1
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Han B, Cui D, Ma X, Cao G, Zhang H, Koh HJ, Han L. Evidence for evolution and selection of drought-resistant genes based on high-throughput resequencing in weedy rice. J Exp Bot 2022; 73:1949-1962. [PMID: 35179195 DOI: 10.1093/jxb/erab515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 11/27/2021] [Indexed: 06/14/2023]
Abstract
Weedy rice (Oryza sativa f. spontanea) is a relative of cultivated rice that propagates in paddy fields and has strong drought resistance. In this study, we used 501 rice accessions to reveal the selection mechanism of drought resistance in weedy rice through a combination of selection analysis, genome-wide association studies, gene knockout and overexpression analysis, and Ca2+ and K+ ion flux assays. The results showed that the weedy rice species investigated have gene introgression with cultivated rice, which is consistent with the hypothesis that weedy rice originated from de-domestication of cultivated rice. Regions related to tolerance have particularly diversified during de-domestication and three drought-tolerance genes were identified. Of these, Os01g0800500 was also identified using an assay of the degree of leaf withering under drought, and it was named as PAPH1, encoding a PAP family protein. The drought-resistance capacity of PAPH1-knockout lines was much lower than that of the wild type, while that of overexpression lines was much higher. Concentrations of Ca2+ and K+ were lower in the knockout lines and higher in the overexpression lines compared with those of the wild type, suggesting that PAPH1 plays important roles in coping with drought stress. Our study therefore provides new insights into the genetic mechanisms underlying adaptive tolerance to drought in wild rice and highlights potential new resistance genes for future breeding programs in cultivated rice.
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Affiliation(s)
- Bing Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Di Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoding Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guilan Cao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hee Jong Koh
- Department of Plant Science, Plant Genomics and Breeding Institute of Agriculture and Life Science, Seoul National University, Seoul, >Korea
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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2
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Metz J, Lampei C, Bäumler L, Bocherens H, Dittberner H, Henneberg L, de Meaux J, Tielbörger K. Rapid adaptive evolution to drought in a subset of plant traits in a large-scale climate change experiment. Ecol Lett 2020; 23:1643-1653. [PMID: 32851791 DOI: 10.1111/ele.13596] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/20/2020] [Indexed: 12/17/2022]
Abstract
Rapid evolution of traits and of plasticity may enable adaptation to climate change, yet solid experimental evidence under natural conditions is scarce. Here, we imposed rainfall manipulations (+30%, control, -30%) for 10 years on entire natural plant communities in two Eastern Mediterranean sites. Additional sites along a natural rainfall gradient and selection analyses in a greenhouse assessed whether potential responses were adaptive. In both sites, our annual target species Biscutella didyma consistently evolved earlier phenology and higher reproductive allocation under drought. Multiple arguments suggest that this response was adaptive: it aligned with theory, corresponding trait shifts along the natural rainfall gradient, and selection analyses under differential watering in the greenhouse. However, another seven candidate traits did not evolve, and there was little support for evolution of plasticity. Our results provide compelling evidence for rapid adaptive evolution under climate change. Yet, several non-evolving traits may indicate potential constraints to full adaptation.
