1
|
Muhala V, Guimarães-Costa A, Bessa-Silva AR, Rabelo LP, Carneiro J, Macate IE, Watanabe L, Balcázar OD, Gomes GE, Vallinoto M, Sampaio I. Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species. Sci Rep 2024; 14:3358. [PMID: 38336845 PMCID: PMC10858209 DOI: 10.1038/s41598-024-52979-4] [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: 07/27/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Fish mitochondrial genome have been largely studied worldwide for evolutionary and other genetic purposes and the structure and gene organization are commonly conservative. However, several studies have demonstrated that this scenario may present variations in some taxa, showing differentiation on the gene rearrangement. In this study, the complete mitogenome of terrestrial fish Boleophthalmus dussumieri was generated and compared with other species of the Exudercidae fishes. The newly complete mitogenome generated is circular and 16,685 bp of length, and it contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA genes (tRNAs), and one control region (CR), with high conservative structure, like other Mudskippers. Most of the PCG showed similar codon usage bias. The gene length was found to be different specially for the CR, 12S rRNA gene and ND5 gene in some taxon. All the Boleophthalmus species showed a gene duplication in the CR, except for B. dussumieri, and they presented a long intergenic spacer specially on the tRNA-Pro/ OH Tandem duplication/random loss (TDRL) and dimer-mitogenome and nonrandom loss (DMNL) are suitable to explain the mitogenome rearrangement observed in this study. The phylogenetic analysis well supported the monophyly of all mudskipper species and the analysis positioned the Periophthalmus clade as the most basal of the terrestrial fishes. This finding provides basis and brings insights for gene variation, gene rearrangements and replications showing evidence for variety of mitochondrial structure diversity within mudskippers.
Collapse
Affiliation(s)
- Valdemiro Muhala
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil.
- Divisão de Agricultura, Instituto Superior Politécnico de Gaza, Chokwe, 1204, Mozambique.
| | - Aurycéia Guimarães-Costa
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Adam Rick Bessa-Silva
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Luan Pinto Rabelo
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Jeferson Carneiro
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Isadola Eusébio Macate
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Luciana Watanabe
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Oscar David Balcázar
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Grazielle Evangelista Gomes
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Marcelo Vallinoto
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
- Laboratório Associado, Campus agrário de Vairão, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Iracilda Sampaio
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| |
Collapse
|
2
|
Jones CLC, Shafer ABA, Frost PC. Characterizing nutritional phenotypes using experimental nutrigenomics: Is there nutrient-specificity to different types of dietary stress? Mol Ecol 2023; 32:1073-1086. [PMID: 36528862 DOI: 10.1111/mec.16825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
The ability to directly measure and monitor poor nutrition in individual animals and ecological communities is hampered by methodological limitations. In this study, we use nutrigenomics to identify nutritional biomarkers in a freshwater zooplankter, Daphnia pulex, a ubiquitous primary consumer in lakes and a sentinel of environmental change. We grew animals in six ecologically relevant nutritional treatments: nutrient replete, low carbon (food), low phosphorus, low nitrogen, low calcium and high Cyanobacteria. We extracted RNA for transcriptome sequencing to identify genes that were nutrient responsive and capable of predicting nutritional status with a high degree of accuracy. We selected a list of 125 candidate genes, which were subsequently pruned to 13 predictive potential biomarkers. Using a nearest-neighbour classification algorithm, we demonstrate that these potential biomarkers are capable of classifying our samples into the correct nutritional group with 100% accuracy. The functional annotation of the selected biomarkers revealed some specific nutritional pathways and supported our hypothesis that animal responses to poor nutrition are nutrient specific and not simply different presentations of slow growth or energy limitation. This is a key step in uncovering the causes and consequences of nutritional limitation in animal consumers and their responses to small- and large-scale changes in biogeochemical cycles.
Collapse
Affiliation(s)
- Catriona L C Jones
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada.,Department of Forensic Science, Trent University, Peterborough, Ontario, Canada
| | - Paul C Frost
- Department of Biology, Trent University, Peterborough, Ontario, Canada
| |
Collapse
|
3
|
Lemmen KD, Zhou L, Papakostas S, Declerck SAJ. An experimental test of the growth rate hypothesis as a predictive framework for microevolutionary adaptation. Ecology 2023; 104:e3853. [PMID: 36054549 PMCID: PMC10078216 DOI: 10.1002/ecy.3853] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 02/01/2023]
Abstract
The growth rate hypothesis (GRH) posits that the relative body phosphorus content of an organism is positively related to somatic growth rate, as protein synthesis, which is necessary for growth, requires P-rich rRNA. This hypothesis has strong support at the interspecific level. Here, we explore the use of the GRH to predict microevolutionary responses in consumer body stoichiometry. For this, we subjected populations of the rotifer Brachionus calyciflorus to selection for fast population growth rate (PGR) in P-rich (HPF) and P-poor (LPF) food environments. With common garden transplant experiments, we demonstrate that in HP populations evolution toward increased PGR was concomitant with an increase in relative phosphorus content. In contrast, LP populations evolved higher PGR without an increase in relative phosphorus content. We conclude that the GRH has the potential to predict microevolutionary change, but that its application is contingent on the environmental context. Our results highlight the potential of cryptic evolution in determining the performance response of populations to elemental limitation of their food resources.
Collapse
Affiliation(s)
- Kimberley D Lemmen
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Libin Zhou
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | | | - Steven A J Declerck
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Department of Biology, Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| |
Collapse
|
4
|
Schneeweiss A, Juvigny-Khenafou NPD, Osakpolor S, Scharmüller A, Scheu S, Schreiner VC, Ashauer R, Escher BI, Leese F, Schäfer RB. Three perspectives on the prediction of chemical effects in ecosystems. GLOBAL CHANGE BIOLOGY 2023; 29:21-40. [PMID: 36131639 DOI: 10.1111/gcb.16438] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
The increasing production, use and emission of synthetic chemicals into the environment represents a major driver of global change. The large number of synthetic chemicals, limited knowledge on exposure patterns and effects in organisms and their interaction with other global change drivers hamper the prediction of effects in ecosystems. However, recent advances in biomolecular and computational methods are promising to improve our capacity for prediction. We delineate three idealised perspectives for the prediction of chemical effects: the suborganismal, organismal and ecological perspective, which are currently largely separated. Each of the outlined perspectives includes essential and complementary theories and tools for prediction but captures only part of the phenomenon of chemical effects. Links between the perspectives may foster predictive modelling of chemical effects in ecosystems and extrapolation between species. A major challenge for the linkage is the lack of data sets simultaneously covering different levels of biological organisation (here referred to as biological levels) as well as varying temporal and spatial scales. Synthesising the three perspectives, some central aspects and associated types of data seem particularly necessary to improve prediction. First, suborganism- and organism-level responses to chemicals need to be recorded and tested for relationships with chemical groups and organism traits. Second, metrics that are measurable at many biological levels, such as energy, need to be scrutinised for their potential to integrate across levels. Third, experimental data on the simultaneous response over multiple biological levels and spatiotemporal scales are required. These could be collected in nested and interconnected micro- and mesocosm experiments. Lastly, prioritisation of processes involved in the prediction framework needs to find a balance between simplification and capturing the essential complexity of a system. For example, in some cases, eco-evolutionary dynamics and interactions may need stronger consideration. Prediction needs to move from a static to a real-world eco-evolutionary view.
