson
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dolph Schluter
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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6
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Abstract
Even if a species' phenotype does not change over evolutionary time, the underlying mechanism may change, as distinct molecular pathways can realize identical phenotypes. Here we use linear system theory to explore the consequences of this idea, describing how a gene network underlying a conserved phenotype evolves, as the genetic drift of small changes to these molecular pathways causes a population to explore the set of mechanisms with identical phenotypes. To do this, we model an organism's internal state as a linear system of differential equations for which the environment provides input and the phenotype is the output, in which context there exists an exact characterization of the set of all mechanisms that give the same input-output relationship. This characterization implies that selectively neutral directions in genotype space should be common and that the evolutionary exploration of these distinct but equivalent mechanisms can lead to the reproductive incompatibility of independently evolving populations. This evolutionary exploration, or system drift, is expected to proceed at a rate proportional to the amount of intrapopulation genetic variation divided by the effective population size ( Ne$N_e$ ). At biologically reasonable parameter values this could lead to substantial interpopulation incompatibility, and thus speciation, on a time scale of Ne$N_e$ generations. This model also naturally predicts Haldane's rule, thus providing a concrete explanation of why heterogametic hybrids tend to be disrupted more often than homogametes during the early stages of speciation.
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Affiliation(s)
- Joshua S. Schiffman
- New York Genome CenterNew YorkNew York 10013,Weill Cornell MedicineNew YorkNew York 10065,Department of Molecular and Computational BiologyUniversity of Southern CaliforniaLos AngelesCalifornia 90089
| | - Peter L. Ralph
- Department of Molecular and Computational BiologyUniversity of Southern CaliforniaLos AngelesCalifornia 90089,Department of Mathematics, Institute of Ecology and EvolutionUniversity of OregonEugeneOregon 97403,Department of Biology, Institute of Ecology and EvolutionUniversity of OregonEugeneOregon 97403
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Rosas U, Fuentes-Pérez ES, Cervantes CR, Sandoval-Zapotitla E, Santiago-Sandoval I, Arias S, Reyes-Santiago J. Evolution of flower allometry and pigmentation in Mammillaria haageana (Cactaceae). BMC PLANT BIOLOGY 2022; 22:52. [PMID: 35078406 PMCID: PMC8787947 DOI: 10.1186/s12870-021-03386-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/01/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND A puzzle in evolution is the understanding of how the environment might drive subtle phenotypic variation, and whether this variation is adaptive. Under the neutral evolutionary theory, subtle phenotypes are almost neutral with little adaptive value. To test this idea, we studied the infraspecific variation in flower shape and color in Mammillaria haageana, a species with a wide geographical distribution and phenotypic variation, which populations are often recognized as infraspecific taxa. RESULTS We collected samples from wild populations, kept them in the greenhouse for at least one reproductive year, and collected newly formed flowers. Our first objective was to characterize tepal natural variation in M. haageana through geometric morphometric and multivariate pigmentation analyses. We used landmark-based morphometrics to quantify the trends of shape variation and tepal color-patterns in 20 M. haageana accessions, belonging to five subspecies, plus 8 M. albilanata accessions for comparison as the sister species. We obtained eight geometric morphometric traits for tepal shape and color-patterns. We found broad variation in these traits between accessions belonging to the same subspecies, without taxonomic congruence with those infraspecific units. Also the phenetic cluster analysis showed different grouping patterns among accessions. When we correlated these phenotypes to the environment, we also found that solar radiation might explain the variation in tepal shape and color, suggesting that subtle variation in flower phenotypes might be adaptive. Finally we present anatomical sections in M. haageana subsp. san-angelensis to propose some of the underlying tepal structural features that may give rise to tepal variation. CONCLUSIONS Our geometric morphometric approach of flower shape and color allowed us to identify the main trends of variation in each accession and putative subspecies, but also allowed us to correlate these variation to the environment, and propose anatomical mechanisms underlying this diversity of flower phenotypes.
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Affiliation(s)
- Ulises Rosas
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
| | - Elisa Sofía Fuentes-Pérez
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Cristian R Cervantes
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Estela Sandoval-Zapotitla
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Itzel Santiago-Sandoval
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Salvador Arias
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Jerónimo Reyes-Santiago
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
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Rehman AU, Dang T, Qamar S, Ilyas A, Fatema R, Kafle M, Hussain Z, Masood S, Iqbal S, Shahzad K. Revisiting Plant Heterosis-From Field Scale to Molecules. Genes (Basel) 2021; 12:genes12111688. [PMID: 34828294 PMCID: PMC8619659 DOI: 10.3390/genes12111688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 11/21/2022] Open
Abstract
Heterosis refers to the increase in biomass, stature, fertility, and other characters that impart superior performance to the F1 progeny over genetically diverged parents. The manifestation of heterosis brought an economic revolution to the agricultural production and seed sector in the last few decades. Initially, the idea was exploited in cross-pollinated plants, but eventually acquired serious attention in self-pollinated crops as well. Regardless of harvesting the benefits of heterosis, a century-long discussion is continued to understand the underlying basis of this phenomenon. The massive increase in knowledge of various fields of science such as genetics, epigenetics, genomics, proteomics, and metabolomics persistently provide new insights to understand the reasons for the expression of hybrid vigor. In this review, we have gathered information ranging from classical genetic studies, field experiments to various high-throughput omics and computational modelling studies in order to understand the underlying basis of heterosis. The modern-day science has worked significantly to pull off our understanding of heterosis yet leaving open questions that requires further research and experimentation. Answering these questions would possibly equip today’s plant breeders with efficient tools and accurate choices to breed crops for a sustainable future.