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Affiliation(s)
- Johannes Metz
- Plant Ecology & Nature Conservation, Institute of Biology & Chemistry, University of Hildesheim, Hildesheim, Germany.,Plant Ecology Group, Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Christian Lampei
- Biodiversity and Ecosystem Research, Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Laura Bäumler
- Plant Ecology Group, Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Hervé Bocherens
- Senckenberg Centre for Human Evolution and Palaeoenvironment, and Department of Geosciences, Biogeology, University of Tübingen, Tübingen, Germany
| | - Hannes Dittberner
- Plant Molecular Ecology, Institute of Botany, University of Cologne, Cologne, Germany
| | - Lorenz Henneberg
- Plant Ecology Group, Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Juliette de Meaux
- Plant Molecular Ecology, Institute of Botany, University of Cologne, Cologne, Germany
| | - Katja Tielbörger
- Plant Ecology Group, Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
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3
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Yasui H, Valind A, Karlsson J, Pietras C, Jansson C, Wille J, Romerius P, Backman T, Gisselsson D. A dynamic mutational landscape associated with an inter-regionally diverse immune response in malignant rhabdoid tumour. J Pathol 2020; 252:22-28. [PMID: 32542645 DOI: 10.1002/path.5490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/11/2020] [Accepted: 06/03/2020] [Indexed: 12/19/2022]
Abstract
Malignant rhabdoid tumour (MRT) is a childhood neoplasm of high malignancy characterised by biallelic mutation and/or loss of the epigenetic master regulator SMARCB1, accompanied by no or few other oncogenic drivers. In spite of their generally low mutational burden, an intratumoural T-cell response has been reported in a subset of MRTs, indicating that immune checkpoint inhibition may be considered a viable therapy option for some patients. We assess here the evolution over time and space of predicted neoantigens and indicators of immune checkpoint status in two MRT patients who progressed under treatment. Both patients showed an accumulation of novel clonal and subclonal mutations, including predicted neoantigens, in metastases compared to their inferred ancestral clones in the primary tumours. The first patient had peritoneal metastases from an MRT of the liver. Clonal deconvolution revealed polyclonal seeding from the primary tumour to a single metastatic site, followed by a local subclonal burst of mutations. The second patient had a renal MRT with multiple pulmonary metastases, each of which could be traced back to a single genetically unique founder cell, with formation of novel subclones in two metastases. Both patients showed a regionally heterogeneous landscape of predicted neoantigens and of tumour-infiltrating lymphocytes expressing CD8 and PD1. In both patients, some tumour regions fulfilled established criteria for PD-L1 positivity (> 1% of tumour cells), while others did not. This suggests that even in a tumour type like MRT, with a single driver mutation, there can be heterogeneity in neoantigen repertoire, immune response, and biomarkers for checkpoint blockade among sampled locations. This must be taken into account when assessing progressed MRT patients for checkpoint inhibition therapy. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Hiroaki Yasui
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Obstetrics and Gynaecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Anders Valind
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Paediatrics, Skåne University Hospital, Lund, Sweden
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Christina Pietras
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Caroline Jansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Joakim Wille
- Paediatric Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Patrik Romerius
- Paediatric Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Torbjörn Backman
- Paediatric Surgery, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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4
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House C, Tunstall P, Rapkin J, Bale MJ, Gage M, Del Castillo E, Hunt J. Multivariate stabilizing sexual selection and the evolution of male and female genital morphology in the red flour beetle. Evolution 2020; 74:883-896. [PMID: 31889313 PMCID: PMC7317928 DOI: 10.1111/evo.13912] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/11/2019] [Accepted: 12/15/2019] [Indexed: 11/28/2022]
Abstract
Male genitals are highly divergent in animals with internal fertilization. Most studies attempting to explain this diversity have focused on testing the major hypotheses of genital evolution (the lock‐and‐key, pleiotropy, and sexual selection hypotheses), and quantifying the form of selection targeting male genitals has played an important role in this endeavor. However, we currently know far less about selection targeting female genitals or how male and female genitals interact during mating. Here, we use formal selection analysis to show that genital size and shape is subject to strong multivariate stabilizing sexual selection in both sexes of the red flour beetle, Tribolium castaneum. Moreover, we show significant sexual selection on the covariance between the sexes for specific aspects of genital shape suggesting that male and female genitalia also interact to determine the successful transfer of a spermatophore during mating. Our work therefore highlights the important role that both male and female genital morphologies play in determining mating success and that these effects can occur independently, as well as through their interaction. Moreover, it cautions against the overly simplistic view that the sexual selection targeting genital morphology will always be directional in form and restricted primarily to males.