Collapse
Affiliation(s)
- Anke Schneeweiss
- Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | | | - Stephen Osakpolor
- Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | - Andreas Scharmüller
- Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
- Institut Terre et Environnement de Strasbourg (ITES), UMR 7063, CNRS-Université de Strasbourg-ENGEES, Strasbourg, France
| | - Sebastian Scheu
- Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | - Verena C Schreiner
- Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | - Roman Ashauer
- Syngenta Crop Protection AG, Basel, Switzerland
- Department of Environment and Geography, University of York, York, UK
| | - Beate I Escher
- Department of Cell Toxicology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- Environmental Toxicology, Center for Applied Geoscience, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Ralf B Schäfer
- Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| |
Collapse
|
5
|
Orr JA, Luijckx P, Arnoldi JF, Jackson AL, Piggott JJ. Rapid evolution generates synergism between multiple stressors: Linking theory and an evolution experiment. GLOBAL CHANGE BIOLOGY 2022; 28:1740-1752. [PMID: 33829610 DOI: 10.1111/gcb.15633] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Global change encompasses many co-occurring anthropogenic stressors. Understanding the interactions between these multiple stressors, whether they be additive, antagonistic or synergistic, is critical for ecosystem managers when prioritizing which stressors to mitigate in the face of global change. While such interactions between stressors appear prevalent, it remains unclear if and how these interactions change over time, as the majority of multiple-stressor studies rarely span multiple generations of study organisms. Although meta-analyses have reported some intriguing temporal trends in stressor interactions, for example that synergism may take time to emerge, the mechanistic basis for such observations is unknown. In this study, by analysing data from an evolution experiment with the rotifer Brachionus calyciflorus (~35 generations and 31,320 observations), we show that adaptation to multiple stressors shifts stressor interactions towards synergism. We show that trade-offs, where populations cannot optimally perform multiple tasks (i.e. adapting to multiple stressors), generate this bias towards synergism. We also show that removal of stressors from evolved populations does not necessarily increase fitness and that there is variation in the evolutionary trajectories of populations that experienced the same stressor regimes. Our results highlight outstanding questions at the interface between evolution and global change biology, and illustrate the importance of considering rapid adaptation when managing or restoring ecosystems subjected to multiple stressors under global change.
Collapse
Affiliation(s)
- James A Orr
- School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Pepijn Luijckx
- School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Jean-François Arnoldi
- School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin, Ireland
- Centre National de la Recherche Scientifique, Experimental and Theoretical Ecology Station, Moulis, France
| | - Andrew L Jackson
- School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Jeremy J Piggott
- School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| |
Collapse
|
6
|
Lemmen KD, Verhoeven KJF, Declerck SAJ. Experimental evidence of rapid heritable adaptation in the absence of initial standing genetic variation. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kimberley D. Lemmen
- Department of Aquatic Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - Koen J. F. Verhoeven
- Department of Terrestrial Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Steven A. J. Declerck
- Department of Aquatic Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
- Department of Biology Laboratory of Aquatic Ecology, Evolution and Conservation KULeuven Leuven Belgium
| |
Collapse
|
7
|
McElroy KE, Müller S, Lamatsch DK, Bankers L, Fields PD, Jalinsky JR, Sharbrough J, Boore JL, Logsdon JM, Neiman M. Asexuality Associated with Marked Genomic Expansion of Tandemly Repeated rRNA and Histone Genes. Mol Biol Evol 2021; 38:3581-3592. [PMID: 33885820 PMCID: PMC8382920 DOI: 10.1093/molbev/msab121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
How does asexual reproduction influence genome evolution? Although is it clear that genomic structural variation is common and important in natural populations, we know very little about how one of the most fundamental of eukaryotic traits-mode of genomic inheritance-influences genome structure. We address this question with the New Zealand freshwater snail Potamopyrgus antipodarum, which features multiple separately derived obligately asexual lineages that coexist and compete with otherwise similar sexual lineages. We used whole-genome sequencing reads from a diverse set of sexual and asexual individuals to analyze genomic abundance of a critically important gene family, rDNA (the genes encoding rRNAs), that is notable for dynamic and variable copy number. Our genomic survey of rDNA in P. antipodarum revealed two striking results. First, the core histone and 5S rRNA genes occur between tandem copies of the 18S-5.8S-28S gene cluster, a unique architecture for these crucial gene families. Second, asexual P. antipodarum harbor dramatically more rDNA-histone copies than sexuals, which we validated through molecular and cytogenetic analysis. The repeated expansion of this genomic region in asexual P. antipodarum lineages following distinct transitions to asexuality represents a dramatic genome structural change associated with asexual reproduction-with potential functional consequences related to the loss of sexual reproduction.
Collapse
Affiliation(s)
- Kyle E McElroy
- Ecology, Evolutionary, and Organismal Biology, Iowa State University, Ames, IA, USA
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Stefan Müller
- Institute of Human Genetics, Munich University Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Dunja K Lamatsch
- Research Department for Limnology, University of Innsbruck, Mondsee, Mondsee, Austria
| | - Laura Bankers
- Division of Infectious Diseases, University of Colorado—Anschutz Medical Campus, Aurora, CO, USA
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | | | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Jeffrey L Boore
- Providence St. Joseph Health and Institute for Systems Biology, Seattle, WA, USA
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA, USA
- Department of Gender, Women's, and Sexuality Studies, University of Iowa, Iowa City, IA, USA
| |
Collapse
|
8
|
Evolutionary Diversity in the Intracellular Microsporidian Parasite Nosema sp. Infecting Wild Silkworm Revealed by IGS Nucleotide Sequence Diversity. J Mol Evol 2020; 88:345-360. [PMID: 32166385 DOI: 10.1007/s00239-020-09936-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/27/2020] [Indexed: 10/24/2022]
Abstract
Intracellular microsporidian Nosema mylitta infects Indian wild silkworm Antheraea mylitta causing pebrine disease. Genetic structure and phylogeny of N. mylitta are analysed using nucleotide variability in 5S ribosomal DNA and intergenic spacer (IGS) sequence from 20 isolates collected from Southern, Northern and Central regions of Jharkhand State. Nucleotide diversity (π) and genetic differentiation Gst were highest in the Central isolates whereas lowest in the North. Among the isolates, absence of nucleotides, transitions and transversions were observed. Haplotyping showed nucleotide variability at 83 positions in IGS and 13 positions in 5S rDNA. Haplotype-based genetic differentiation was 0.96 to 0.97 whereas nucleotide sequence-based genetic differentiation was higher (Ks = 22.29) between Southern and Central isolates. Bottleneck analysis showed negative value for Tajima's D and other summary statistics revealing induction of loss of rare alleles and population explosion. From IGS, 17 ancestral sequences were inferred by Network algorithm. Core of nine closely related nodes having ancient nucleotides and peripheral nodes with highly divergent nucleotides were derived. Most diverged peripheral haplotype was Bero (H11) from the Central region whereas Deoghar (H3) of the Northern region diverged early. Phylogeny of N. mylitta grouped Southern and Northern isolates together revealed weak phylogenetic signal for these locations. Phylogeny of N. mylitta with Nosema sp. infecting other lepidopterans clustered N. mylitta isolates with N. antheraea and N. philosamiae of China indicating genetic similarity whereas other species were dissimilar showing diversity irrespective of country of origin.
Collapse
|
9
|
Madani M, Ward L, Vierstraete A, De Boer SH, Moens M. The ribosomal intergenic spacer (IGS) in the potato and tobacco cyst nematodes, Globodera pallida, G. rostochiensis and G. tabacum. Mol Cell Probes 2019; 48:101441. [PMID: 31470078 DOI: 10.1016/j.mcp.2019.101441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 08/18/2019] [Accepted: 08/27/2019] [Indexed: 11/20/2022]
Abstract
The potato cyst nematodes Globodera pallida and G. rostochiensis (PCN), and tobacco cyst nematode (TCN), G. tabacum, are the most important parasitic nematodes of potato and tobacco worldwide. Ribosomal DNA provides useful molecular data for diagnostics, the study of polymorphisms and for evolutionary research in eukaryotic organisms including nematodes. Here we present data on the structure and organization of a rarely studied part of the intergenic spacer (IGS) region of the PCN and TCN genome of cyst nematodes. This region has shown potential for diagnostic purposes and population studies in other organisms including nematodes. In nematodes, the ribosomal RNA gene cluster comprises three genes: 5.8S, 18S and 28S rRNA, which are separated by spacer regions: the intergenic spacer (IGS), non-transcribed spacer (NTS), externally transcribed spacer (EST) and the internally transcribed spacer (ITS). The intergenic spacer (IGS) region consists of an external transcribed spacer (ETS) and a non-transcribed spacer (NTS) which is located between the 28S of one repeat and the 18S gene of the next repeat within the rRNA genes cluster. In this study, the first flanking portion of the IGS was amplified, cloned and sequenced from PCN and TCN. Primers were then designed to amplify the whole IGS sequence. PCR amplification of IGS from G. tabacum, G. pallida, and G. rostochiensis yielded respectively: a single amplicon of 3 kb, three amplicons sized 2.5, 2.6 and 2.9 kb, and two amplicons sized 2.8 and 2.9 kb. Results showed that Globodera spp. has more than one variant copy of the IGS, with both long and short repetitive DNA elements. An approximately 400 bp long region without any internal repetitive elements, were identified in a position between the two repetitive regions suggesting that there is a 5S gene in the IGS of these species.