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Affiliation(s)
- Attiq ur Rehman
- Horticulture Technologies, Production Systems Unit, Natural Resources Institute (Luke), Toivonlinnantie 518, 21500 Piikkiö, Finland;
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, The University of Helsinki, 00790 Helsinki, Finland;
| | - Trang Dang
- Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
- Correspondence:
| | - Shanzay Qamar
- Department of Agricultural Biotechnology, National Institute of Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Science, Faisalabad 38000, Pakistan;
| | - Amina Ilyas
- Department of Botany, Government College University, Lahore 54000, Pakistan;
| | - Reemana Fatema
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), SE-230 53 Alnarp, Sweden;
- Department of Seed Science and Technology, Ege University, Bornova, Izmir 35100, Turkey
| | - Madan Kafle
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, The University of Helsinki, 00790 Helsinki, Finland;
| | - Zawar Hussain
- Environmental and Plant Biology Department, Ohio University, Athens, OH 45701, USA;
| | - Sara Masood
- University Institute of Diet and Nutritional Sciences (UIDNS), Faculty of Allied Health Sciences, University of Lahore, Lahore 54000, Pakistan;
| | - Shehyar Iqbal
- IMPLANTEUS Graduate School, Avignon Université, 84000 Avignon, France;
| | - Khurram Shahzad
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur 22620, Pakistan;
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Mackay IJ, Cockram J, Howell P, Powell W. Understanding the classics: the unifying concepts of transgressive segregation, inbreeding depression and heterosis and their central relevance for crop breeding. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:26-34. [PMID: 32996672 PMCID: PMC7769232 DOI: 10.1111/pbi.13481] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 09/07/2020] [Accepted: 09/12/2020] [Indexed: 05/12/2023]
Abstract
Transgressive segregation and heterosis are the reasons that plant breeding works. Molecular explanations for both phenomena have been suggested and play a contributing role. However, it is often overlooked by molecular genetic researchers that transgressive segregation and heterosis are most simply explained by dispersion of favorable alleles. Therefore, advances in molecular biology will deliver the most impact on plant breeding when integrated with sources of heritable trait variation - and this will be best achieved within a quantitative genetics framework. An example of the power of quantitative approaches is the implementation of genomic selection, which has recently revolutionized animal breeding. Genomic selection is now being applied to both hybrid and inbred crops and is likely to be the major source of improvement in plant breeding practice over the next decade. Breeders' ability to efficiently apply genomic selection methodologies is due to recent technology advances in genotyping and sequencing. Furthermore, targeted integration of additional molecular data (such as gene expression, gene copy number and methylation status) into genomic prediction models may increase their performance. In this review, we discuss and contextualize a suite of established quantitative genetics themes relating to hybrid vigour, transgressive segregation and their central relevance to plant breeding, with the aim of informing crop researchers outside of the quantitative genetics discipline of their relevance and importance to crop improvement. Better understanding between molecular and quantitative disciplines will increase the potential for further improvements in plant breeding methodologies and so help underpin future food security.
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Affiliation(s)
- Ian J. Mackay
- SRUC (Scotland’s Rural College)EdinburghUK
- IMplant ConsultancyChelmsfordUK
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10
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Schneemann H, De Sanctis B, Roze D, Bierne N, Welch JJ. The geometry and genetics of hybridization. Evolution 2020; 74:2575-2590. [PMID: 33150956 PMCID: PMC7839769 DOI: 10.1111/evo.14116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 07/26/2020] [Accepted: 10/12/2020] [Indexed: 11/30/2022]
Abstract
When divergent populations form hybrids, hybrid fitness can vary with genome composition, current environmental conditions, and the divergence history of the populations. We develop analytical predictions for hybrid fitness, which incorporate all three factors. The predictions are based on Fisher's geometric model, and apply to a wide range of population genetic parameter regimes and divergence conditions, including allopatry and parapatry, local adaptation, and drift. Results show that hybrid fitness can be decomposed into intrinsic effects of admixture and heterozygosity, and extrinsic effects of the (local) adaptedness of the parental lines. Effect sizes are determined by a handful of geometric distances, which have a simple biological interpretation. These distances also reflect the mode and amount of divergence, such that there is convergence toward a characteristic pattern of intrinsic isolation. We next connect our results to the quantitative genetics of line crosses in variable or patchy environments. This means that the geometrical distances can be estimated from cross data, and provides a simple interpretation of the "composite effects." Finally, we develop extensions to the model, involving selectively induced disequilibria, and variable phenotypic dominance. The geometry of fitness landscapes provides a unifying framework for understanding speciation, and wider patterns of hybrid fitness.
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Affiliation(s)
- Hilde Schneemann
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeUnited Kingdom
- Institut des Sciences de l'ÉvolutionUniversité MontpellierUMR 5554, Montpellier Cedex 05France
| | - Bianca De Sanctis
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeUnited Kingdom
- Department of ZoologyUniversity of CambridgeDowning StreetCambridgeUnited Kingdom
| | - Denis Roze
- CNRS, UMI 3614Evolutionary Biology and Ecology of AlgaeRoscoffFrance
- Station Biologique de RoscoffSorbonne UniversitéRoscoff29688France
| | - Nicolas Bierne
- ISEM Université Montpellier, CNRS, EPHE, IRDMontpellierFrance
| | - John J. Welch
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeUnited Kingdom
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11
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Matur F, Yanchukov A, Çolak F, Sözen M. Two major clades of blind mole rats (Nannospalax sp.) revealed by mtDNA and microsatellite genotyping in Western and Central Turkey. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2018.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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12
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Simon A, Bierne N, Welch JJ. Coadapted genomes and selection on hybrids: Fisher's geometric model explains a variety of empirical patterns. Evol Lett 2018; 2:472-498. [PMID: 30283696 PMCID: PMC6145440 DOI: 10.1002/evl3.66] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/02/2018] [Accepted: 06/06/2018] [Indexed: 12/27/2022] Open
Abstract
Natural selection plays a variety of roles in hybridization, speciation, and admixture. Most research has focused on two extreme cases: crosses between closely related inbred lines, where hybrids are fitter than their parents, or crosses between effectively isolated species, where hybrids suffer severe breakdown. But many natural populations must fall into intermediate regimes, with multiple types of gene interaction, and these are more difficult to study. Here, we develop a simple fitness landscape model, and show that it naturally interpolates between previous modeling approaches, which were designed for the extreme cases, and invoke either mildly deleterious recessives, or discrete hybrid incompatibilities. Our model yields several new predictions, which we test with genomic data from Mytilus mussels, and published data from plants (Zea, Populus, and Senecio) and animals (Mus, Teleogryllus, and Drosophila). The predictions are generally supported, and the model explains a number of surprising empirical patterns. Our approach enables novel and complementary uses of genome-wide datasets, which do not depend on identifying outlier loci, or "speciation genes" with anomalous effects. Given its simplicity and flexibility, and its predictive successes with a wide range of data, the approach should be readily extendable to other outstanding questions in the study of hybridization.