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Affiliation(s)
- Clarissa House
- School of Science and Health and Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Philip Tunstall
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall, TR10 9EZ, United Kingdom
| | - James Rapkin
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall, TR10 9EZ, United Kingdom
| | - Mathilda J Bale
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall, TR10 9EZ, United Kingdom
| | - Matthew Gage
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Enrique Del Castillo
- Department of Industrial Engineering and Department of Statistics, Pennsylvania State University, State College, Pennsylvania, 16802
| | - John Hunt
- School of Science and Health and Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.,Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall, TR10 9EZ, United Kingdom
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5
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Keith RA, Mitchell-Olds T. Antagonistic selection and pleiotropy constrain the evolution of plant chemical defenses. Evolution 2019; 73:947-960. [PMID: 30950034 DOI: 10.1111/evo.13728] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 03/13/2019] [Indexed: 01/24/2023]
Abstract
When pleiotropy is present, genetic correlations may constrain the evolution of ecologically important traits. We used a quantitative genetics approach to investigate constraints on the evolution of secondary metabolites in a wild mustard, Boechera stricta. Much of the genetic variation in chemical composition of glucosinolates in B. stricta is controlled by a single locus, BCMA1/3. In a large-scale common garden experiment under natural conditions, we quantified fitness and glucosinolate profile in two leaf types and in fruits. We estimated genetic variances and covariances (the G-matrix) and selection on chemical profile in each tissue. Chemical composition of defenses was strongly genetically correlated between tissues. We found antagonistic selection between defense composition in leaves and fruits: compounds that were favored in leaves were disadvantageous in fruits. The positive genetic correlations and antagonistic selection led to strong constraints on the evolution of defenses in leaves and fruits. In a hypothetical population with no genetic variation at BCMA1/3, we found no evidence for genetic constraints, indicating that pleiotropy affecting chemical profile in multiple tissues drives constraints on the evolution of secondary metabolites.
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Affiliation(s)
- Rose A Keith
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, 27708.,Biology Department, Duke University, Durham, North Carolina, 27708.,Current Address: Biology Department, St Mary's College of Maryland, St Mary's City, MD, 20686
| | - Thomas Mitchell-Olds
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, 27708.,Biology Department, Duke University, Durham, North Carolina, 27708
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6
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Monro K, Marshall DJ. Unravelling anisogamy: egg size and ejaculate size mediate selection on morphology in free-swimming sperm. Proc Biol Sci 2017; 283:rspb.2016.0671. [PMID: 27412273 DOI: 10.1098/rspb.2016.0671] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/20/2016] [Indexed: 01/28/2023] Open
Abstract
Gamete dimorphism (anisogamy) defines the sexes in most multicellular organisms. Theoretical explanations for its maintenance usually emphasize the size-related selection pressures of sperm competition and zygote survival, assuming that fertilization of all eggs precludes selection for phenotypes that enhance fertility. In external fertilizers, however, fertilization is often incomplete due to sperm limitation, and the risk of polyspermy weakens the advantage of high sperm numbers that is predicted to limit sperm size, allowing alternative selection pressures to target free-swimming sperm. We asked whether egg size and ejaculate size mediate selection on the free-swimming sperm of Galeolaria caespitosa, a marine tubeworm with external fertilization, by comparing relationships between sperm morphology and male fertility across manipulations of egg size and sperm density. Our results suggest that selection pressures exerted by these factors may aid the maintenance of anisogamy in external fertilizers by limiting the adaptive value of larger sperm in the absence of competition. In doing so, our study offers a more complete explanation for the stability of anisogamy across the range of sperm environments typical of this mating system and identifies new potential for the sexes to coevolve via mutual selection pressures exerted by gametes at fertilization.
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Affiliation(s)
- Keyne Monro
- Centre for Geometric Biology, School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Dustin J Marshall
- Centre for Geometric Biology, School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
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7
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Abstract
Sperm competition is pervasive and fundamental to determining a male's overall fitness. Sperm traits and seminal fluid proteins (Sfps) are key factors. However, studies of sperm competition may often exclude females that fail to remate during a defined period. Hence, the resulting data sets contain fewer data from the potentially fittest males that have most success in preventing female remating. It is also important to consider a male's reproductive success before entering sperm competition, which is a major contributor to fitness. The exclusion of these data can both hinder our understanding of the complete fitness landscapes of competing males and lessen our ability to assess the contribution of different determinants of reproductive success to male fitness. We addressed this here, using the Drosophila melanogaster model system, by (i) capturing a comprehensive range of intermating intervals that define the fitness of interacting wild-type males and (ii) analysing outcomes of sperm competition using selection analyses. We conducted additional tests using males lacking the sex peptide (SP) ejaculate component vs. genetically matched (SP+ ) controls. This allowed us to assess the comprehensive fitness effects of this important Sfp on sperm competition. The results showed a signature of positive, linear selection in wild-type and SP+ control males on the length of the intermating interval and on male sperm competition defence. However, the fitness surface for males lacking SP was distinct, with local fitness peaks depending on contrasting combinations of remating intervals and offspring numbers. The results suggest that there are alternative routes to success in sperm competition and provide an explanation for the maintenance of variation in sperm competition traits.