Collapse
Affiliation(s)
- Mehrdad Madani
- Department of Soil Science, University of Manitoba, R3T 2N2, Winnipeg, MB, Canada; Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown Laboratory, Charlottetown, PE, Canada.
| | - Len Ward
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown Laboratory, Charlottetown, PE, Canada
| | - Andy Vierstraete
- Biology Department, Gent University, K.L. Ledeganckstraat, 35, 9000, Gent, Belgium
| | - Solke H De Boer
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown Laboratory, Charlottetown, PE, Canada
| | - Maurice Moens
- Research Institute for Agriculture, Fisheries and Food (ILVO), 9280, Merelbeke, Belgium; Department of Plants and Crops, Ghent University, Coupure Links 653, Ghent, Belgium
| |
Collapse
|
10
|
Lemmen KD, Butler OM, Koffel T, Rudman SM, Symons CC. Stoichiometric Traits Vary Widely Within Species: A Meta-Analysis of Common Garden Experiments. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00339] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
|
11
|
Evolution without standing genetic variation: change in transgenerational plastic response under persistent predation pressure. Heredity (Edinb) 2018; 121:266-281. [PMID: 29959428 DOI: 10.1038/s41437-018-0108-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 05/22/2018] [Accepted: 06/03/2018] [Indexed: 11/08/2022] Open
Abstract
Transgenerational phenotypic plasticity is a fast non-genetic response to environmental modifications that can buffer the effects of environmental stresses on populations. However, little is known about the evolution of plasticity in the absence of standing genetic variation although several non-genetic inheritance mechanisms have now been identified. Here we monitored the pea aphid transgenerational phenotypic response to ladybird predators (production of winged offspring) during 27 generations of experimental evolution in the absence of initial genetic variation (clonal multiplication starting from a single individual). We found that the frequency of winged aphids first increased rapidly in response to predators and then remained stable over 25 generations, implying a stable phenotypic reconstruction at each generation. We also found that the high frequency of winged aphids persisted for one generation after removing predators. Winged aphid frequency then entered a refractory phase during which it dropped below the level of control lines for at least two generations before returning to it. Interestingly, the persistence of the winged phenotype decreased and the refractory phase lasted longer with the increasing number of generations of exposure to predators. Finally, we found that aphids continuously exposed to predators for 22 generations evolved a significantly weaker plastic response than aphids never exposed to predators, which, in turn, increased their fitness in presence of predators. Our findings therefore showcased an example of experimental evolution of plasticity in the absence of initial genetic variation and highlight the importance of integrating several components of non-genetic inheritance to detect evolutionary responses to environmental changes.
Collapse
|
12
|
Branco P, Egas M, Elser JJ, Huisman J. Eco-Evolutionary Dynamics of Ecological Stoichiometry in Plankton Communities. Am Nat 2018; 192:E1-E20. [PMID: 29897797 DOI: 10.1086/697472] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Nitrogen (N) and phosphorus (P) limit primary production in many aquatic ecosystems, with major implications for ecological interactions in plankton communities. Yet it remains unclear how evolution may affect the N∶P stoichiometry of phytoplankton-zooplankton interactions. Here, we address this issue by analyzing an eco-evolutionary model of phytoplankton-zooplankton interactions with explicit nitrogen and phosphorus dynamics. In our model, investment of phytoplankton in nitrogen versus phosphorus uptake is an evolving trait, and zooplankton display selectivity for phytoplankton with N∶P ratios matching their nutritional requirements. We use this model to explore implications of the contrasting N∶P requirements of copepods versus cladocerans. The model predicts that selective zooplankton strongly affect the N∶P ratio of phytoplankton, resulting in deviations from their optimum N∶P ratio. Specifically, selective grazing by nitrogen-demanding copepods favors dominance of phytoplankton with low N∶P ratios, whereas phosphorus-demanding cladocerans favor dominance of phytoplankton with high N∶P ratios. Interestingly, selective grazing by nutritionally balanced zooplankton leads to the occurrence of alternative stable states, where phytoplankton may evolve either low, optimum, or high N∶P ratios, depending on the initial conditions. These results offer a new perspective on commonly observed differences in N∶P stoichiometry between plankton of freshwater and those of marine ecosystems and indicate that selective grazing by zooplankton can have a major impact on the stoichiometric composition of phytoplankton.
Collapse
|
13
|
Bélanger-Lépine F, Leung C, Glémet H, Angers B. Balancing selection on the number of repeats in the ribosomal intergenic spacer present in naturally occurring yellow perch (Perca flavescens) populations. Genome 2017; 61:1-6. [PMID: 28950069 DOI: 10.1139/gen-2017-0061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The ribosomal intergenic spacer (IGS), responsible for the rate of transcription of rRNA genes, is associated with the growth and fecundity of individuals. A previous study of IGS length variants in a yellow perch (Perca flavescens) population revealed the presence of two predominant alleles differing by 1 kb due to variation in the number of repeat units. This study aims to assess whether length variation of IGS is the result of selection in natural populations. Length variation of IGS and 11 neutral microsatellite loci were assessed in geographically distant yellow perch populations. Most populations displayed the very same IGS alleles; they did not differ in frequencies among populations and the FST was not significantly different from zero. In contrast, diversity at microsatellite loci was high and differed among populations (FST = 0.18). Selection test based on FST identified IGS as a significant outlier from neutral expectations for population differentiation. Heterozygote excess was also detected in one specific cohort, suggesting temporal variation in the selection regime. While the exact mechanism remains to be specified, together the results of this study support the contention that balancing selection is acting to maintain two distinct IGS alleles in natural fish populations.
Collapse
Affiliation(s)
- Frédérique Bélanger-Lépine
- a Département des sciences de l'environnement, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada; GRIL - Groupe de recherche interuniversitaire en limnologie et en environnement aquatique
| | - Christelle Leung
- b Department of Biological Sciences, Université de Montréal, Montréal, QC H3C 3J7, Canada; GRIL - Groupe de recherche interuniversitaire en limnologie et en environnement aquatique
| | - Hélène Glémet
- a Département des sciences de l'environnement, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada; GRIL - Groupe de recherche interuniversitaire en limnologie et en environnement aquatique
| | - Bernard Angers
- b Department of Biological Sciences, Université de Montréal, Montréal, QC H3C 3J7, Canada; GRIL - Groupe de recherche interuniversitaire en limnologie et en environnement aquatique
| |
Collapse
|
14
|
Turner CB, Wade BD, Meyer JR, Sommerfeld BA, Lenski RE. Evolution of organismal stoichiometry in a long-term experiment with Escherichia coli. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170497. [PMID: 28791173 PMCID: PMC5541568 DOI: 10.1098/rsos.170497] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 06/21/2017] [Indexed: 05/25/2023]
Abstract
Organismal stoichiometry refers to the relative proportion of chemical elements in the biomass of organisms, and it can have important effects on ecological interactions from population to ecosystem scales. Although stoichiometry has been studied extensively from an ecological perspective, much less is known about the rates and directions of evolutionary changes in elemental composition. We measured carbon, nitrogen and phosphorus content of 12 Escherichia coli populations that evolved under controlled carbon-limited, serial-transfer conditions for 50 000 generations. The bacteria evolved higher relative nitrogen and phosphorus content, consistent with selection for increased use of the more abundant elements. Total carbon assimilated also increased, indicating more efficient use of the limiting element. We also measured stoichiometry in one population repeatedly through time. Stoichiometry changed more rapidly in early generations than later on, similar to the trajectory seen for competitive fitness. Altogether, our study shows that stoichiometry evolved over long time periods, and that it did so in a predictable direction, given the carbon-limited environment.