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Affiliation(s)
- Alexis Simon
- Institut des Sciences de l'Évolution UMR5554, Université de MontpellierCNRS‐IRD‐EPHE‐UMFrance
- Department of GeneticsUniversity of CambridgeDowning St. CambridgeCB23EHUnited Kingdom
| | - Nicolas Bierne
- Institut des Sciences de l'Évolution UMR5554, Université de MontpellierCNRS‐IRD‐EPHE‐UMFrance
- Department of GeneticsUniversity of CambridgeDowning St. CambridgeCB23EHUnited Kingdom
| | - John J. Welch
- Department of GeneticsUniversity of CambridgeDowning St. CambridgeCB23EHUnited Kingdom
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13
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Wang J, Lamer JT, Gaughan S, Wachholtz M, Wang C, Lu G. Transcriptomic comparison of invasive bigheaded carps ( Hypophthalmichthys nobilis and Hypophthalmichthys molitrix) and their hybrids. Ecol Evol 2016; 6:8452-8459. [PMID: 28031797 PMCID: PMC5167015 DOI: 10.1002/ece3.2574] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 09/30/2016] [Accepted: 10/05/2016] [Indexed: 11/15/2022] Open
Abstract
Bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), collectively called bigheaded carps, are invasive species in the Mississippi River Basin (MRB). Interspecific hybridization between bigheaded carps has been considered rare within their native rivers in China; however, it is prevalent in the MRB. We conducted de novo transcriptome analysis of pure and hybrid bigheaded carps and obtained 40,759 to 51,706 transcripts for pure, F1 hybrid, and backcross bigheaded carps. The search against protein databases resulted in 20,336–28,133 annotated transcripts (over 50% of the transcriptome) with over 13,000 transcripts mapped to 23 Gene Ontology biological processes and 127 KEGG metabolic pathways. More transcripts were detected in silver carp than in bighead carp; however, comparable numbers of transcripts were annotated. Transcriptomic variation detected between two F1 hybrids may indicate a potential loss of fitness in hybrids. The neighbor‐joining distance tree constructed using over 2,500 one‐to‐one orthologous sequences suggests transcriptomes could be used to infer the history of introgression and hybridization. Moreover, we detected 24,792 candidate SNPs that can be used to identify different species. The transcriptomes, orthologous sequences, and candidate SNPs obtained in this study should provide further knowledge of interspecific hybridization and introgression.
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Affiliation(s)
- Jun Wang
- Department of Biology University of Nebraska at Omaha Omaha NE 68182 USA; Key Laboratory of Freshwater Fisheries Germplasm Resources Ministry of Agriculture Shanghai Ocean University Shanghai 201306 China
| | - James T Lamer
- Department of Biological Sciences Western Illinois University Macomb IL 61455 USA
| | - Sarah Gaughan
- Department of Biology University of Nebraska at Omaha Omaha NE 68182 USA
| | - Michael Wachholtz
- Department of Biology University of Nebraska at Omaha Omaha NE 68182 USA
| | - Chenghui Wang
- Key Laboratory of Freshwater Fisheries Germplasm Resources Ministry of Agriculture Shanghai Ocean University Shanghai 201306 China
| | - Guoqing Lu
- Department of Biology University of Nebraska at Omaha Omaha NE 68182 USA; School of Interdisciplinary Informatics University of Nebraska at Omaha Omaha NE 68182 USA
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14
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López-Rull I, Lifshitz N, Macías Garcia C, Graves JA, Torres R. Females of a polymorphic seabird dislike foreign-looking males. Anim Behav 2016. [DOI: 10.1016/j.anbehav.2015.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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15
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Yang X, Zhao XG, Li CQ, Liu J, Qiu ZJ, Dong Y, Wang YZ. Distinct Regulatory Changes Underlying Differential Expression of TEOSINTE BRANCHED1-CYCLOIDEA-PROLIFERATING CELL FACTOR Genes Associated with Petal Variations in Zygomorphic Flowers of Petrocosmea spp. of the Family Gesneriaceae. PLANT PHYSIOLOGY 2015; 169:2138-51. [PMID: 26351309 PMCID: PMC4634094 DOI: 10.1104/pp.15.01181] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/04/2015] [Indexed: 05/08/2023]
Abstract
CYCLOIDEA (CYC)-like genes, belonging to the plant-specific TCP transcription factor family that is named after TEOSINTE BRANCHED1 (TB1) from maize (Zea mays), CYC from Antirrhinum majus, and the PROLIFERATING CELL FACTORS (PCF) from rice (Oryza sativa), have conserved dorsal identity function in patterning floral zygomorphy mainly through specific expression in dorsal petals of a flower. Their expression changes are usually related to morphological diversity of zygomorphic flowers. However, it is still a challenge to elucidate the molecular mechanism underlying their expression differentiation. It is also unknown whether CINCINNATA (CIN)-like TCP genes, locally controlling cell growth and proliferation, are involved in the evolution of floral zygomorphy. To address these questions, we selected two closely related species, i.e. Petrocosmea glabristoma and Petrocosmea sinensis, with distinct petal morphology to conduct expression, hybridization, mutant, and allele-specific expression analyses. The results show that the size change of the dorsal petals between the two species is mainly mediated by the expression differentiation of CYC1C and CYC1D, while the shape variation of all petals is related to the expression change of CIN1. In reciprocal F1 hybrids, the expression of CYC1C, CYC1D, and CIN1 conforms to an additive inheritance mode, consistent with the petal phenotypes of hybrids. Through allele-specific expression analyses, we find that the expression differentiation of these TCP genes is underlain by distinctly different types of regulatory changes. We suggest that highly redundant paralogs with identical expression patterns and interspecific expression differentiation may be controlled by remarkably different regulatory pathways because natural selection may favor different regulatory modifications rather than coding sequence changes of key developmental genes in generating morphological diversity.
