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Yu L, Renton J, Burian A, Khachaturyan M, Bayer T, Kotta J, Stachowicz JJ, DuBois K, Baums IB, Werner B, Reusch TBH. A somatic genetic clock for clonal species. Nat Ecol Evol 2024:10.1038/s41559-024-02439-z. [PMID: 38858515 DOI: 10.1038/s41559-024-02439-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/07/2024] [Indexed: 06/12/2024]
Abstract
Age and longevity are key parameters for demography and life-history evolution of organisms. In clonal species, a widespread life history among animals, plants, macroalgae and fungi, the sexually produced offspring (genet) grows indeterminately by producing iterative modules, or ramets, and so obscure their age. Here we present a novel molecular clock based on the accumulation of fixed somatic genetic variation that segregates among ramets. Using a stochastic model, we demonstrate that the accumulation of fixed somatic genetic variation will approach linearity after a lag phase, and is determined by the mitotic mutation rate, without direct dependence on asexual generation time. The lag phase decreased with lower stem cell population size, number of founder cells for the formation of new modules, and the ratio of symmetric versus asymmetric cell divisions. We calibrated the somatic genetic clock on cultivated eelgrass Zostera marina genets (4 and 17 years respectively). In a global data set of 20 eelgrass populations, genet ages were up to 1,403 years. The somatic genetic clock is applicable to any multicellular clonal species where the number of founder cells is small, opening novel research avenues to study longevity and, hence, demography and population dynamics of clonal species.
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Affiliation(s)
- Lei Yu
- GEOMAR Helmholtz-Center for Ocean Research Kiel, Marine Evolutionary Ecology, Kiel, Germany
| | - Jessie Renton
- Evolutionary Dynamics Group, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Agata Burian
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Marina Khachaturyan
- GEOMAR Helmholtz-Center for Ocean Research Kiel, Marine Evolutionary Ecology, Kiel, Germany
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Till Bayer
- GEOMAR Helmholtz-Center for Ocean Research Kiel, Marine Evolutionary Ecology, Kiel, Germany
| | - Jonne Kotta
- Estonian Marine Institute, University of Tartu, Tallinn, Estonia
| | - John J Stachowicz
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Katherine DuBois
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Iliana B Baums
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, Germany
- Alfred Wegener Institute, Helmholtz-Centre for Polar and Marine Research (AWI), Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Benjamin Werner
- Evolutionary Dynamics Group, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Thorsten B H Reusch
- GEOMAR Helmholtz-Center for Ocean Research Kiel, Marine Evolutionary Ecology, Kiel, Germany.
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Krueger-Hadfield SA. Let's talk about sex: Why reproductive systems matter for understanding algae. JOURNAL OF PHYCOLOGY 2024; 60:581-597. [PMID: 38743848 DOI: 10.1111/jpy.13462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024]
Abstract
Sex is a crucial process that has molecular, genetic, cellular, organismal, and population-level consequences for eukaryotic evolution. Eukaryotic life cycles are composed of alternating haploid and diploid phases but are constrained by the need to accommodate the phenotypes of these different phases. Critical gaps in our understanding of evolutionary drivers of the diversity in algae life cycles include how selection acts to stabilize and change features of the life cycle. Moreover, most eukaryotes are partially clonal, engaging in both sexual and asexual reproduction. Yet, our understanding of the variation in their reproductive systems is largely based on sexual reproduction in animals or angiosperms. The relative balance of sexual versus asexual reproduction not only controls but also is in turn controlled by standing genetic variability, thereby shaping evolutionary trajectories. Thus, we must quantitatively assess the consequences of the variation in life cycles on reproductive systems. Algae are a polyphyletic group spread across many of the major eukaryotic lineages, providing powerful models by which to resolve this knowledge gap. There is, however, an alarming lack of data about the population genetics of most algae and, therefore, the relative frequency of sexual versus asexual processes. For many algae, the occurrence of sexual reproduction is unknown, observations have been lost in overlooked papers, or data on population genetics do not yet exist. This greatly restricts our ability to forecast the consequences of climate change on algal populations inhabiting terrestrial, aquatic, and marine ecosystems. This perspective summarizes our extant knowledge and provides some future directions to pursue broadly across micro- and macroalgal species.