Collapse
Affiliation(s)
- Caroline B. Turner
- Ecology, Evolutionary Biology and Behavior Program, Michigan State University, East Lansing, MI, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brian D. Wade
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Justin R. Meyer
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Brooke A. Sommerfeld
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - Richard E. Lenski
- Ecology, Evolutionary Biology and Behavior Program, Michigan State University, East Lansing, MI, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| |
Collapse
|
15
|
Prater C, Wagner ND, Frost PC. Interactive effects of genotype and food quality on consumer growth rate and elemental content. Ecology 2017; 98:1399-1408. [DOI: 10.1002/ecy.1795] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 02/07/2017] [Accepted: 02/21/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Clay Prater
- Environmental and Life Science Graduate Program; Trent University; Peterborough Ontario K9J 7B8 Canada
| | - Nicole D. Wagner
- Environmental and Life Science Graduate Program; Trent University; Peterborough Ontario K9J 7B8 Canada
| | - Paul C. Frost
- Department of Biology; Trent University; Peterborough Ontario K9L 1Z8 Canada
| |
Collapse
|
16
|
Leal MC, Seehausen O, Matthews B. The Ecology and Evolution of Stoichiometric Phenotypes. Trends Ecol Evol 2016; 32:108-117. [PMID: 28017452 DOI: 10.1016/j.tree.2016.11.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 11/18/2016] [Accepted: 11/22/2016] [Indexed: 12/21/2022]
Abstract
Ecological stoichiometry has generated new insights into how the balance of elements affects ecological interactions and ecosystem processes, but little is known about the ecological and evolutionary dynamics of stoichiometric traits. Understanding the origins and drivers of stoichiometric trait variation between and within species will improve our understanding about the ecological responses of communities to environmental change and the ecosystem effects of organisms. In addition, studying the plasticity, heritability, and genetic basis of stoichiometric traits might improve predictions about how organisms adapt to changing environmental conditions, and help to identify interactions and feedbacks between phenotypic evolution and ecosystem processes.
Collapse
Affiliation(s)
- Miguel C Leal
- Department of Fish Ecology and Evolution, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Center for Ecology, Evolution, and Biogeochemistry, 6047 Kastanienbaum, Switzerland.
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Center for Ecology, Evolution, and Biogeochemistry, 6047 Kastanienbaum, Switzerland; Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Blake Matthews
- Department of Aquatic Ecology, Eawag, Center for Ecology, Evolution, and Biogeochemistry, 6047 Kastanienbaum, Switzerland
| |
Collapse
|
17
|
Kakou B, Angers B, Glémet H. Extensive length variation in the ribosomal DNA intergenic spacer of yellow perch (Perca flavescens). Genome 2016; 59:149-58. [PMID: 26841134 DOI: 10.1139/gen-2015-0114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The intergenic spacer (IGS) is located between ribosomal RNA (rRNA) gene copies. Within the IGS, regulatory elements for rRNA gene transcription are found, as well as a varying number of other repetitive elements that are at the root of IGS length heterogeneity. This heterogeneity has been shown to have a functional significance through its effect on growth rate. Here, we present the structural organization of yellow perch (Perca flavescens) IGS based on its entire sequence, as well as the IGS length variation within a natural population. Yellow perch IGS structure has four discrete regions containing tandem repeat elements. For three of these regions, no specific length class was detected as allele size was seemingly normally distributed. However, for one repeat region, PCR amplification uncovered the presence of two distinctive IGS variants representing a length difference of 1116 bp. This repeat region was also devoid of any CpG sites despite a high GC content. Balanced selection may be holding the alleles in the population and would account for the high diversity of length variants observed for adjacent regions. Our study is an important precursor for further work aiming to assess the role of IGS length variation in influencing growth rate in fish.
Collapse
Affiliation(s)
- Bidénam Kakou
- a Département des sciences de l'environnement, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada
| | - Bernard Angers
- b Department of Biological Sciences, Université de Montréal, Montréal, QC H3C 3J7, Canada.,c GRIL - Groupe de recherche interuniversitaire en limnologie et en environnement aquatique
| | - Hélène Glémet
- a Département des sciences de l'environnement, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada.,c GRIL - Groupe de recherche interuniversitaire en limnologie et en environnement aquatique
| |
Collapse
|
18
|
Kalinka AT. Towards an ecological understanding of morphological evolution. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:383-392. [PMID: 24890454 DOI: 10.1002/jez.b.22578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 05/05/2014] [Accepted: 05/07/2014] [Indexed: 06/03/2023]
Abstract
The roots of modern evo-devo can be traced back to the comparative anatomy of the 19th century. Inheriting from this tradition, the field has maintained a mechanistic approach to understanding the origins of distinct animal morphologies. While this focus has produced a valuable body of work, we argue here that a fuller understanding of why species diverge morphologically must be centered on the selective forces driving divergence, and these forces ultimately reside in the ecological context in which organisms live and reproduce. We discuss reasons why we expect many morphological novelties to evolve largely secondarily to, and often as a by-product of, primary selection on life-history traits. By shifting the focus to proximate evolutionary causes, our perspective necessarily prioritises selection experiments as a means of empirical testing. We outline experimental approaches designed to dissect the role of ecological variables in the evolution of animal development and morphology, and we show how methods and advances in fields as diverse as population genomics and ecological stoichiometry can contribute to progress in this direction.
Collapse
Affiliation(s)
- Alex T Kalinka
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| |
Collapse
|
19
|
Yamamichi M, Meunier CL, Peace A, Prater C, Rúa MA. Rapid evolution of a consumer stoichiometric trait destabilizes consumer-producer dynamics. OIKOS 2015. [DOI: 10.1111/oik.02388] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masato Yamamichi
- Hakubi Center for Advanced Research/Center for Ecological Research, Kyoto Univ.; JP-606-8501 Kyoto Japan
| | - Cédric L. Meunier
- Dept of Ecology and Environmental Sciences; Umeå Univ.; SE-901 87 Umeå Sweden
| | - Angela Peace
- National Inst. for Mathematical and Biological Synthesis, Univ. of Tennessee; Knoxville TN 37996-3410 USA
| | - Clay Prater
- Environmental and Life Sciences, Trent Univ.; 1600 West Bank Drive Peterborough, ON K9J 7B8 Canada
| | - Megan A. Rúa
- Dept of Biology; Univ. of Mississippi; 214 Shoemaker Hall PO Box 1848, University MS 38677-1848 USA
| |
Collapse
|
20
|
Characterization of the intergenic spacer rDNAs of two pig nodule worms, Oesophagostomum dentatum and O. quadrispinulatum. ScientificWorldJournal 2014; 2014:147963. [PMID: 25197691 PMCID: PMC4147281 DOI: 10.1155/2014/147963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 07/16/2014] [Accepted: 07/17/2014] [Indexed: 01/22/2023] Open
Abstract
The characteristics of the intergenic spacer rDNAs (IGS rDNAs) of Oesophagostomum dentatum and O. quadrispinulatum isolated from pigs in different geographical locations in Mainland China were determined, and the phylogenetic relationships of the two species were reconstructed using the IGS rDNA sequences. The organization of the IGS rDNA sequences was similar to their organization in other eukaryotes. The 28S-18S IGS rDNA sequences of both O. dentatum and O. quadrispinulatum were found to have variable lengths, that is, 759-762 bp and 937-1128 bp, respectively. All of the sequences contained direct repeats and inverted repeats. The length polymorphisms were related to the different numbers and organization of repetitive elements. Different types and numbers of repeats were found between the two pig nodule species, and two IGS structures were found within O. quadrispinulatum. Phylogenetic analysis showed that all O. dentatum isolates were clustered into one clade, but O. quadrispinulatum isolates from different origins were grouped into two distinct clusters. These results suggested independent species and the existence of genotypes or subspecies within pig nodule worms. Different types and numbers of repeats and IGS rDNA structures could serve as potential markers for differentiating these two species of pig nodule worms.
Collapse
|
21
|
Paredes-Esquivel CC, Townson H. Functional constraints and evolutionary dynamics of the repeats in the rDNA internal transcribed spacer 2 of members of the Anopheles barbirostris group. Parasit Vectors 2014; 7:106. [PMID: 24646478 PMCID: PMC3994965 DOI: 10.1186/1756-3305-7-106] [Citation(s) in RCA: 10] [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: 01/29/2014] [Accepted: 03/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Anopheles barbirostris group is widely distributed in Southeast Asia. Although seven species have been formally described, a molecular analysis of the rDNA ITS2 and the mitochondrial cytochrome oxidase I gene suggests that the group includes species that are morphologically very similar or identical.We have previously shown that species in the Anopheles barbirostris Subgroup have an exceptionally large ITS2 (>1.5 kb), greater than in any other Anopheline group. However, the molecular processes responsible for generating such a large ITS2 have not previously been explored. METHODS To determine the processes by which this large ITS2 is generated, we examined the sequence and secondary structure of the ITS2 of 51 specimens from five species of the Anopheles barbirostris Subgroup. These include the anthropophilic species An. campestris and three morphospecies of the Barbirostris Complex: An. vanderwulpi, An. barbirostris I and III, together with a previously undescribed member of this group (Clade IV). RESULTS AND CONCLUSIONS All the specimens were found to have an ITS2 greater than 1.5 kb in length. The possibility that the spacer sequences amplified were pseudogenes was examined and discarded. The large size of ITS2 in the species studied is due to the presence of internal repeats of approximately 110 bp in length, confined to the central region of the spacer. Repeats varied markedly between the species examined, with respect to their organization, number and sequence similarity. The nucleotide diversity increased in direct relation to size variation and the presence of non-repeated elements.A secondary structure analysis showed that the repeats form hairpin structures with a wide range of free energy values. These hairpin structures are known to facilitate the subsequent processing of mature rRNA. An analysis of the repeats from the different species suggests they originate from a common ancestor, with the repeats appearing before speciation of the Barbirostris Group.