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Affiliation(s)
- Xia Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.Y., X.-G.Z., C.-Q.L., J.L., Z.-J.Q., Y.D., Y.-Z.W.) andUniversity of Chinese Academy of Sciences, Beijing 100049, China (X.-G.Z., C.-Q.L., J.L., Y.-Z.W.)
| | - Xiao-Ge Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.Y., X.-G.Z., C.-Q.L., J.L., Z.-J.Q., Y.D., Y.-Z.W.) andUniversity of Chinese Academy of Sciences, Beijing 100049, China (X.-G.Z., C.-Q.L., J.L., Y.-Z.W.)
| | - Chao-Qun Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.Y., X.-G.Z., C.-Q.L., J.L., Z.-J.Q., Y.D., Y.-Z.W.) andUniversity of Chinese Academy of Sciences, Beijing 100049, China (X.-G.Z., C.-Q.L., J.L., Y.-Z.W.)
| | - Jing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.Y., X.-G.Z., C.-Q.L., J.L., Z.-J.Q., Y.D., Y.-Z.W.) andUniversity of Chinese Academy of Sciences, Beijing 100049, China (X.-G.Z., C.-Q.L., J.L., Y.-Z.W.)
| | - Zhi-Jing Qiu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.Y., X.-G.Z., C.-Q.L., J.L., Z.-J.Q., Y.D., Y.-Z.W.) andUniversity of Chinese Academy of Sciences, Beijing 100049, China (X.-G.Z., C.-Q.L., J.L., Y.-Z.W.)
| | - Yang Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.Y., X.-G.Z., C.-Q.L., J.L., Z.-J.Q., Y.D., Y.-Z.W.) andUniversity of Chinese Academy of Sciences, Beijing 100049, China (X.-G.Z., C.-Q.L., J.L., Y.-Z.W.)
| | - Yin-Zheng Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.Y., X.-G.Z., C.-Q.L., J.L., Z.-J.Q., Y.D., Y.-Z.W.) andUniversity of Chinese Academy of Sciences, Beijing 100049, China (X.-G.Z., C.-Q.L., J.L., Y.-Z.W.)
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16
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Transcriptional Derepression Uncovers Cryptic Higher-Order Genetic Interactions. PLoS Genet 2015; 11:e1005606. [PMID: 26484664 PMCID: PMC4618523 DOI: 10.1371/journal.pgen.1005606] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 09/24/2015] [Indexed: 12/11/2022] Open
Abstract
Disruption of certain genes can reveal cryptic genetic variants that do not typically show phenotypic effects. Because this phenomenon, which is referred to as ‘phenotypic capacitance’, is a potential source of trait variation and disease risk, it is important to understand how it arises at the genetic and molecular levels. Here, we use a cryptic colony morphology trait that segregates in a yeast cross to explore the mechanisms underlying phenotypic capacitance. We find that the colony trait is expressed when a mutation in IRA2, a negative regulator of the Ras pathway, co-occurs with specific combinations of cryptic variants in six genes. Four of these genes encode transcription factors that act downstream of the Ras pathway, indicating that the phenotype involves genetically complex changes in the transcriptional regulation of Ras targets. We provide evidence that the IRA2 mutation reveals the phenotypic effects of the cryptic variants by disrupting the transcriptional silencing of one or more genes that contribute to the trait. Supporting this role for the IRA2 mutation, deletion of SFL1, a repressor that acts downstream of the Ras pathway, also reveals the phenotype, largely due to the same cryptic variants that were detected in the IRA2 mutant cross. Our results illustrate how higher-order genetic interactions among mutations and cryptic variants can result in phenotypic capacitance in specific genetic backgrounds, and suggests these interactions might reflect genetically complex changes in gene expression that are usually suppressed by negative regulation. Some genetic polymorphisms have phenotypic effects that are masked under most conditions, but can be revealed by mutations or environmental change. The genetic and molecular mechanisms that suppress and uncover these cryptic genetic variants are important to understand. Here, we show that a single mutation in a yeast cross causes a major phenotypic change through its genetic interactions with two specific combinations of cryptic variants in six genes. This result suggests that in some cases cryptic variants themselves play roles in revealing their own phenotypic effects through their genetic interactions with each other and the mutations that reveal them. We also demonstrate that most of the genes harboring cryptic variation in our system are transcription factors, a finding that supports an important role for perturbation of gene regulatory networks in the uncovering of cryptic variation. As a final part of our study, we interrogate how a mutation exposes combinations of cryptic variants and obtain evidence that it does so by disrupting the silencing of one or more genes that must be expressed for the cryptic variants to exert their effects. To prove this point, we delete the transcriptional repressor that mediates this silencing and demonstrate that this deletion reveals a similar set of cryptic variants to the ones that were discovered in the initial mutant background. These findings advance our understanding of the genetic and molecular mechanisms that reveal cryptic variation.
