Clones in space—how sampling can bias genetic diversity estimates in corals: editorial comment on the feature article by Gorospe et al.

Riginos, Cynthia

doi:10.1007/s00227-015-2638-4

Cited by 5 publications

(4 citation statements)

References 18 publications

(16 reference statements)

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“…minutum ), genotypic parameters alone may not be informative on the existence or extent of clonality except for nearly strictly clonal organisms such as the human pathogen Trypanosoma cruzi . Such power would be gained as the spatial distance of clonal dispersal becomes lower than the sampling mesh size (for an example of the influence of sampling strategy in corals, see Gorospe et al, 2015; see Riginos, 2015 for a comment), and clonal replicates would become decreasingly randomly diluted at large population sizes and across vast spatial scales.…”

Section: Discussionmentioning

confidence: 99%

The discernible and hidden effects of clonality on the genotypic and genetic states of populations: Improving our estimation of clonal rates

Stoeckel

Porro

Arnaud‐Haond

2021

Molecular Ecology Resources

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Partial clonality is widespread across the tree of life, but most population genetic models are designed for exclusively clonal or sexual organisms. This gap hampers our understanding of the influence of clonality on evolutionary trajectories and the interpretation of population genetic data. We performed forward simulations of diploid populations at increasing rates of clonality (c), analysed their relationships with genotypic (clonal richness, R, and distribution of clonal sizes, Pareto β) and genetic (FIS and linkage disequilibrium) indices, and tested predictions of c from population genetic data through supervised machine learning. Two complementary behaviours emerged from the probability distributions of genotypic and genetic indices with increasing c. While the impact of c on R and Pareto β was easily described by simple mathematical equations, its effects on genetic indices were noticeable only at the highest levels (c > 0.95). Consequently, genotypic indices allowed reliable estimates of c, while genetic descriptors led to poorer performances when c < 0.95. These results provide clear baseline expectations for genotypic and genetic diversity and dynamics under partial clonality. Worryingly, however, the use of realistic sample sizes to acquire empirical data systematically led to gross underestimates (often of one to two orders of magnitude) of c, suggesting that many interpretations hitherto proposed in the literature, mostly based on genotypic richness, should be reappraised. We propose future avenues to derive realistic confidence intervals for c and show that, although still approximate, a supervised learning method would greatly improve the estimation of c from population genetic data.

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Section: Discussionmentioning

confidence: 99%

The discernible and hidden effects of clonality on the genotypic and genetic states of populations: Improving our estimation of clonal rates

Stoeckel

Porro

Arnaud‐Haond

2021

Molecular Ecology Resources

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“…Alternatively, distinct colonies sampled at least 5 m apart on the reef decreases the chances that collections will include clonal ramets (Baums et al 2019). For species known to engage more heavily in asexual proliferation, particularly Acroporids (Baums et al 2006, Gorospe et al 2015, Manzello et al 2019), even greater spacing of field‐sampled corals may be needed, or secondary genetic analysis performed, to verify the uniqueness of the sourced corals (Gorospe et al 2015, Riginos 2015, Manzello et al 2019).…”

Section: Proposed Common Frameworkmentioning

confidence: 99%

Increasing comparability among coral bleaching experiments

Grottoli

Toonen

Woesik

et al. 2021

Ecological Applications

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Coral bleaching is the single largest global threat to coral reefs worldwide. Integrating the diverse body of work on coral bleaching is critical to understanding and combating this global problem. Yet investigating the drivers, patterns, and processes of coral bleaching poses a major challenge. A recent review of published experiments revealed a wide range of experimental variables used across studies. Such a wide range of approaches enhances discovery, but without full transparency in the experimental and analytical methods used, can also make comparisons among studies challenging. To increase comparability but not stifle innovation, we propose a common framework for coral bleaching experiments that includes consideration of coral provenance, experimental conditions, and husbandry. For example, reporting the number of genets used, collection site conditions, the experimental temperature offset(s) from the maximum monthly mean (MMM) of the collection site, experimental light conditions, flow, and the feeding regime will greatly facilitate comparability across studies. Similarly, quantifying common response variables of endosymbiont (Symbiodiniaceae) and holobiont phenotypes (i.e., color, chlorophyll, endosymbiont cell density, mortality, and skeletal growth) could further facilitate cross-study comparisons. While no single bleaching experiment can provide the data necessary to determine global coral responses of all corals to current and future ocean warming, linking studies through a common framework as outlined here, would help increase comparability among experiments, facilitate synthetic insights into the causes and underlying mechanisms of coral bleaching, and reveal unique bleaching responses among genets, species, and regions. Such a collaborative framework that fosters transparency in methods used would strengthen comparisons among studies that can help inform coral reef management and facilitate conservation strategies to mitigate coral bleaching worldwide.