Collapse
Affiliation(s)
- Claudia Caterina Paredes-Esquivel
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA United Kingdom
- Current address: Laboratory of Zoology. University of the Balearic Islands, Ctra de Valldemossa Km 7.5, 07122 Palma de Mallorca, Spain
| | - Harold Townson
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA United Kingdom
| |
Collapse
|
22
|
Hood JM, Sterner RW. Carbon and phosphorus linkages inDaphniagrowth are determined by growth rate, not species or diet. Funct Ecol 2014. [DOI: 10.1111/1365-2435.12243] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James M. Hood
- Department of Ecology, Evolution and Behavior; University of Minnesota-Twin Cities; St. Paul Minnesota 55108 USA
| | - Robert W. Sterner
- Department of Ecology, Evolution and Behavior; University of Minnesota-Twin Cities; St. Paul Minnesota 55108 USA
| |
Collapse
|
23
|
Bullejos FJ, Carrillo P, Gorokhova E, Medina-Sánchez JM, Villar-Argaiz M. Nucleic acid content in crustacean zooplankton: bridging metabolic and stoichiometric predictions. PLoS One 2014; 9:e86493. [PMID: 24466118 PMCID: PMC3897710 DOI: 10.1371/journal.pone.0086493] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Accepted: 12/14/2013] [Indexed: 11/17/2022] Open
Abstract
Metabolic and stoichiometric theories of ecology have provided broad complementary principles to understand ecosystem processes across different levels of biological organization. We tested several of their cornerstone hypotheses by measuring the nucleic acid (NA) and phosphorus (P) content of crustacean zooplankton species in 22 high mountain lakes (Sierra Nevada and the Pyrenees mountains, Spain). The P-allocation hypothesis (PAH) proposes that the genome size is smaller in cladocerans than in copepods as a result of selection for fast growth towards P-allocation from DNA to RNA under P limitation. Consistent with the PAH, the RNA:DNA ratio was >8-fold higher in cladocerans than in copepods, although 'fast-growth' cladocerans did not always exhibit higher RNA and lower DNA contents in comparison to 'slow-growth' copepods. We also showed strong associations among growth rate, RNA, and total P content supporting the growth rate hypothesis, which predicts that fast-growing organisms have high P content because of the preferential allocation to P-rich ribosomal RNA. In addition, we found that ontogenetic variability in NA content of the copepod Mixodiaptomus laciniatus (intra- and interstage variability) was comparable to the interspecific variability across other zooplankton species. Further, according to the metabolic theory of ecology, temperature should enhance growth rate and hence RNA demands. RNA content in zooplankton was correlated with temperature, but the relationships were nutrient-dependent, with a positive correlation in nutrient-rich ecosystems and a negative one in those with scarce nutrients. Overall our results illustrate the mechanistic connections among organismal NA content, growth rate, nutrients and temperature, contributing to the conceptual unification of metabolic and stoichiometric theories.
Collapse
Affiliation(s)
| | | | - Elena Gorokhova
- Department of Applied Environmental Science, Stockholm University, Stockholm, Sweden
| | | | - Manuel Villar-Argaiz
- Department of Ecology, Faculty of Sciences, University of Granada, Granada, Spain
| |
Collapse
|
24
|
DeLong JP, Hanley TC. The rate-size trade-off structures intraspecific variation in Daphnia ambigua life history parameters. PLoS One 2013; 8:e81024. [PMID: 24312518 PMCID: PMC3849075 DOI: 10.1371/journal.pone.0081024] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 10/15/2013] [Indexed: 11/23/2022] Open
Abstract
The identification of trade-offs is necessary for understanding the evolution and maintenance of diversity. Here we employ the supply-demand (SD) body size optimization model to predict a trade-off between asymptotic body size and growth rate. We use the SD model to quantitatively predict the slope of the relationship between asymptotic body size and growth rate under high and low food regimes and then test the predictions against observations for Daphnia ambigua. Close quantitative agreement between observed and predicted slopes at both food levels lends support to the model and confirms that a ‘rate-size’ trade-off structures life history variation in this population. In contrast to classic life history expectations, growth and reproduction were positively correlated after controlling for the rate-size trade-off. We included 12 Daphnia clones in our study, but clone identity explained only some of the variation in life history traits. We also tested the hypothesis that growth rate would be positively related to intergenic spacer length (i.e. the growth rate hypothesis) across clones, but we found that clones with intermediate intergenic spacer lengths had larger asymptotic sizes and slower growth rates. Our results strongly support a resource-based optimization of body size following the SD model. Furthermore, because some resource allocation decisions necessarily precede others, understanding interdependent life history traits may require a more nested approach.
Collapse
Affiliation(s)
- John P. DeLong
- Yale University, Department of Ecology and Evolutionary Biology, New Haven, Connecticut, United States of America
- * E-mail:
| | - Torrance C. Hanley
- Yale University, Department of Ecology and Evolutionary Biology, New Haven, Connecticut, United States of America
| |
Collapse
|
25
|
Wang C, Lin Y, Lin Y, Chung W. Modified primers for the identification of nonpathogenic Fusarium oxysporum isolates that have biological control potential against Fusarium wilt of cucumber in Taiwan. PLoS One 2013; 8:e65093. [PMID: 23762289 PMCID: PMC3676385 DOI: 10.1371/journal.pone.0065093] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 04/21/2013] [Indexed: 11/24/2022] Open
Abstract
Previous investigations demonstrated that Fusarium oxysporum (Fo), which is not pathogenic to cucumbers, could serve as a biological control agent for managing Fusarium wilt of cucumber caused by Fo f. sp. cucumerinum (Foc) in Taiwan. However, thus far it has not been possible to separate the populations of pathogenic Fo from the nonpathogenic isolates that have biological control potential through their morphological characteristics. Although these two populations can be distinguished from one another using a bioassay, the work is laborious and time-consuming. In this study, a fragment of the intergenic spacer (IGS) region of ribosomal DNA from an Fo biological control agent, Fo366, was PCR-amplified with published general primers, FIGS11/FIGS12 and sequenced. A new primer, NPIGS-R, which was designed based on the IGS sequence, was paired with the FIGS11 primer. These primers were then evaluated for their specificity to amplify DNA from nonpathogenic Fo isolates that have biological control potential. The results showed that the modified primer pair, FIGS11/NPIGS-R, amplified a 500-bp DNA fragment from five of seven nonpathogenic Fo isolates. These five Fo isolates delayed symptom development of cucumber Fusarium wilt in greenhouse bioassay tests. Seventy-seven Fo isolates were obtained from the soil and plant tissues and then subjected to amplification using the modified primer pair; six samples showed positive amplification. These six isolates did not cause symptoms on cucumber seedlings when grown in peat moss infested with the isolates and delayed disease development when the same plants were subsequently inoculated with a virulent isolate of Foc. Therefore, the modified primer pair may prove useful for the identification of Fo isolates that are nonpathogenic to cucumber which can potentially act as biocontrol agents for Fusarium wilt of cucumber.
Collapse
Affiliation(s)
- Chaojen Wang
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Yisheng Lin
- Department of Biotechnology, Asia University, Wufeng, Taichung, Taiwan
| | - Yinghong Lin
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Wenhsin Chung
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| |
Collapse
|
26
|
Elser JJ, Loladze I, Peace AL, Kuang Y. Lotka re-loaded: Modeling trophic interactions under stoichiometric constraints. Ecol Modell 2012. [DOI: 10.1016/j.ecolmodel.2012.02.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
27
|
Yu Q, Wu H, He N, Lü X, Wang Z, Elser JJ, Wu J, Han X. Testing the growth rate hypothesis in vascular plants with above- and below-ground biomass. PLoS One 2012; 7:e32162. [PMID: 22427823 PMCID: PMC3302800 DOI: 10.1371/journal.pone.0032162] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 01/21/2012] [Indexed: 11/18/2022] Open
Abstract
The growth rate hypothesis (GRH) proposes that higher growth rate (the rate of change in biomass per unit biomass, μ) is associated with higher P concentration and lower C:P and N:P ratios. However, the applicability of the GRH to vascular plants is not well-studied and few studies have been done on belowground biomass. Here we showed that, for aboveground, belowground and total biomass of three study species, μ was positively correlated with N:C under N limitation and positively correlated with P:C under P limitation. However, the N:P ratio was a unimodal function of μ, increasing for small values of μ, reaching a maximum, and then decreasing. The range of variations in μ was positively correlated with variation in C:N:P stoichiometry. Furthermore, μ and C:N:P ranges for aboveground biomass were negatively correlated with those for belowground. Our results confirm the well-known association of growth rate with tissue concentration of the limiting nutrient and provide empirical support for recent theoretical formulations.