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17
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Variation in Arabidopsis flowering time associated with cis-regulatory variation in CONSTANS. Nat Commun 2014; 5:3651. [PMID: 24736505 PMCID: PMC3997802 DOI: 10.1038/ncomms4651] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/13/2014] [Indexed: 12/22/2022] Open
Abstract
The onset of flowering, the change from vegetative to reproductive development, is a major life history transition in flowering plants. Recent work suggests that mutations in cis-regulatory mutations should play critical roles in the evolution of this (as well as other) important adaptive traits, but thus far there has been little evidence that directly links regulatory mutations to evolutionary change at the species level. While several genes have previously been shown to affect natural variation in flowering time in Arabidopsis thaliana, most either show protein-coding changes and/or are found at low frequency (<5%). Here we identify and characterize natural variation in the cis-regulatory sequence in the transcription factor CONSTANS that underlies flowering time diversity in Arabidopsis. Mutation in this regulatory motif evolved recently and has spread to high frequency in Arabidopsis natural accessions, suggesting a role for these cis-regulatory changes in adaptive variation of flowering time. The transcription factor CONSTANS regulates the timing of flowering in Arabidopsis. Rosas et al. report that genetic variation in the cis-regulatory regions of this gene contributes to natural phenotypic variation in flowering time.
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18
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Boratyński Z, Melo-Ferreira J, Alves PC, Berto S, Koskela E, Pentikäinen OT, Tarroso P, Ylilauri M, Mappes T. Molecular and ecological signs of mitochondrial adaptation: consequences for introgression? Heredity (Edinb) 2014; 113:277-86. [PMID: 24690754 DOI: 10.1038/hdy.2014.28] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 02/18/2014] [Accepted: 02/20/2014] [Indexed: 02/01/2023] Open
Abstract
The evolution of the mitochondrial genome and its potential adaptive impact still generates vital debates. Even if mitochondria have a crucial functional role, as they are the main cellular energy suppliers, mitochondrial DNA (mtDNA) introgression is common in nature, introducing variation in populations upon which selection may act. Here we evaluated whether the evolution of mtDNA in a rodent species affected by mtDNA introgression is explained by neutral expectations alone. Variation in one mitochondrial and six nuclear markers in Myodes glareolus voles was examined, including populations that show mtDNA introgression from its close relative, Myodes rutilus. In addition, we modelled protein structures of the mtDNA marker (cytochrome b) and estimated the environmental envelopes of mitotypes. We found that massive mtDNA introgression occurred without any trace of introgression in the analysed nuclear genes. The results show that the native glareolus mtDNA evolved under past positive selection, suggesting that mtDNA in this system has selective relevance. The environmental models indicate that the rutilus mitotype inhabits colder and drier habitats than the glareolus one that can result from local adaptation or from the geographic context of introgression. Finally, homology models of the cytochrome b protein revealed a substitution in rutilus mtDNA in the vicinity of the catalytic fraction, suggesting that differences between mitotypes may result in functional changes. These results suggest that the evolution of mtDNA in Myodes may have functional, ecological and adaptive significance. This work opens perspective onto future experimental tests of the role of natural selection in mtDNA introgression in this system.
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Affiliation(s)
- Z Boratyński
- 1] Centre of Excellence in Evolutionary Research, Division of Ecology and Evolutionary Biology, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland [2] CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Associate Laboratory, Universidade do Porto, Vairão, Portugal
| | - J Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Associate Laboratory, Universidade do Porto, Vairão, Portugal
| | - P C Alves
- 1] CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Associate Laboratory, Universidade do Porto, Vairão, Portugal [2] Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal [3] Wildlife Biology Program, University of Montana, Missoula, MT, USA
| | - S Berto
- 1] Centre of Excellence in Evolutionary Research, Division of Ecology and Evolutionary Biology, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland [2] 'TFome and Trancriptome Evolution', Universität Leipzig, Leipzig, Germany
| | - E Koskela
- Division of Ecology and Evolutionary Biology, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - O T Pentikäinen
- Computational Bioscience Laboratory, Division of Cell and Molecular Biology, Department of Biological and Environmental Science & Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - P Tarroso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Associate Laboratory, Universidade do Porto, Vairão, Portugal
| | - M Ylilauri
- Computational Bioscience Laboratory, Division of Cell and Molecular Biology, Department of Biological and Environmental Science & Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - T Mappes
- Centre of Excellence in Evolutionary Research, Division of Ecology and Evolutionary Biology, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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19
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Chevin LM, Decorzent G, Lenormand T. NICHE DIMENSIONALITY AND THE GENETICS OF ECOLOGICAL SPECIATION. Evolution 2014; 68:1244-56. [DOI: 10.1111/evo.12346] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 01/03/2014] [Indexed: 12/19/2022]
Affiliation(s)
| | | | - Thomas Lenormand
- CEFE-UMR 5175 1919 route de Mende; F-34293 Montpellier CEDEX 5 France
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20
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de Bossoreille de Ribou S, Douam F, Hamant O, Frohlich MW, Negrutiu I. Plant science and agricultural productivity: why are we hitting the yield ceiling? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 210:159-76. [PMID: 23849123 DOI: 10.1016/j.plantsci.2013.05.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 04/26/2013] [Accepted: 05/16/2013] [Indexed: 05/11/2023]
Abstract
Trends in conventional plant breeding and in biotechnology research are analyzed with a focus on production and productivity of individual organisms. Our growing understanding of the productive/adaptive potential of (crop) plants is a prerequisite to increasing this potential and also its expression under environmental constraints. This review concentrates on growth rate, ribosome activity, and photosynthetic rate to link these key cellular processes to plant productivity. Examples of how they may be integrated in heterosis, organ growth control, and responses to abiotic stresses are presented. The yield components in rice are presented as a model. The ultimate goal of research programs, that concentrate on yield and productivity and integrating the panoply of systems biology tools, is to achieve "low input, high output" agriculture, i.e. shifting from a conventional "productivist" agriculture to an efficient sustainable agriculture. This is of critical, strategic importance, because the extent to which we, both locally and globally, secure and manage the long-term productive potential of plant resources will determine the future of humanity.