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“…Photogrammetric approaches uniquely enable both fine-scale mapping and simultaneous characterization of the focal organism and surrounding reefscape, and will provide a step change in our ability to conduct landscape genomic assessments in marine environments. Such approaches have the potential to overcome pervasive sampling biases associated with underwater population genetic studies (Gorospe et al, 2015;Riginos, 2015) in that rigorous sampling designs can be established based on a priori characterized positioning, micro-environment, and phenotypes of organisms across the reefscape (Figure 1). As the spatial extent and grain of the reefscape characterization can vary per imaging platform (diver-based or autonomous underwater vehicle) and strategy (low or high altitude), reefscape genomic approaches allow for spatially explicit assessments from fine-scale (e.g., assessing the spread of somatic mutations or distribution of endosymbiotic associations within/between colonies), to medium-scale (e.g., patterns of genetic variation, kinship, and clonality within/across reef habitats), and broadscale (e.g., in conservation genomics assessments of rare and threatened species at the scale of hectares) (Figure 2).…”

Section: Opportunities Enabled By Reefscape Genomicsmentioning

confidence: 99%

Reefscape Genomics: Leveraging Advances in 3D Imaging to Assess Fine-Scale Patterns of Genomic Variation on Coral Reefs

et al. 2021

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Coral reefs across the world are undergoing rapid deterioration, and understanding the ecological and evolutionary processes that govern these ecosystems is critical to our ability to protect them. Molecular ecological studies have been instrumental in advancing such understanding, and while initially focused primarily on broad-scale patterns, they have gradually uncovered the prevalence of local genetic structuring. Genome-wide sequencing approaches have provided new opportunities to understand both neutral and adaptive contributions to this largely unexplained diversity, but fine-scale assessments have been hampered by challenges associated with aquatic environments, in terms of (geo)referencing, seafloor characterization, and in situ phenotyping. Here, we discuss the potential of “reefscape genomics,” leveraging recent advances in underwater imaging to enable spatially explicit genomic studies on coral reefs. More specifically, we consider how (close-range) photogrammetry approaches enable (1) fine-scale spatial mapping of benthic target organisms, (2) repeatable characterization of the abiotic and biotic reefscape, and (3) simultaneous in situ mass-phenotyping. The spatially explicit consideration of genomic data –combined with detailed environmental and phenotypic characterization– opens up the opportunity for fine-scale landscape genomic approaches on coral reefs (and other marine ecosystems). Such approaches enable assessment of the spatio-temporal drivers and adaptive potential of the extensive genetic structuring and cryptic diversity encountered in benthic invertebrates, such as reef-building corals. Considering the threats that coral reefs are facing worldwide, we believe that reefscape genomics represents a promising advancement of our molecular ecological toolkit to help inform how we can most effectively conserve and restore coral reef ecosystems into the future.

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Clones in space—how sampling can bias genetic diversity estimates in corals: editorial comment on the feature article by Gorospe et al.

Cited by 5 publications

References 18 publications

The discernible and hidden effects of clonality on the genotypic and genetic states of populations: Improving our estimation of clonal rates

The discernible and hidden effects of clonality on the genotypic and genetic states of populations: Improving our estimation of clonal rates

Increasing comparability among coral bleaching experiments

Reefscape Genomics: Leveraging Advances in 3D Imaging to Assess Fine-Scale Patterns of Genomic Variation on Coral Reefs

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