Collapse
Affiliation(s)
- Qiang Yu
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Honghui Wu
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Nianpeng He
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Xiaotao Lü
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhiping Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - James J. Elser
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Jianguo Wu
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- Sino-US Center for Conservation, Energy and Sustainability Science (SUCCESS), Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Xingguo Han
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
28
|
Miner BE, De Meester L, Pfrender ME, Lampert W, Hairston NG. Linking genes to communities and ecosystems: Daphnia as an ecogenomic model. Proc Biol Sci 2012; 279:1873-82. [PMID: 22298849 DOI: 10.1098/rspb.2011.2404] [Citation(s) in RCA: 192] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
How do genetic variation and evolutionary change in critical species affect the composition and functioning of populations, communities and ecosystems? Illuminating the links in the causal chain from genes up to ecosystems is a particularly exciting prospect now that the feedbacks between ecological and evolutionary changes are known to be bidirectional. Yet to fully explore phenomena that span multiple levels of the biological hierarchy requires model organisms and systems that feature a comprehensive triad of strong ecological interactions in nature, experimental tractability in diverse contexts and accessibility to modern genomic tools. The water flea Daphnia satisfies these criteria, and genomic approaches capitalizing on the pivotal role Daphnia plays in the functioning of pelagic freshwater food webs will enable investigations of eco-evolutionary dynamics in unprecedented detail. Because its ecology is profoundly influenced by both genetic polymorphism and phenotypic plasticity, Daphnia represents a model system with tremendous potential for developing a mechanistic understanding of the relationship between traits at the genetic, organismal and population levels, and consequences for community and ecosystem dynamics. Here, we highlight the combination of traits and ecological interactions that make Daphnia a definitive model system, focusing on the additional power and capabilities enabled by recent molecular and genomic advances.
Collapse
Affiliation(s)
- Brooks E Miner
- Department of Biology, University of Washington, PO Box 351800, Seattle, WA 98195, USA.
| | | | | | | | | |
Collapse
|
29
|
Huang S, Molaei G, Andreadis TG. Reexamination of Culex pipiens hybridization zone in the Eastern United States by ribosomal DNA-based single nucleotide polymorphism markers. Am J Trop Med Hyg 2011; 85:434-41. [PMID: 21896800 DOI: 10.4269/ajtmh.2011.10-0679] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Mosquitoes in the Culex pipiens complex are important vectors of several disease-causing pathogens, including West Nile virus. In North America, the complex consists of Cx. pipiens pipiens form pipiens, Cx. pipiens pipiens form molestus, Cx. pipiens quinquefasciatus, and their hybrids that exhibit substantial diversity in physiology, behavior, and geographic range. Hybridization among these mosquitoes is of concern because of potential implications for disease transmission. Currently, several morphological and molecular markers exist for differentiating members of the Cx. pipiens complex; however, these markers have specific limitations. We report here two highly reliable ribosomal DNA-based single nucleotide polymorphism (SNP) markers, CxpG2T and CxpA2d, for detecting Cx. pipiens complex mosquitoes containing Cx. p. quinquefasciatus alleles. Both CxpG2T and CxpA2d contain one allele that is present in all members of the Cx. pipiens complex, and the other allele is specific to Cx. p. quinquefasciatus. Testing of field populations from the eastern United States showed that these two SNP markers are capable of identifying a south to north gradient of Cx. p. quinquefasciatus and hybrids. The northern limit of detection of Cx. p. quinquefasciatus alleles in this study was in Fort Totten, NY (40.79°N), whereas the southern boundary was determined between Atlanta, GA (33.81°N) and Gainesville, FL (29.64°N). CxpG2T and CxpA2d were more accurate than the ACE-2 marker, and they may conceivably provide comparable resolution with microsatellite markers for detecting Cx. p. quinquefasciatus alleles.
Collapse
Affiliation(s)
- Shaoming Huang
- Center for Vector Biology & Zoonotic Diseases, Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA.
| | | | | |
Collapse
|
30
|
Matthews B, Narwani A, Hausch S, Nonaka E, Peter H, Yamamichi M, Sullam KE, Bird KC, Thomas MK, Hanley TC, Turner CB. Toward an integration of evolutionary biology and ecosystem science. Ecol Lett 2011; 14:690-701. [PMID: 21554512 DOI: 10.1111/j.1461-0248.2011.01627.x] [Citation(s) in RCA: 203] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
At present, the disciplines of evolutionary biology and ecosystem science are weakly integrated. As a result, we have a poor understanding of how the ecological and evolutionary processes that create, maintain, and change biological diversity affect the flux of energy and materials in global biogeochemical cycles. The goal of this article was to review several research fields at the interfaces between ecosystem science, community ecology and evolutionary biology, and suggest new ways to integrate evolutionary biology and ecosystem science. In particular, we focus on how phenotypic evolution by natural selection can influence ecosystem functions by affecting processes at the environmental, population and community scale of ecosystem organization. We develop an eco-evolutionary model to illustrate linkages between evolutionary change (e.g. phenotypic evolution of producer), ecological interactions (e.g. consumer grazing) and ecosystem processes (e.g. nutrient cycling). We conclude by proposing experiments to test the ecosystem consequences of evolutionary changes.
Collapse
Affiliation(s)
- Blake Matthews
- EAWAG, Aquatic Ecology Department, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum 6047, Switzerland.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
PANTEL JH, JUENGER TE, LEIBOLD MA. Environmental gradients structure Daphnia pulex × pulicaria clonal distribution. J Evol Biol 2011; 24:723-32. [DOI: 10.1111/j.1420-9101.2010.02196.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
32
|
Hall EK, Singer GA, Pölzl M, Hämmerle I, Schwarz C, Daims H, Maixner F, Battin TJ. Looking inside the box: using Raman microspectroscopy to deconstruct microbial biomass stoichiometry one cell at a time. THE ISME JOURNAL 2011; 5:196-208. [PMID: 20703314 PMCID: PMC3105696 DOI: 10.1038/ismej.2010.115] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 06/03/2010] [Accepted: 06/10/2010] [Indexed: 11/09/2022]
Abstract
Stoichiometry of microbial biomass is a key determinant of nutrient recycling in a wide variety of ecosystems. However, little is known about the underlying causes of variance in microbial biomass stoichiometry. This is primarily because of technological constraints limiting the analysis of macromolecular composition to large quantities of microbial biomass. Here, we use Raman microspectroscopy (MS), to analyze the macromolecular composition of single cells of two species of bacteria grown on minimal media over a wide range of resource stoichiometry. We show that macromolecular composition, determined from a subset of identified peaks within the Raman spectra, was consistent with macromolecular composition determined using traditional analytical methods. In addition, macromolecular composition determined by Raman MS correlated with total biomass stoichiometry, indicating that analysis with Raman MS included a large proportion of a cell's total macromolecular composition. Growth phase (logarithmic or stationary), resource stoichiometry and species identity each influenced each organism's macromolecular composition and thus biomass stoichiometry. Interestingly, the least variable peaks in the Raman spectra were those responsible for differentiation between species, suggesting a phylogenetically specific cellular architecture. As Raman MS has been previously shown to be applicable to cells sampled directly from complex environments, our results suggest Raman MS is an extremely useful application for evaluating the biomass stoichiometry of environmental microorganisms. This includes the ability to partition microbial biomass into its constituent macromolecules and increase our understanding of how microorganisms in the environment respond to resource heterogeneity.