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21
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Costa MMR, Yang S, Critchley J, Feng X, Wilson Y, Langlade N, Copsey L, Hudson A. The genetic basis for natural variation in heteroblasty in Antirrhinum. THE NEW PHYTOLOGIST 2012; 196:1251-1259. [PMID: 23025531 DOI: 10.1111/j.1469-8137.2012.04347.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 08/18/2012] [Indexed: 05/28/2023]
Abstract
Heteroblasty refers to the changes in leaf shape and size (allometry) along stems. Although evolutionary changes involving heteroblasty might contribute to leaf diversity, little is known of the extent to which heteroblasty differs between species or how it might relate to other aspects of allometry or other developmental transitions. Here, we develop a computational model that can quantify differences in leaf allometry between Antirrhinum (snapdragon) species, including variation in heteroblasty. It allows the underlying genes to be mapped in inter-species hybrids, and their effects to be studied in similar genetic backgrounds. Heteroblasty correlates with overall variation in leaf allometry, so species with smaller, rounder leaves produce their largest leaves earlier in development. This involves genes that affect both characters together and is exaggerated by additional genes with multiplicative effects on leaf size. A further heteroblasty gene also alters leaf spacing, but none affect other developmental transitions, including flowering. We suggest that differences in heteroblasty have co-evolved with overall leaf shape and size in Antirrhinum because these characters are constrained by common underlying genes. By contrast, heteroblasty is not correlated with other developmental transitions, with the exception of internode length, suggesting independent genetic control and evolution.
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Affiliation(s)
- M Manuela R Costa
- Institute of Molecular Plant Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3JH, UK
- Center for Biodiversity, Functional & Integrative Genomics, Department of Biology, University of Minho, 4710-057, Braga, Portugal
| | - Suxin Yang
- Institute of Molecular Plant Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3JH, UK
| | - Joanna Critchley
- Institute of Molecular Plant Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3JH, UK
| | - Xianzhong Feng
- Institute of Molecular Plant Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3JH, UK
| | - Yvette Wilson
- Institute of Molecular Plant Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3JH, UK
| | - Nicolas Langlade
- Department of Cell & Developmental Biology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - Lucy Copsey
- Department of Cell & Developmental Biology, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - Andrew Hudson
- Institute of Molecular Plant Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3JH, UK
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22
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Félix MA. Evolution in developmental phenotype space. Curr Opin Genet Dev 2012; 22:593-9. [PMID: 22925969 DOI: 10.1016/j.gde.2012.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 08/03/2012] [Accepted: 08/09/2012] [Indexed: 12/23/2022]
Abstract
Developmental systems can produce a variety of patterns and morphologies when the molecular and cellular activities within them are varied. With the advent of quantitative modeling, the range of phenotypic output of a developmental system can be assessed by exploring model parameter space. Here I review recent examples where developmental evolution is studied using quantitative models, which increasingly rely on empirically determined molecular signaling pathways and their crosstalk. Quantitative pathway evolution may result in dramatic morphological changes. Alternatively, in many developmental systems, the phenotypic output is robust to a range of parameter variation, and cryptic developmental evolution may occur without morphological change. Formalization and measurements of the relationship between genetic variation and parameter variation in developmental models remain in their infancy.
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Affiliation(s)
- Marie-Anne Félix
- Institute of Biology of the Ecole Normale Supérieure, CNRS UMR8197, Inserm U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris cedex 05, France.
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23
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Rosas U, Zhou RW, Castillo G, Collazo-Ortega M. Developmental reaction norms for water stressed seedlings of succulent cacti. PLoS One 2012; 7:e33936. [PMID: 22479481 PMCID: PMC3316504 DOI: 10.1371/journal.pone.0033936] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 02/21/2012] [Indexed: 11/21/2022] Open
Abstract
Succulent cacti are remarkable plants with capabilities to withstand long periods of drought. However, their adult success is contingent on the early seedling stages, when plants are highly susceptible to the environment. To better understand their early coping strategies in a challenging environment, two developmental aspects (anatomy and morphology) in Polaskia chichipe and Echinocactus platyacanthus were studied in the context of developmental reaction norms under drought conditions. The morphology was evaluated using landmark based morphometrics and Principal Component Analysis, which gave three main trends of the variation in each species. The anatomy was quantified as number and area of xylem vessels. The quantitative relationship between morphology and anatomy in early stages of development, as a response to drought was revealed in these two species. Qualitatively, collapsible cells and collapsible parenchyma tissue were observed in seedlings of both species, more often in those subjected to water stress. These tissues were located inside the epidermis, resembling a web of collapsible-cell groups surrounding turgid cells, vascular bundles, and spanned across the pith. Occasionally the groups formed a continuum stretching from the epidermis towards the vasculature. Integrating the morphology and the anatomy in a developmental context as a response to environmental conditions provides a better understanding of the organism's dynamics, adaptation, and plasticity.
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Affiliation(s)
- Ulises Rosas
- Center for Genomics and Systems Biology, New York University, New York City, New York, United States of America.