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Affiliation(s)
- C. Fricke
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichUK
- Institute for Evolution and BiodiversityUniversity of MuensterMuensterGermany
| | - T. Chapman
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichUK
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8
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Abstract
Understanding the mechanics of adaptive evolution requires not only knowing the quantitative genetic bases of the traits of interest but also obtaining accurate measures of the strengths and modes of selection acting on these traits. Most recent empirical studies of multivariate selection have employed multiple linear regression to obtain estimates of the strength of selection. We reconsider the motivation for this approach, paying special attention to the effects of nonnormal traits and fitness measures. We apply an alternative statistical method, logistic regression, to estimate the strength of selection on multiple phenotypic traits. First, we argue that the logistic regression model is more suitable than linear regression for analyzing data from selection studies with dichotomous fitness outcomes. Subsequently, we show that estimates of selection obtained from the logistic regression analyses can be transformed easily to values that directly plug into equations describing adaptive microevolutionary change. Finally, we apply this methodology to two published datasets to demonstrate its utility. Because most statistical packages now provide options to conduct logistic regression analyses, we suggest that this approach should be widely adopted as an analytical tool for empirical studies of multivariate selection.
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Affiliation(s)
- Fredric J Janzen
- Department of Zoology and Genetics, Program in Ecology and Evolutionary Biology, Iowa Computational Biology Laboratory, Iowa State University, Ames, Iowa, 50011
| | - Hal S Stern
- Department of Statistics, Iowa State University, Ames, Iowa, 50011
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9
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Sahadeo NSD, Allicock OM, De Salazar PM, Auguste AJ, Widen S, Olowokure B, Gutierrez C, Valadere AM, Polson-Edwards K, Weaver SC, Carrington CVF. Understanding the evolution and spread of chikungunya virus in the Americas using complete genome sequences. Virus Evol 2017; 3:vex010. [PMID: 28480053 PMCID: PMC5413804 DOI: 10.1093/ve/vex010] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Local transmission of chikungunya virus (CHIKV) was first detected in the Americas in December 2013, after which it spread rapidly throughout the Caribbean islands and American mainland, causing a major chikungunya fever epidemic. Previous phylogenetic analysis of CHIKV from a limited number of countries in the Americas suggests that an Asian genotype strain was responsible, except in Brazil where both Asian and East/Central/South African (ECSA) lineage strains were detected. In this study, we sequenced thirty-three complete CHIKV genomes from viruses isolated in 2014 from fourteen Caribbean islands, the Bahamas and two mainland countries in the Americas. Phylogenetic analyses confirmed that they all belonged to the Asian genotype and clustered together with other Caribbean and mainland sequences isolated during the American outbreak, forming an 'Asian/American' lineage defined by two amino acid substitutions, E2 V368A and 6K L20M, and divided into two well-supported clades. This lineage is estimated to be evolving at a mean rate of 5 × 10-4 substitutions per site per year (95% higher probability density, 2.9-7.9 × 10-4) and to have arisen from an ancestor introduced to the Caribbean (most likely from Oceania) in about March 2013, 9 months prior to the first report of CHIKV in the Americas. Estimation of evolutionary rates for individual gene regions and selection analyses indicate that (in contrast to the Indian Ocean Lineage that emerged from the ECSA genotype followed by adaptive evolution and with a significantly higher substitution rate) the evolutionary dynamics of the Asian/American lineage are very similar to the rest of the Asian genotype and natural selection does not appear to have played a major role in its emergence. However, several codon sites with evidence of positive selection were identified within the non-structural regions of Asian genotype sequences outside of the Asian/American lineage.