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Krueger-Hadfield SA, Shainker-Connelly SJ, Crowell RM, Vis ML. The eco-evolutionary importance of reproductive system variation in the macroalgae: Freshwater reds as a case study. JOURNAL OF PHYCOLOGY 2024; 60:15-25. [PMID: 37948315 DOI: 10.1111/jpy.13407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 11/12/2023]
Abstract
The relative frequency of sexual versus asexual reproduction governs the distribution of genetic diversity within and among populations. Most studies on the consequences of reproductive variation focus on the mating system (i.e., selfing vs. outcrossing) of diploid-dominant taxa (e.g., angiosperms), often ignoring asexual reproduction. Although reproductive systems are hypothesized to be correlated with life-cycle types, variation in the relative rates of sexual and asexual reproduction remains poorly characterized across eukaryotes. This is particularly true among the three major lineages of macroalgae (green, brown, and red). The Rhodophyta are particularly interesting, as many taxa have complex haploid-diploid life cycles that influence genetic structure. Though most marine reds have separate sexes, we show that freshwater red macroalgae exhibit patterns of switching between monoicy and dioicy in sister taxa that rival those recently shown in brown macroalgae and in angiosperms. We advocate for the investigation of reproductive system evolution using freshwater reds, as this will expand the life-cycle types for which these data exist, enabling comparative analyses broadly across eukaryotes. Unlike their marine cousins, species in the Batrachospermales have macroscopic gametophytes attached to filamentous, often microscopic sporophytes. While asexual reproduction through monospores may occur in all freshwater reds, the Compsopogonales are thought to be exclusively asexual. Understanding the evolutionary consequences of selfing and asexual reproduction will aid in our understanding of the evolutionary ecology of all algae and of eukaryotic evolution generally.
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Affiliation(s)
| | | | - Roseanna M Crowell
- Department of Environmental and Plant Biology, Ohio University, Athens, Ohio, USA
| | - Morgan L Vis
- Department of Environmental and Plant Biology, Ohio University, Athens, Ohio, USA
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Stoeckel S, Becheler R, Bocharova E, Barloy D. GenAPoPop 1.0: A user-friendly software to analyse genetic diversity and structure from partially clonal and selfed autopolyploid organisms. Mol Ecol Resour 2024; 24:e13886. [PMID: 37902131 DOI: 10.1111/1755-0998.13886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 10/05/2023] [Accepted: 10/16/2023] [Indexed: 10/31/2023]
Abstract
Autopolyploidy is quite common in most clades of eukaryotes. The emergence of sequence-based genotyping methods with individual and marker tags now enables confident allele dosage, overcoming the main obstacle to the democratization of the population genetic approaches when studying ecology and evolution of autopolyploid populations and species. Reproductive modes, including clonality, selfing and allogamy, have deep consequences on the ecology and evolution of population and species. Analysing genetic diversity and its dynamics over generations is one efficient way to infer the relative importance of clonality, selfing and allogamy in populations. GenAPoPop is a user-friendly solution to compute the specific corpus of population genetic indices, including indices about genotypic diversity, needed to analyse partially clonal, selfed and allogamous polysomic populations genotyped with confident allele dosage. It also easily provides the posterior probabilities of quantitative reproductive modes in autopolyploid populations genotyped at two-time steps and a graphical representation of the minimum spanning trees of the genetic distances between polyploid individuals, facilitating the interpretation of the genetic coancestry between individuals in hierarchically structured populations. GenAPoPop complements the previously existing solutions, including SPAGEDI and POLYGENE, to use genotypings to study the ecology and evolution of autopolyploid populations. It was specially developed with a simple graphical interface and workflow, and comes with a simulator to facilitate practical courses and teaching of population genetics for autopolyploid populations.
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Affiliation(s)
- Solenn Stoeckel
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, France
- DECOD (Ecosystem Dynamics and Sustainability), Institut Agro, IFREMER, INRAE, Rennes, France
| | - Ronan Becheler
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, France
- DECOD (Ecosystem Dynamics and Sustainability), Institut Agro, IFREMER, INRAE, Rennes, France
| | - Ekaterina Bocharova
- Evolutionary Developmental Biology laboratory, Koltzov Institute of Developmental Biology of Russian Academy of Sciences (IDB RAS), Moscow, Russia
| | - Dominique Barloy
- DECOD (Ecosystem Dynamics and Sustainability), Institut Agro, IFREMER, INRAE, Rennes, France
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5
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Orive ME, Barfield M, Holt RD. Partial Clonality Expands the Opportunity for Spatial Adaptation. Am Nat 2023; 202:681-698. [PMID: 37963114 DOI: 10.1086/726335] [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] [Indexed: 11/16/2023]
Abstract
AbstractReproductive mode may strongly impact adaptation in spatially varying populations linked by dispersal, especially when sexual and clonal offspring differ in dispersal. We determined how spatial structure affects adaptation in populations with mixed clonal and sexual reproduction. In a source-sink quantitative genetic deterministic model (with stabilizing selection around different optima), greater clonal reproduction or parent-offspring association (a measure of the part of the parent's phenotype other than the additive genetic component inherited by clonal offspring) increased the selective difference (difference between phenotypic optima) allowing sink populations to adapt. Given dispersal differences between clonally and sexually produced juveniles, adaptation increased with an increasing fraction of clonal dispersers. When considering migrational meltdown, partially clonal reproduction reduced cases where dispersal caused habitat loss. Stochastic individual-based simulations support these results, although the effect of differential dispersal was reversed, with decreased clonal dispersal allowing greater adaptation. These results parallel earlier findings that for an instantaneous shift in phenotypic optimum, increasing clonality allowed population persistence for a greater shift; here, selective change is spatial rather than temporal. These results may help explain the success of many partially clonal organisms in invading new habitats, complementing traditional explanations based on avoiding Allee effects.