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24
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Chitwood DH, Headland LR, Kumar R, Peng J, Maloof JN, Sinha NR. The developmental trajectory of leaflet morphology in wild tomato species. PLANT PHYSIOLOGY 2012; 158:1230-40. [PMID: 22247269 PMCID: PMC3291254 DOI: 10.1104/pp.111.192518] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 01/09/2012] [Indexed: 05/18/2023]
Abstract
Leaves between species vary in their size, serration, complexity, and shape. However, phylogeny is not the only predictor of leaf morphology. The shape of a leaf is the result of intricate developmental processes, including heteroblastic progression (changes in leaf size and shape at different nodes) and the developmental stage of an organ. The leaflets that arise from complex leaves are additionally modified by their positioning along the proximal-distal axis of a leaf and whether they fall on the left or right side of leaves. Even further, leaves are environmentally responsive, and their final shape is influenced by environmental inputs. Here, we comprehensively describe differences in leaflet shape between wild tomato (Solanum section Lycopersicon) species using a principal component analysis on elliptical Fourier descriptors arising from >11,000 sampled leaflets. We leverage differences in developmental rate to approximate a developmental series, which allows us to resolve the confounding differences in intrinsic leaflet form and developmental stage along positions of the heteroblastic leaf series and proximal-distal axis of leaves. We find that the resulting developmental trajectory of organs at different positions along these axes are useful for describing the changes in leaflet shape that occur during the shade avoidance response in tomato. We argue that it is the developmental trajectory, the changes in shape that occur over developmental time in organs reiterated at multiple positions, that is the relevant phenotype for discerning differences between populations and species, and to understand the underlying developmental processes that change during evolution.
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Affiliation(s)
| | | | | | | | | | - Neelima R. Sinha
- Department of Plant Biology (D.H.C., L.R.H., R.K., J.N.M., N.R.S.) and Department of Statistics (J.P.), University of California, Davis, California 95616
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25
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Duveau F, Félix MA. Role of pleiotropy in the evolution of a cryptic developmental variation in Caenorhabditis elegans. PLoS Biol 2012; 10:e1001230. [PMID: 22235190 PMCID: PMC3250502 DOI: 10.1371/journal.pbio.1001230] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 11/18/2011] [Indexed: 12/20/2022] Open
Abstract
Using vulval phenotypes in Caenorhabditis elegans, the authors show that cryptic genetic variation can evolve through selection for pleiotropic effects that alter fitness, and identify a cryptic variant that has conferred enhanced fitness on domesticated worms under laboratory conditions. Robust biological systems are expected to accumulate cryptic genetic variation that does not affect the system output in standard conditions yet may play an evolutionary role once phenotypically expressed under a strong perturbation. Genetic variation that is cryptic relative to a robust trait may accumulate neutrally as it does not change the phenotype, yet it could also evolve under selection if it affects traits related to fitness in addition to its cryptic effect. Cryptic variation affecting the vulval intercellular signaling network was previously uncovered among wild isolates of Caenorhabditis elegans. Using a quantitative genetic approach, we identify a non-synonymous polymorphism of the previously uncharacterized nath-10 gene that affects the vulval phenotype when the system is sensitized with different mutations, but not in wild-type strains. nath-10 is an essential protein acetyltransferase gene and the homolog of human NAT10. The nath-10 polymorphism also presents non-cryptic effects on life history traits. The nath-10 allele carried by the N2 reference strain leads to a subtle increase in the egg laying rate and in the total number of sperm, a trait affecting the trade-off between fertility and minimal generation time in hermaphrodite individuals. We show that this allele appeared during early laboratory culture of N2, which allowed us to test whether it may have evolved under selection in this novel environment. The derived allele indeed strongly outcompetes the ancestral allele in laboratory conditions. In conclusion, we identified the molecular nature of a cryptic genetic variation and characterized its evolutionary history. These results show that cryptic genetic variation does not necessarily accumulate neutrally at the whole-organism level, but may evolve through selection for pleiotropic effects that alter fitness. In addition, cultivation in the laboratory has led to adaptive evolution of the reference strain N2 to the laboratory environment, which may modify other phenotypes of interest. Robustness is a property of biological systems that ensures the production of reproducible phenotypes in spite of underlying environmental, stochastic, and genetic variability. A consequence of robustness is that potentially functional genetic variation is free to accumulate in natural populations because it is buffered at the phenotypic level. Even if this so-called “cryptic” genetic variation has no obvious effects under standard conditions, it may become phenotypically expressed upon major genetic or environmental perturbations. Here we used the model organism Caenorhabditis elegans to identify genetic variations involved in the cryptic evolution of vulval cell fate induction between wild strains. We found that a mutation in the essential nath-10 gene not only contributes to cryptic genetic variation in the vulval system, but also affects key life history traits that are expected to be under a strong selective pressure (brood size, age at sexual maturity, sperm number and rate of progeny production). Indeed, an allele of nath-10 that emerged during the laboratory domestication of C. elegans about 50 years ago confers a strong competitive advantage over the ancestral allele under laboratory conditions. A genetic variation that is cryptic for a robust trait can therefore affect more sensitive phenotypes and thus evolve under selection.