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Affiliation(s)
- N S D Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine Campus, Trinidad and Tobago
| | - O M Allicock
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine Campus, Trinidad and Tobago
| | - P M De Salazar
- Caribbean Public Health Agency, Port-of-Spain, Trinidad and Tobago.,ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - A J Auguste
- Institute for Human Infections and Immunity and Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - S Widen
- Institute for Human Infections and Immunity and Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - B Olowokure
- Caribbean Public Health Agency, Port-of-Spain, Trinidad and Tobago
| | - C Gutierrez
- Caribbean Public Health Agency, Port-of-Spain, Trinidad and Tobago
| | - A M Valadere
- Caribbean Public Health Agency, Port-of-Spain, Trinidad and Tobago
| | - K Polson-Edwards
- Caribbean Public Health Agency, Port-of-Spain, Trinidad and Tobago
| | - S C Weaver
- Institute for Human Infections and Immunity and Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - C V F Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine Campus, Trinidad and Tobago
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10
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Rapkin J, Jensen K, House CM, Sakaluk SK, Sakaluk JK, Hunt J. The complex interplay between macronutrient intake, cuticular hydrocarbon expression and mating success in male decorated crickets. J Evol Biol 2017; 30:711-727. [PMID: 28029711 DOI: 10.1111/jeb.13036] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 11/30/2016] [Accepted: 12/22/2016] [Indexed: 01/15/2023]
Abstract
The condition dependence of male sexual traits plays a central role in sexual selection theory. Relatively little, however, is known about the condition dependence of chemical signals used in mate choice and their subsequent effects on male mating success. Furthermore, few studies have isolated the specific nutrients responsible for condition-dependent variation in male sexual traits. Here, we used nutritional geometry to determine the effect of protein (P) and carbohydrate (C) intake on male cuticular hydrocarbon (CHC) expression and mating success in male decorated crickets (Gryllodes sigillatus). We show that both traits are maximized at a moderate-to-high intake of nutrients in a P:C ratio of 1 : 1.5. We also show that female precopulatory mate choice exerts a complex pattern of linear and quadratic sexual selection on this condition-dependent variation in male CHC expression. Structural equation modelling revealed that although the effect of nutrient intake on mating success is mediated through condition-dependent CHC expression, it is not exclusively so, suggesting that other traits must also play an important role. Collectively, our results suggest that the complex interplay between nutrient intake, CHC expression and mating success plays an important role in the operation of sexual selection in G. sigillatus.
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Affiliation(s)
- J Rapkin
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, UK
| | - K Jensen
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, UK.,Department of Bioscience, Terrestrial Ecology, Aarhus University, Silkeborg, Denmark
| | - C M House
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, UK.,School of Science and Health, and Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - S K Sakaluk
- Behaviour, Ecology, Evolution and Systematics Section, School of Biological Sciences, Illinois State University, Normal, IL, USA
| | - J K Sakaluk
- Department of Psychology, University of Victoria, Victoria, BC, Canada
| | - J Hunt
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, UK.,School of Science and Health, and Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
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11
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Abstract
Many quantitative traits are labile (e.g. somatic growth rate, reproductive timing and investment), varying over the life cycle as a result of behavioural adaptation, developmental processes and plastic responses to the environment. At the population level, selection can alter the distribution of such traits across age classes and among generations. Despite a growing body of theoretical research exploring the evolutionary dynamics of labile traits, a data‐driven framework for incorporating such traits into demographic models has not yet been developed. Integral projection models (IPMs) are increasingly being used to understand the interplay between changes in labile characters, life histories and population dynamics. One limitation of the IPM approach is that it relies on phenotypic associations between parents and offspring traits to capture inheritance. However, it is well‐established that many different processes may drive these associations, and currently, no clear consensus has emerged on how to model micro‐evolutionary dynamics in an IPM framework. We show how to embed quantitative genetic models of inheritance of labile traits into age‐structured, two‐sex models that resemble standard IPMs. Commonly used statistical tools such as GLMs and their mixed model counterparts can then be used for model parameterization. We illustrate the methodology through development of a simple model of egg‐laying date evolution, parameterized using data from a population of Great tits (Parus major). We demonstrate how our framework can be used to project the joint dynamics of species' traits and population density. We then develop a simple extension of the age‐structured Price equation (ASPE) for two‐sex populations, and apply this to examine the age‐specific contributions of different processes to change in the mean phenotype and breeding value. The data‐driven framework we outline here has the potential to facilitate greater insight into the nature of selection and its consequences in settings where focal traits vary over the lifetime through ontogeny, behavioural adaptation and phenotypic plasticity, as well as providing a potential bridge between theoretical and empirical studies of labile trait variation.