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Heiser S, Amsler CD, Stoeckel S, McClintock JB, Baker BJ, Krueger-Hadfield SA. Tetrasporophytic bias coupled with heterozygote deficiency in Antarctic Plocamium sp. (Florideophyceae, Rhodophyta). JOURNAL OF PHYCOLOGY 2023; 59:681-697. [PMID: 37114881 DOI: 10.1111/jpy.13339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/11/2023] [Accepted: 03/29/2023] [Indexed: 05/05/2023]
Abstract
Meiosis and syngamy generate an alternation between two ploidy stages, but the timing of these two processes varies widely across taxa, thereby generating life cycle diversity. One hypothesis suggests that life cycles with long-lived haploid stages are correlated with selfing, asexual reproduction, or both. Though mostly studied in angiosperms, selfing and asexual reproduction are often associated with marginal habitats. Yet, in haploid-diploid macroalgae, these two reproductive modes have subtle but unique consequences whereby predictions from angiosperms may not apply. Along the western Antarctic Peninsula, there is a thriving macroalgal community, providing an opportunity to explore reproductive system variation in haploid-diploid macroalgae at high latitudes where endemism is common. Plocamium sp. is a widespread and abundant red macroalga observed within this ecosystem. We sampled 12 sites during the 2017 and 2018 field seasons and used 10 microsatellite loci to describe the reproductive system. Overall genotypic richness and evenness were high, suggesting sexual reproduction. Eight sites were dominated by tetrasporophytes, but there was strong heterozygote deficiency, suggesting intergametophytic selfing. We observed slight differences in the prevailing reproductive mode among sites, possibly due to local conditions (e.g., disturbance) that may contribute to site-specific variation. It remains to be determined whether high levels of selfing are characteristic of macroalgae more generally at high latitudes, due to the haploid-diploid life cycle, or both. Further investigations of algal life cycles will likely reveal the processes underlying the maintenance of sexual reproduction more broadly across eukaryotes, but more studies of natural populations are required.
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Affiliation(s)
- Sabrina Heiser
- Department of Biology, University of Alabama, Birmingham, Alabama, USA
| | - Charles D Amsler
- Department of Biology, University of Alabama, Birmingham, Alabama, USA
| | - Solenn Stoeckel
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, France
| | | | - Bill J Baker
- Department of Chemistry, University of South Florida, Tampa, Florida, USA
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Yu L, Stachowicz JJ, DuBois K, Reusch TBH. Detecting clonemate pairs in multicellular diploid clonal species based on a shared heterozygosity index. Mol Ecol Resour 2023; 23:592-600. [PMID: 36366977 DOI: 10.1111/1755-0998.13736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Clonal reproduction, the formation of nearly identical individuals via mitosis in the absence of genetic recombination, is a very common reproductive mode across plants, fungi and animals. To detect clonal genetic structure, genetic similarity indices based on shared alleles are widely used, such as the Jaccard index, or identity by state. Here we propose a new pairwise genetic similarity index, the SH index, based on segregating genetic marker loci (typically single nucleotide polymorphisms) that are identically heterozygous for pairs of samples (NSH ). To test our method, we analyse two old seagrass clones (Posidonia australis, estimated to be around 8500 years old; Zostera marina, >750 years old) along with two young Z. marina clones of known age (17 years old). We show that focusing on shared heterozygosity amplifies the power to distinguish sample pairs belonging to different clones compared to methods focusing on all shared alleles. Our proposed workflow can successfully detect clonemates at a location dominated by a single clone. When the collected samples involve two or more clones, the SH index shows a clear gap between clonemate pairs and interclone sample pairs. Ideally NSH should be on the order of approximately ≥3000, a number easily achievable via restriction-site associated DNA (RAD) sequencing or whole-genome resequencing. Another potential application of the SH index is to detect possible parent-descendant pairs under selfing. Our proposed workflow takes advantage of the availability of the larger number of genetic markers in the genomic era, and improves the ability to distinguish clonemates from nonclonemates in multicellular diploid clonal species.