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26
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Masly JP, Dalton JE, Srivastava S, Chen L, Arbeitman MN. The genetic basis of rapidly evolving male genital morphology in Drosophila. Genetics 2011; 189:357-74. [PMID: 21750260 PMCID: PMC3176115 DOI: 10.1534/genetics.111.130815] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 06/22/2011] [Indexed: 01/22/2023] Open
Abstract
The external genitalia are some of the most rapidly evolving morphological structures in insects. The posterior lobe of the male genital arch shows striking differences in both size and shape among closely related species of the Drosophila melanogaster species subgroup. Here, we dissect the genetic basis of posterior lobe morphology between D. mauritiana and D. sechellia, two island endemic species that last shared a common ancestor ∼300,000 years ago. We test a large collection of genome-wide homozygous D. mauritiana genetic introgressions, which collectively cover ∼50% of the genome, for their morphological effects when placed in a D. sechellia genetic background. We find several introgressions that have large effects on posterior lobe morphology and that posterior lobe size and posterior lobe shape can be separated genetically for some of the loci that specify morphology. Using next generation sequencing technology, we perform whole transcriptome gene expression analyses of the larval genital imaginal disc of D. mauritiana, D. sechellia, and two D. mauritiana-D. sechellia hybrid introgression genotypes that each have large effects on either posterior lobe size or posterior lobe shape. Many of the genes we identify as differentially expressed are expressed at levels similar to D. mauritiana in one introgression hybrid, but are expressed at levels similar to D. sechellia in the other introgression hybrid. However, we also find that both introgression hybrids express some of the same genes at levels similar to D. mauritiana, and notably, that both introgression hybrids possess genes in the insulin receptor signaling pathway, which are expressed at D. mauritiana expression levels. These results suggest the possibility that the insulin signaling pathway might integrate size and shape genetic inputs to establish differences in overall posterior lobe morphology between D. mauritiana and D. sechellia.
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Affiliation(s)
- John P Masly
- Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA.
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27
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Hybrid fitness, adaptation and evolutionary diversification: lessons learned from Louisiana Irises. Heredity (Edinb) 2011; 108:159-66. [PMID: 21792222 DOI: 10.1038/hdy.2011.65] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Estimates of hybrid fitness have been used as either a platform for testing the potential role of natural hybridization in the evolution of species and species complexes or, alternatively, as a rationale for dismissing hybridization events as being of any evolutionary significance. From the time of Darwin's publication of The Origin, through the neo-Darwinian synthesis, to the present day, the observation of variability in hybrid fitness has remained a challenge for some models of speciation. Yet, Darwin and others have reported the elevated fitness of hybrid genotypes under certain environmental conditions. In modern scientific terminology, this observation reflects the fact that hybrid genotypes can demonstrate genotype × environment interactions. In the current review, we illustrate the development of one plant species complex, namely the Louisiana Irises, into a 'model system' for investigating hybrid fitness and the role of genetic exchange in adaptive evolution and diversification. In particular, we will argue that a multitude of approaches, involving both experimental and natural environments, and incorporating both manipulative analyses and surveys of natural populations, are necessary to adequately test for the evolutionary significance of introgressive hybridization. An appreciation of the variability of hybrid fitness leads to the conclusion that certain genetic signatures reflect adaptive evolution. Furthermore, tests of the frequency of allopatric versus sympatric/parapatric divergence (that is, divergence with ongoing gene flow) support hybrid genotypes as a mechanism of evolutionary diversification in numerous species complexes.
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Mathes WF, Aylor DL, Miller DR, Churchill GA, Chesler EJ, de Villena FPM, Threadgill DW, Pomp D. Architecture of energy balance traits in emerging lines of the Collaborative Cross. Am J Physiol Endocrinol Metab 2011; 300:E1124-34. [PMID: 21427413 PMCID: PMC3118585 DOI: 10.1152/ajpendo.00707.2010] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The potential utility of the Collaborative Cross (CC) mouse resource was evaluated to better understand complex traits related to energy balance. A primary focus was to examine if genetic diversity in emerging CC lines (pre-CC) would translate into equivalent phenotypic diversity. Second, we mapped quantitative trait loci (QTL) for 15 metabolism- and exercise-related phenotypes in this population. We evaluated metabolic and voluntary exercise traits in 176 pre-CC lines, revealing phenotypic variation often exceeding that seen across the eight founder strains from which the pre-CC was derived. Many phenotypic correlations existing within the founder strains were no longer significant in the pre-CC population, potentially representing reduced linkage disequilibrium (LD) of regions harboring multiple genes with effects on energy balance or disruption of genetic structure of extant inbred strains with substantial shared ancestry. QTL mapping revealed five significant and eight suggestive QTL for body weight (Chr 4, 7.54 Mb; CI 3.32-10.34 Mb; Bwq14), body composition, wheel running (Chr 16, 33.2 Mb; CI 32.5-38.3 Mb), body weight change in response to exercise (1: Chr 6, 77.7Mb; CI 72.2-83.4 Mb and 2: Chr 6, 42.8 Mb; CI 39.4-48.1 Mb), and food intake during exercise (Chr 12, 85.1 Mb; CI 82.9-89.0 Mb). Some QTL overlapped with previously mapped QTL for similar traits, whereas other QTL appear to represent novel loci. These results suggest that the CC will be a powerful, high-precision tool for examining the genetic architecture of complex traits such as those involved in regulation of energy balance.
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Affiliation(s)
- Wendy Foulds Mathes
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
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Luna-Nevarez P, Rincon G, Medrano JF, Riley DG, Chase CC, Coleman SW, VanLeeuwen DM, DeAtley KL, Islas-Trejo A, Silver GA, Thomas MG. Single nucleotide polymorphisms in the growth hormone–insulin-like growth factor axis in straightbred and crossbred Angus, Brahman, and Romosinuano heifers: Population genetic analyses and association of genotypes with reproductive phenotypes1. J Anim Sci 2011; 89:926-34. [DOI: 10.2527/jas.2010-3483] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Lourenço J, Galtier N, Glémin S. COMPLEXITY, PLEIOTROPY, AND THE FITNESS EFFECT OF MUTATIONS. Evolution 2011; 65:1559-71. [DOI: 10.1111/j.1558-5646.2011.01237.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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