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Affiliation(s)
- Dylan Z Childs
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ben C Sheldon
- Department of Zoology, The Edward Grey Institute, Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK
| | - Mark Rees
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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12
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Wise MJ, Rausher MD. Costs of resistance and correlational selection in the multiple-herbivore community of Solanum carolinense. Evolution 2016; 70:2411-2420. [PMID: 27501350 DOI: 10.1111/evo.13035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/12/2016] [Accepted: 07/24/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Michael J Wise
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708. .,Current Address: Department of Biology, Roanoke College, 221 College Lane, Salem, Virginia, 24153.
| | - Mark D Rausher
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708
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13
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Martin AM, Festa-Bianchet M, Coltman DW, Pelletier F. Demographic drivers of age-dependent sexual selection. J Evol Biol 2016; 29:1437-46. [PMID: 27090379 DOI: 10.1111/jeb.12883] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 03/21/2016] [Accepted: 04/11/2016] [Indexed: 01/21/2023]
Abstract
Sexual selection has a critical role in evolution, and it is fundamental to identify what ecological factors drive its variation. Disentangling the ecological correlates of sexual selection over the long term, however, is challenging and has rarely been done in nature. We sought to assess how demographic changes influenced the intensity, direction and form of sexual selection and whether selective pressures varied with age. We tested whether breeder sex ratio, number of competitors and age structure influenced selection differentials on horn length of wild bighorn rams (Ovis canadensis) of different age classes on Ram Mountain, Alberta. We used 21 years of data including a detailed pedigree, demographic parameters and repeated morphological measurements. Sexual selection on horn length of males of all ages was directional and positive. Selection intensity increased with the number of competitors, reflecting male-male encounter rate during the rut, but was independent of breeder sex ratio or age structure. This result can also be linked to changes in population size because the number of competitors was highly correlated to total number of sheep. This demographic effect likely arises from age-dependent mating tactics. Males aged 2-4 years are weakly competitive and experienced stronger sexual selection as they accounted for a greater proportion of all males. Selection experienced by mature males appeared independent of demography. Our study provides a rare description of the demographic determinants of sexual selection in nature.
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Affiliation(s)
- A M Martin
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - M Festa-Bianchet
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - D W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - F Pelletier
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada.,Canada Research Chair in Evolutionary Demography and Conservation, Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
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Carlson JE, Adams CA, Holsinger KE. Intraspecific variation in stomatal traits, leaf traits and physiology reflects adaptation along aridity gradients in a South African shrub. Ann Bot 2016; 117:195-207. [PMID: 26424782 PMCID: PMC4701147 DOI: 10.1093/aob/mcv146] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/11/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Trait-environment relationships are commonly interpreted as evidence for local adaptation in plants. However, even when selection analyses support this interpretation, the mechanisms underlying differential benefits are often unknown. This study addresses this gap in knowledge using the broadly distributed South African shrub Protea repens. Specifically, the study examines whether broad-scale patterns of trait variation are consistent with spatial differences in selection and ecophysiology in the wild. METHODS In a common garden study of plants sourced from 19 populations, associations were measured between five morphological traits and three axes describing source climates. Trait-trait and trait-environment associations were analysed in a multi-response model. Within two focal populations in the wild, selection and path analyses were used to test associations between traits, fecundity and physiological performance. KEY RESULTS Across 19 populations in a common garden, stomatal density increased with the source population's mean annual temperature and decreased with its average amount of rainfall in midsummer. Concordantly, selection analysis in two natural populations revealed positive selection on stomatal density at the hotter, drier site, while failing to detect selection at the cooler, moister site. Dry-site plants with high stomatal density also had higher stomatal conductances, cooler leaf temperatures and higher light-saturated photosynthetic rates than those with low stomatal density, but no such relationships were present among wet-site plants. Leaf area, stomatal pore index and specific leaf area in the garden also co-varied with climate, but within-population differences were not associated with fitness in either wild population. CONCLUSIONS The parallel patterns of broad-scale variation, differences in selection and differences in trait-ecophysiology relationships suggest a mechanism for adaptive differentiation in stomatal density. Densely packed stomata may improve performance by increasing transpiration and cooling, but predominately in drier, hotter climates. This study uniquely shows context-dependent benefits of stomatal density--a trait rarely linked to local adaptation in plants.