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Affiliation(s)
- Lei Yu
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - John J Stachowicz
- Center for Population Biology, University of California, Davis, California, USA.,Department of Evolution and Ecology, University of California, Davis, California, USA
| | - Katie DuBois
- Center for Population Biology, University of California, Davis, California, USA.,Department of Evolution and Ecology, University of California, Davis, California, USA
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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8
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Kottler EJ, Gedan KB. Sexual reproduction is light-limited as marsh grasses colonize maritime forest. AMERICAN JOURNAL OF BOTANY 2022; 109:514-525. [PMID: 35244201 DOI: 10.1002/ajb2.1831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 01/24/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Climate change is driving abiotic shifts that can threaten the conservation of foundation species and the habitats they support. Directional range shifting is one mechanism of escape, but requires the successful colonization of habitats where interspecific interactions may differ from those to which a species has adapted. For plants with multiple reproductive strategies, these range-edge interactions may alter the investment or allocation toward a given reproductive strategy. In this study, we quantified sexual reproduction of the clonal marsh grass Spartina patens across an inland colonization front into maritime forest being driven by sea-level rise. We find that flowering is variable across S. patens meadows, but consistently reduced in low light conditions like those of the forest understory. Observational surveys of S. patens flowering at four sites in the Delmarva Peninsula agreed with the results of two experimental manipulations of light availability (shading experiment in S. patens-dominated marsh and a forest dieback manipulation). These three approaches pinpointed light limitation as a principal control on S. patens flowering capacity, suggesting that light competition with taller upland species can suppress S. patens flowering along its upland migration front. Consequently, all propagation in shaded conditions must occur clonally or via seeds from the marsh, a reproductive restriction that could limit the potential for local adaptation and reduce genetic diversity. Future research is needed to determine whether the lack of flowering is the result of a trade-off between sexual and clonal reproduction or results from insufficient photosynthetic products needed to achieve either reproductive method.
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Affiliation(s)
- Ezra J Kottler
- Department of Biological Sciences, George Washington University, 800 22nd ST NW, Suite 6000, Washington, D.C. 20052, USA
| | - Keryn B Gedan
- Department of Biological Sciences, George Washington University, 800 22nd ST NW, Suite 6000, Washington, D.C. 20052, USA
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9
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Evolution via somatic genetic variation in modular species. Trends Ecol Evol 2021; 36:1083-1092. [PMID: 34538501 DOI: 10.1016/j.tree.2021.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/14/2021] [Accepted: 08/20/2021] [Indexed: 01/10/2023]
Abstract
Somatic genetic variation (SoGV) may play a consequential yet underappreciated role in long-lived, modular species among plants, animals, and fungi. Recent genomic data identified two levels of genetic heterogeneity, between cell lines and between modules, that are subject to multilevel selection. Because SoGV can transfer into gametes when germlines are sequestered late in ontogeny (plants, algae, and fungi and some basal animals), sexual and asexual processes provide interdependent routes of mutational input and impact the accumulation of genetic load and molecular evolution rates of the integrated asexual/sexual life cycle. Avenues for future research include possible fitness effects of SoGV, the identification and implications of multilevel selection, and modeling of asexual selective sweeps using approaches from tumor evolution.
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10
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Peniston JH, Barfield M, Holt RD, Orive ME. Environmental fluctuations dampen the effects of clonal reproduction on evolutionary rescue. J Evol Biol 2021; 34:710-722. [PMID: 33682225 DOI: 10.1111/jeb.13778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/19/2021] [Accepted: 02/22/2021] [Indexed: 12/27/2022]
Abstract
Evolutionary rescue occurs when genetic change allows a population to persist in response to an environmental change that would otherwise have led to extinction. Most studies of evolutionary rescue assume that species have either fully clonal or fully sexual reproduction; however, many species have partially clonal reproductive strategies in which they reproduce both clonally and sexually. Furthermore, the few evolutionary rescue studies that have evaluated partially clonal reproduction did not consider fluctuations in the environment, which are nearly ubiquitous in nature. Here, we use individual-based simulations to investigate how environmental fluctuations (either uncorrelated or positively autocorrelated) influence the effect of clonality on evolutionary rescue. We show that, for moderate magnitudes of environmental fluctuations, as was found in the absence of fluctuations, increasing the degree of clonality increases the probability of population persistence in response to an abrupt environmental change, but decreases persistence in response to a continuous, directional environmental change. However, with large magnitudes of fluctuations, both the benefits of clonality following a step change and the detrimental effects of clonality following a continuous, directional change are generally reduced; in fact, in the latter scenario, increasing clonality can even become beneficial if environmental fluctuations are autocorrelated. We also show that increased generational overlap dampens the effects of environmental fluctuations. Overall, we demonstrate that understanding the evolutionary rescue of partially clonal organisms requires not only knowledge of the species life history and the type of environmental change, but also an understanding of the magnitude and autocorrelation of environmental fluctuations.
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Affiliation(s)
- James H Peniston
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Michael Barfield
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Robert D Holt
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Maria E Orive
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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