Collapse
Affiliation(s)
- Edward K Hall
- Department of Limnology and WasserKluster Lunz GmbH, University of Vienna, Vienna, Austria.
| | | | | | | | | | | | | | | |
Collapse
|
33
|
Monro K, Poore AGB. The potential for evolutionary responses to cell-lineage selection on growth form and its plasticity in a red seaweed. Am Nat 2010; 173:151-63. [PMID: 19115857 DOI: 10.1086/595758] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Despite much theoretical discussion on the evolutionary significance of intraclonal genetic variation, particularly for modular organisms whose lack of germ-soma segregation allows for variants arising in clonal growth to contribute to evolutionary change, the potential of this variation to fuel adaptation remains surprisingly untested. Given intraclonal variation, mitotic cell lineages, rather than sexual offspring, may frequently act as units of selection. Here, we applied artificial selection to such lineages in the branching red seaweed Asparagopsis armata, targeting aspects of clonal growth form and growth-form plasticity that enhance light acquisition on patchy subtidal reefs and predicting that a genetic basis to intraclonal variation may promote significant responses that cannot accompany phenotypic variation alone. Cell-lineage selection increased variation in branch proliferation among A. armata genets and successfully altered its plasticity to light. Correlated responses in the plasticity of branch elongation, moreover, showed that cell-lineage selection may be transmitted among the plasticities of growth-form traits in A. armata via pleiotropy. By demonstrating significant responses to cell-lineage selection on growth-form plasticity in this seaweed, our study lends support to the notion that intraclonal genetic variation may potentially help clonal organisms to evolve adaptively in the absence of sex and thereby prove surprisingly resilient to environmental change.
Collapse
Affiliation(s)
- Keyne Monro
- Evolution and Ecology Research Centre and School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia.
| | | |
Collapse
|
34
|
González AL, Kominoski JS, Danger M, Ishida S, Iwai N, Rubach A. Can ecological stoichiometry help explain patterns of biological invasions? OIKOS 2010. [DOI: 10.1111/j.1600-0706.2009.18549.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
35
|
Genome streamlining and the elemental costs of growth. Trends Ecol Evol 2010; 25:75-80. [DOI: 10.1016/j.tree.2009.08.004] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 08/07/2009] [Accepted: 08/12/2009] [Indexed: 11/18/2022]
|
36
|
Transgenerational effects of poor elemental food quality on Daphnia magna. Oecologia 2009; 162:865-72. [DOI: 10.1007/s00442-009-1517-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 11/10/2009] [Indexed: 12/17/2022]
|
37
|
Sensitivity of Daphnia species to phosphorus-deficient diets. Oecologia 2009; 162:349-57. [DOI: 10.1007/s00442-009-1452-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Accepted: 08/22/2009] [Indexed: 10/20/2022]
|
38
|
Poczai P, Hyvönen J. Nuclear ribosomal spacer regions in plant phylogenetics: problems and prospects. Mol Biol Rep 2009; 37:1897-912. [PMID: 19626457 DOI: 10.1007/s11033-009-9630-3] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Accepted: 07/09/2009] [Indexed: 01/06/2023]
Affiliation(s)
- Péter Poczai
- Department of Plant Sciences and Biotechnology, Georgikon Faculty, University of Pannonia, Festetics 7, 8360, Keszthely, Hungary.
| | | |
Collapse
|
39
|
NEIMAN M, THEISEN KM, MAYRY ME, KAY AD. Can phosphorus limitation contribute to the maintenance of sex? A test of a key assumption. J Evol Biol 2009; 22:1359-63. [DOI: 10.1111/j.1420-9101.2009.01748.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
40
|
Hessen DO, Ventura M, Elser JJ. Do phosphorus requirements for RNA limit genome size in crustacean zooplankton? Genome 2008; 51:685-91. [DOI: 10.1139/g08-053] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As for most other organisms, genome size in zooplankton differs widely. This may have a range of consequences for growth rate, development, and life history strategies, yet the causes of this pronounced variability are not settled. Here we propose that small genome size may be an evolutionary consequence of phosphorus (P) allocation from DNA to RNA under P deficiency. To test this hypothesis we have compared the two major groups of zooplankton, copepods and cladocerans, that have overlapping niches and body size. Relative to the cladocerans, copepods have a more complex life history and a lower mass-specific P content, while cladocerans tend to have higher P and RNA contents and higher specific growth rates and frequently experience P-limited growth, likely due to a shortage of P for ribosome synthesis. Cladocerans also generally have smaller genomes than copepods (1C = 0.17–0.63 pg DNA·cell–1vs. 1C = 0.10–10 pg DNA·cell–1). Furthermore, cladocerans have a higher slope of the relationship of body size with DNA content (1.5 vs. 0.28 in copepods) and present almost 15-fold higher RNA:DNA ratios (24.8 in cladocerans vs. 1.6 in copepods). Hence, small genome size in cladocerans could reflect an evolutionary pressure towards “efficient” genomes to conserve a key element needed to maximize growth rate. We do not claim that this is a universal cause of genome size variability, but propose that streamlining of genomes could be related to P conservation rather than energy conservation. This could be relevant for a range of organisms that may suffer P-limited growth rates.
Collapse
Affiliation(s)
- Dag O. Hessen
- University of Oslo, Department of Biology, CEES, P.O. Box 1066, Blindern, 0316 Oslo, Norway
- Department of Freshwater Ecology, National Environmental Research Institute (NERI), Vejlsøvej 25, DK-8600 Silkeborg, Denmark
- Limnology Group (CSIC-UB), Centre for Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), Accés a la Cala Sant Francesc, 14, 17300 Blanes, Girona, Spain
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| | - Marc Ventura
- University of Oslo, Department of Biology, CEES, P.O. Box 1066, Blindern, 0316 Oslo, Norway
- Department of Freshwater Ecology, National Environmental Research Institute (NERI), Vejlsøvej 25, DK-8600 Silkeborg, Denmark
- Limnology Group (CSIC-UB), Centre for Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), Accés a la Cala Sant Francesc, 14, 17300 Blanes, Girona, Spain
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| | - James J. Elser
- University of Oslo, Department of Biology, CEES, P.O. Box 1066, Blindern, 0316 Oslo, Norway
- Department of Freshwater Ecology, National Environmental Research Institute (NERI), Vejlsøvej 25, DK-8600 Silkeborg, Denmark
- Limnology Group (CSIC-UB), Centre for Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), Accés a la Cala Sant Francesc, 14, 17300 Blanes, Girona, Spain
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| |
Collapse
|
41
|
Baudouin-Cornu P. [Stoichiometric, my dear Watson!]. Med Sci (Paris) 2008; 24:483-9. [PMID: 18466725 DOI: 10.1051/medsci/2008245483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Living organisms can be seen as complex chemicals interacting with their environment through chemical reactions. As such, they are subjected to the laws of stoichiometry: their constitutive elements (atoms) cannot be created (they must be found in their environment) nor destroyed. Acknowledging these rules led ecologists to the concept of "biological stoichiometry". In this review, I want to show that combining (1) the study of the elemental composition of biopolymers and (2) the ecologist's point of view, particularly the concept of biological stoichiometry, benefits molecular biology. In particular, this coupled approach unveils parts of the history of organisms, helps interpreting transcriptional profiles and sheds a different light on the growth of carcinogenic tumors.
Collapse
Affiliation(s)
- Peggy Baudouin-Cornu
- CEA, iBiTecS, SBIGeM, LBI, Bâtiment 142, CEA Saclay, 91191 Gif-sur-Yvette, France.
| |
Collapse
|
42
|
High-frequency intragenomic heterogeneity of the ribosomal DNA intergenic spacer region in Trichophyton violaceum. EUKARYOTIC CELL 2008; 7:721-6. [PMID: 18296618 DOI: 10.1128/ec.00441-07] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The intergenic spacer (IGS) of the rRNA genes was analyzed from the dermatophyte Trichophyton violaceum isolated from cases of tinea capitis in Taiwan and Iran. T. violaceum strains were cultured from different colonies, from single conidial colonies derived by dilution plating, and from micromanipulation of single conidia from clinical samples. A ribosomal DNA probe hybridizing to multiple EcoRI fragments was used to compare restriction fragment length polymorphisms in different T. violaceum isolates. The arthroconidia of T. violaceum that form in vivo during infection were shown to contain a single nucleus by 4',6'-diamidino-2-phenylindole staining. IGS regions from an isolate cultured from a single conidium were amplified, cloned, and sequenced. The results identified that heterogeneity exists between IGS regions within a single T. violaceum genome due to different copy numbers of a 171-bp tandem repeat. This suggests that the IGS of T. violaceum is partially excluded from the concerted evolution of the rRNA gene locus. The heterogeneous character of the IGS regions in T. violaceum contrasts with the closely related dermatophyte Trichophyton rubrum, posing further questions on the phylogeny and the evolution of dermatophyte fungi.