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Affiliation(s)
- Jane E Carlson
- Department of Biological Sciences, Nicholls State University, P.O. Box 2021, Thibodaux, LA 70310, USA and
| | - Christopher A Adams
- Department of Biological Sciences, Nicholls State University, P.O. Box 2021, Thibodaux, LA 70310, USA and
| | - Kent E Holsinger
- Department of Ecology and Evolutionary Biology, University of Connecticut, U-3043, Storrs, CT 06269, USA
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Filloux D, Murrell S, Koohapitagtam M, Golden M, Julian C, Galzi S, Uzest M, Rodier-Goud M, D’Hont A, Vernerey MS, Wilkin P, Peterschmitt M, Winter S, Murrell B, Martin DP, Roumagnac P. The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed. Virus Evol 2015; 1:vev002. [PMID: 27774276 PMCID: PMC5014472 DOI: 10.1093/ve/vev002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Endogenous viral sequences are essentially 'fossil records' that can sometimes reveal the genomic features of long extinct virus species. Although numerous known instances exist of single-stranded DNA (ssDNA) genomes becoming stably integrated within the genomes of bacteria and animals, there remain very few examples of such integration events in plants. The best studied of these events are those which yielded the geminivirus-related DNA elements found within the nuclear genomes of various Nicotiana species. Although other ssDNA virus-like sequences are included within the draft genomes of various plant species, it is not entirely certain that these are not contaminants. The Nicotiana geminivirus-related DNA elements therefore remain the only definitively proven instances of endogenous plant ssDNA virus sequences. Here, we characterize two new classes of endogenous plant virus sequence that are also apparently derived from ancient geminiviruses in the genus Begomovirus. These two endogenous geminivirus-like elements (EGV1 and EGV2) are present in the Dioscorea spp. of the Enantiophyllum clade. We used fluorescence in situ hybridization to confirm that the EGV1 sequences are integrated in the D. alata genome and showed that one or two ancestral EGV sequences likely became integrated more than 1.4 million years ago during or before the diversification of the Asian and African Enantiophyllum Dioscorea spp. Unexpectedly, we found evidence of natural selection actively favouring the maintenance of EGV-expressed replication-associated protein (Rep) amino acid sequences, which clearly indicates that functional EGV Rep proteins were probably expressed for prolonged periods following endogenization. Further, the detection in D. alata of EGV gene transcripts, small 21-24 nt RNAs that are apparently derived from these transcripts, and expressed Rep proteins, provides evidence that some EGV genes are possibly still functionally expressed in at least some of the Enantiophyllum clade species.
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Affiliation(s)
- Denis Filloux
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Sasha Murrell
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Maneerat Koohapitagtam
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
- Department of Pest Management, Faculty of Natural Resources, Prince of Songkla University, Hat Yai campus, Thailand 90120
| | - Michael Golden
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa
| | - Charlotte Julian
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Serge Galzi
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Marilyne Uzest
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | | | - Angélique D’Hont
- CIRAD, UMR AGAP, TA A-108/03, Avenue Agropolis, F-34398 Montpellier Cedex 5, France
| | - Marie Stephanie Vernerey
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Michel Peterschmitt
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Stephan Winter
- DSMZ Plant Virus Department, Messeweg 11/12, 38102, Braunschweig, Germany
| | - Ben Murrell
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Darren P. Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa
| | - Philippe Roumagnac
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
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Abstract
PREMISE OF THE STUDY The ecological consequences of plant competition have frequently been tested, but the evolutionary outcomes of these interactions have gone largely unexplored. The study of species invasions can make an important contribution to this field of research by allowing us to watch ecological and evolutionary processes unfold as a novel species is integrated into a plant community. We explored the ecological and evolutionary impact of an invasive jewelweed, Impatiens glandulifera, on a closely related native congener, I. capensis and asked: (1) Does the presence of the invasive jewelweed alter the fitness of native jewelweed populations? (2) Does the invasive jewelweed affect the vegetative growth of the native congener? and (3) Does the invasive jewelweed alter phenotypic selection on the vegetative traits of the native congener? METHODS We used a greenhouse competition experiment, an invasive species removal field experiment, and a survey of natural populations. KEY RESULTS We show that when the invasive jewelweed is present, phenotypic selection favors native jewelweed individuals investing less in rapid upward growth and more in branching and fruiting potential through the production of nodes. CONCLUSIONS This research demonstrates that invasive plants have the potential to greatly alter natural selection on native competitors. Studies investigating altered selection in invaded communities can reveal the potential evolutionary impact of invasive competitors, while deepening our understanding of the more general role of competition in driving plant evolution and permitting species coexistence.
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Affiliation(s)
- Carolyn M Beans
- Department of Biology, Gilmer Hall, University of Virginia, Charlottesville, Virginia 22904-4328 USA
| | - Deborah A Roach
- Department of Biology, Gilmer Hall, University of Virginia, Charlottesville, Virginia 22904-4328 USA
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17
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Han CS, Brooks RC. Correlational selection does not explain the evolution of a behavioural syndrome. J Evol Biol 2013; 26:2260-70. [PMID: 23980636 DOI: 10.1111/jeb.12223] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 07/04/2013] [Accepted: 07/08/2013] [Indexed: 11/26/2022]
Abstract
Correlated suites of behaviours, or behavioural syndromes, appear to be widespread, and yet few studies have explored how they arise and are maintained. One possibility holds that correlational selection can generate and maintain behavioural syndrome if certain behavioural combinations enjoy greater fitness than other combinations. Here we test this correlational selection hypothesis by comparing behavioural syndrome structure with a multivariate fitness surface based on reproductive success of male water striders. We measured the structure of a behavioural syndrome including dispersal ability, exploration behaviour, latency to remount and sex recognition sensitivity in males. We then measured the relationship between these behaviours and mating success in a range of sex ratio environments. Despite the presence of some significant correlational selection, behavioural syndrome structure was not associated with correlational selection on behaviours. Although we cannot conclusively reject the correlational selection hypothesis, our evidence suggests that correlational selection and resulting linkage disequilibrium might not be responsible for maintaining the strong correlations between behaviours. Instead, we suggest alternative ways in which this behavioural syndrome may have arisen and outline the need for physiological and quantitative genetic tests of these suggestions.
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Affiliation(s)
- C S Han
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
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Veltsos P, Wicker-Thomas C, Butlin RK, Hoikkala A, Ritchie MG. Sexual selection on song and cuticular hydrocarbons in two distinct populations of Drosophila montana. Ecol Evol 2012; 2:80-94. [PMID: 22408728 PMCID: PMC3297180 DOI: 10.1002/ece3.75] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 10/08/2011] [Accepted: 10/14/2011] [Indexed: 11/26/2022] Open
Abstract
Sexual selection has the potential to contribute to population divergence and speciation. Most studies of sexual selection in Drosophila have concentrated on a single signaling modality, usually either courtship song or cuticular hydrocarbons (CHCs), which can act as contact pheromones. We have examined the relationship between both signal types and reproductive success using F(1-3) offspring of wild-collected flies, raised in the lab. We used two populations of the Holarctic species Drosophila montana that represent different phylogeographic clades that have been separate for ca. 0.5 million years (MY), and differ to some extent in both traits. Here, we characterize the nature and identify the targets of sexual selection on song, CHCs, and both traits combined within the populations. Three measures of courtship outcome were used as fitness proxies. They were the probability of mating, mating latency, and the production of rejection song by females, and showed patterns of association with different traits that included both linear and quadratic selection. Courtship song predicted courtship outcome better than CHCs and the signal modalities acted in an additive rather than synergistic manner. Selection was generally consistent in direction and strength between the two populations and favored males that sang more vigorously. Sexual selection differed in the extent, strength, and nature on some of the traits between populations. However, the differences in the directionality of selection detected were not a good predictor of population differences. In addition, a character previously shown to be important for species recognition, interpulse interval, was found to be under sexual selection. Our results highlight the complexity of understanding the relationship between within-population sexual selection and population differences. Sexual selection alone cannot predict differences between populations.
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Affiliation(s)
- Paris Veltsos
- School of Biology, University of St Andrews, Dyers Brae HouseSt Andrews, Fife, KY16 9TH, United Kingdom
| | - Claude Wicker-Thomas
- UPR 9034 Laboratoire Evolution, Génomes et Spéciation (LEGS), CNRS, Avenue de la TerrasseBât. 13, Jpg sur Yvette Cedex, 91198, France
| | - Roger K Butlin
- Animal & Plant Sciences, University of Sheffield, Alfred Denny BuildingSheffield, S10 2TN, UK
| | - Anneli Hoikkala
- Department of Biological and Environmental Science, University of JyvãskylãSurvontie 9, Jyvãskylã, 40014, Finland
| | - Michael G Ritchie
- School of Biology, University of St Andrews, Dyers Brae HouseSt Andrews, Fife, KY16 9TH, United Kingdom
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