Collapse
|
43
|
Nikoloudakis N, Skaracis G, Katsiotis A. Evolutionary insights inferred by molecular analysis of the ITS1-5.8S-ITS2 and IGS Avena sp. sequences. Mol Phylogenet Evol 2008; 46:102-15. [DOI: 10.1016/j.ympev.2007.10.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Revised: 10/02/2007] [Accepted: 10/10/2007] [Indexed: 10/22/2022]
|
44
|
Affiliation(s)
- James J Elser
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America.
| | | |
Collapse
|
45
|
Eads BD, Andrews J, Colbourne JK. Ecological genomics in Daphnia: stress responses and environmental sex determination. Heredity (Edinb) 2007; 100:184-90. [PMID: 17519967 DOI: 10.1038/sj.hdy.6800999] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Ecological genomics is the study of adaptation of natural populations to their environment, and therefore seeks to link organism and population level processes through an understanding of genome organization and function. The planktonic microcrustacean Daphnia, which has long been an important system for ecology, is now being used as a genomic model as well. Here we review recent progress in selected areas of Daphnia genomics research. Production of parthenogenetic male offspring occurs through environmental cues, which clearly involves endocrine regulation and has also been studied as a toxicological response to juvenoid hormone analog insecticides. Recent progress has uncovered a putative juvenoid cis-response element, which together with microarray analysis will stimulate further research into nuclear hormone receptors and their associated transcriptional regulatory networks. Ecotoxicological studies indicate that mRNA profiling is a sensitive and specific research tool with promising applications in environmental monitoring and for uncovering conserved cellular processes. Rapid progress is expected to continue in these and other areas, as genomic tools for Daphnia become widely available to investigators.
Collapse
Affiliation(s)
- B D Eads
- Center for Genomics and Bioinformatics, Department of Biology, Indiana University Bloomington, Bloomington, IN 47405-3700, USA.
| | | | | |
Collapse
|
46
|
Elser J. Biological stoichiometry: a chemical bridge between ecosystem ecology and evolutionary biology. Am Nat 2007; 168 Suppl 6:S25-35. [PMID: 17109326 DOI: 10.1086/509048] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The mission of the American Society of Naturalists is "to advance and diffuse knowledge of organic evolution and other broad biological principles so as to enhance the conceptual unification of the biological sciences." In this article, I argue that the area of biology least integrated with knowledge of organic evolution is the field of ecosystem ecology, as evidenced by a semiquantitative literature survey of use of terms in the scientific literature. I present an overview of recent theoretical developments and empirical findings in the emerging field of biological stoichiometry (the study of the balance of energy and multiple chemical elements in living systems). These developments hold some promise as a means to conceptually integrate ecosystem ecology, with its emphasis on flows and pools of energy and chemical elements, with evolutionary biology, with its emphasis on genetic fitness and the biochemical products of the genome. For example, recent evidence indicates that organismal C : P and N : P ratios have a major impact on biologically mediated flows of energy and phosphorus; in turn, variations among taxa in these ratios are connected to evolved differences in organismal growth rate because of the connection between growth rate and the need for increased allocation to P-rich ribosomal RNA. In this way, evolutionary change in growth-related traits, by altering organismal P requirements, has direct biogeochemical implications, while ecosystem conditions can constrain evolutionary acceleration of growth rates by imposing a direct P limitation on production of the needed biochemical machinery of growth. Thus, stoichiometric theory provides a broad biological principle that can interconvert the currencies and concerns of ecosystem ecology and evolutionary biology, facilitating integration of diverse fields of study and contributing to conceptual unification of the biological sciences.
Collapse
Affiliation(s)
- James Elser
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA.
| |
Collapse
|
47
|
Luchetti A, Scanabissi F, Mantovani B. Molecular characterization of ribosomal intergenic spacer in the tadpole shrimp Triops cancriformis (Crustacea, Branchiopoda, Notostraca). Genome 2007; 49:888-93. [PMID: 17036063 DOI: 10.1139/g06-047] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nuclear ribosomal DNA constitutes a multigene family, with tandemly arranged units linked by an intergenic spacer (IGS), which contains initiation/termination transcription signals and usually tandemly arranged subrepeats. The structure and variability of the IGS region are analyzed here in hermaphroditic and parthenogenetic populations of the "living fossil" Triops cancriformis (Branchiopoda, Notostraca). The results indicate the presence of concerted evolution at the population level for this G+C-rich IGS region as a whole, with the major amount of genetic variability found outside the subrepeat region. The subrepeats region is composed of 3 complete repeats (a, c, d) intermingled with 3 repeat fragments (b, e, f) and unrelated sequences. The most striking datum is the absolute identity of subrepeats (except type d) occupying the same position in different individuals/populations. A putative promoter sequence is present upstream of the 18S rRNA gene, but not in subrepeats, which is at variance with other arthropod IGSs. The absence of a promoter sequence in the subrepeats and subrepeat sequence conservation suggests that this region acts as an enhancer simply by its repetitive nature, as observed in some vertebrates. The putative external transcribed spacer (840 bp) shows hairpin structures, as in yeasts, protozoans, Drosophila, and vertebrates.
Collapse
Affiliation(s)
- Andrea Luchetti
- Dipartimento di Biologia Evoluzionistica Sperimentale, Bologna, Italy.
| | | | | |
Collapse
|
48
|
Doroszuk A, Wojewodzic MW, Kammenga JE. Rapid adaptive divergence of life-history traits in response to abiotic stress within a natural population of a parthenogenetic nematode. Proc Biol Sci 2006; 273:2611-8. [PMID: 17002946 PMCID: PMC1635470 DOI: 10.1098/rspb.2006.3602] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Sexual reproduction is acknowledged to facilitate adaptation to novel environments while asexual eukaryotes are often regarded as having low adaptive potential. This view has been challenged in a number of studies, but the adaptive potential of asexual populations in the field is poorly documented. We investigated the response of natural populations of the parthenogenetic nematode Acrobeloides nanus to imposed divergent selective pressures. For this purpose, we employed a replicated evolution experiment in the field. After 20 years of evolution under abiotic stress and control conditions, life-history traits were assessed in reaction norm- and reciprocal transplant experiments. Both these experiments indicated adaptive divergence within the population of A. nanus. Namely, the transplant experiment demonstrated that in the stressed soil environment, body growth rate was more reduced in the nematodes originating from the control treatment. In the reaction norm experiment, survival and reproduction were higher under test conditions corresponding to the native environment of the nematodes. The differences in the analysed traits are discussed in the context of life-history theory. Overall, our results strongly support high adaptive potential of A. nanus and suggest that population structure and distribution of asexual species is shaped by local adaptation events.
Collapse
Affiliation(s)
- Agnieszka Doroszuk
- Laboratory of Nematology, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands.
| | | | | |
Collapse
|
49
|
ELSER JJ, WATTS T, BITLER B, MARKOW TA. Ontogenetic coupling of growth rate with RNA and P contents in five species of Drosophila. Funct Ecol 2006. [DOI: 10.1111/j.1365-2435.2006.01165.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
50
|
Watts T, Woods HA, Hargand S, Elser JJ, Markow TA. Biological stoichiometry of growth in Drosophila melanogaster. JOURNAL OF INSECT PHYSIOLOGY 2006; 52:187-93. [PMID: 16310212 DOI: 10.1016/j.jinsphys.2005.09.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2004] [Revised: 09/15/2005] [Accepted: 09/16/2005] [Indexed: 05/05/2023]
Abstract
We examined the relationship between growth rate, C:N:P stoichiometry, and nucleic acid content in Drosophila melanogaster. The "Growth Rate Hypothesis" predicts that N and P contents per unit body mass will be high during ontogenetic stages characterized by rapid growth, reflecting the large requirement for P-rich ribosomal RNA during these periods. The ratio of RNA:DNA also is predicted to change with changes in growth rate. Growth is rapid in early D. melanogaster larvae, slowing considerably just prior to pupation. As predicted, a positive relationship was found between growth rate and N and P content, but not C. Thus, body C:P and N:P ratios declined with increasing growth rate. The relationship between RNA content and growth rate also was positive. Additionally, the fraction of total body P contributed by ribosomal RNA increased with increasing growth rate.
Collapse
Affiliation(s)
- Thomas Watts
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA
| | | | | | | | | |
Collapse
|