135 results on '"Saenz‐Agudelo, Pablo"'
Search Results
102. Persistence of self-recruitment and patterns of larval connectivity in a marine protected area network
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Berumen, Michael L, Almany, Glenn R, Planes, Serge, Jones, Geoffrey P, Saenz-Agudelo, Pablo, Thorrold, Simon R, Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Biology Department (WHOI), Woods Hole Oceanographic Institution (WHOI), Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University (JCU)-School of Marine and Tropical Biology, Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), and Laboratoire d'excellence 'CORAIL'
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[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2012
103. Estimating connectivity in coral reef fish populations: a tool for understanding stability and resilience of marine ecosystems
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Saenz-Agudelo, Pablo
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- 2011
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104. Connectivity dominates larval replenishment in a coastal reef fish metapopulation
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Saenz-Agudelo, Pablo, Jones, Geoffrey P, Thorrold, Simon R, Planes, Serge, Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), School of Marine and Tropical Biology, James Cook University (JCU), and Woods Hole Oceanographic Institution (WHOI)
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[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2011
105. Exploring seascape genetics and kinship in the reef sponge Stylissa carteri in the Red Sea
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Giles, Emily C., primary, Saenz‐Agudelo, Pablo, additional, Hussey, Nigel E., additional, Ravasi, Timothy, additional, and Berumen, Michael L., additional
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- 2015
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106. Characterization and cross-amplification of microsatellite markers in four species of anemonefish (Pomacentridae, Amphiprion spp.)
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Bonin, Mary C., primary, Saenz-Agudelo, Pablo, additional, Harrison, Hugo B., additional, Nanninga, Gerrit B., additional, van der Meer, Martin H., additional, Mansour, Hicham, additional, Perumal, Sadhavisan, additional, Jones, Geoffrey P., additional, and Berumen, Michael L., additional
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- 2015
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107. On minimising assignment errors and the trade‐off between false positives and negatives in parentage analysis
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Harrison, Hugo B., Saenz-Agudelo, Pablo, Planes, Serge, Jones, Geoffrey P., Berumen, Michael L., Harrison, Hugo B., Saenz-Agudelo, Pablo, Planes, Serge, Jones, Geoffrey P., and Berumen, Michael L.
- Abstract
Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Molecular Ecology 22 (2013): 5738–5742, doi:10.1111/mec.12527., Genetic parentage analyses provide a practical means with which to identify parent–offspring relationships in the wild. In Harrison et al.'s study (2013a), we compare three methods of parentage analysis and showed that the number and diversity of microsatellite loci were the most important factors defining the accuracy of assignments. Our simulations revealed that an exclusion-Bayes theorem method was more susceptible to false-positive and false-negative assignments than other methods tested. Here, we analyse and discuss the trade-off between type I and type II errors in parentage analyses. We show that controlling for false-positive assignments, without reporting type II errors, can be misleading. Our findings illustrate the need to estimate and report both the rate of false-positive and false-negative assignments in parentage analyses.
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- 2014
108. Mothers matter: contribution to local replenishment is linked to female size, mate replacement and fecundity in a fish metapopulation
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Saenz-Agudelo, Pablo, primary, Jones, Geoffrey P., additional, Thorrold, Simon R., additional, and Planes, Serge, additional
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- 2014
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109. Isolation and characterization of 29 microsatellite markers for the bumphead parrotfish, Bolbometopon muricatum, and cross amplification in 12 related species
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Priest, Mark A., primary, Almany, Glenn R., additional, Braun, Camrin D., additional, Hamilton, Richard J., additional, Lozano-Cortés, Diego F., additional, Saenz-Agudelo, Pablo, additional, and Berumen, Michael L., additional
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- 2014
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110. Environmental gradients predict the genetic population structure of a coral reef fish in the Red Sea
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Nanninga, Gerrit B., primary, Saenz-Agudelo, Pablo, additional, Manica, Andrea, additional, and Berumen, Michael L., additional
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- 2014
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111. Taxonomic, spatial and temporal patterns of bleaching in anemones inhabited by anemonefishes
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Hobbs, Jean-Paul A., Frisch, Ashley J., Ford, Benjamin M., Thums, Michele, Saenz-Agudelo, Pablo, Furby, Kathryn A., Berumen, Michael L., Hobbs, Jean-Paul A., Frisch, Ashley J., Ford, Benjamin M., Thums, Michele, Saenz-Agudelo, Pablo, Furby, Kathryn A., and Berumen, Michael L.
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© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e70966, doi:10.1371/journal.pone.0070966., Rising sea temperatures are causing significant destruction to coral reef ecosystems due to coral mortality from thermally-induced bleaching (loss of symbiotic algae and/or their photosynthetic pigments). Although bleaching has been intensively studied in corals, little is known about the causes and consequences of bleaching in other tropical symbiotic organisms. This study used underwater visual surveys to investigate bleaching in the 10 species of anemones that host anemonefishes. Bleaching was confirmed in seven anemone species (with anecdotal reports of bleaching in the other three species) at 10 of 19 survey locations spanning the Indo-Pacific and Red Sea, indicating that anemone bleaching is taxonomically and geographically widespread. In total, bleaching was observed in 490 of the 13,896 surveyed anemones (3.5%); however, this percentage was much higher (19–100%) during five major bleaching events that were associated with periods of elevated water temperatures and coral bleaching. There was considerable spatial variation in anemone bleaching during most of these events, suggesting that certain sites and deeper waters might act as refuges. Susceptibility to bleaching varied between species, and in some species, bleaching caused reductions in size and abundance. Anemones are long-lived with low natural mortality, which makes them particularly vulnerable to predicted increases in severity and frequency of bleaching events. Population viability will be severely compromised if anemones and their symbionts cannot acclimate or adapt to rising sea temperatures. Anemone bleaching also has negative effects to other species, particularly those that have an obligate relationship with anemones. These effects include reductions in abundance and reproductive output of anemonefishes. Therefore, the future of these iconic and commercially valuable coral reef fishes is inextricably linked to the ability of host anemones to cope with rising sea temperatures associated with cli, This work was supported by funding from the Red Sea Research Center at the King Abdullah University of Science and Technology (KAUST), The ARC Centre of Excellence for Coral Reef Studies, the National Science Foundation (OCE 0424688), the Coral Reef Initiatives for the Pacific (CRISP), the TOTAL Foundation, Populations Fractionees et Insulares (PPF EPHE), the Connectivity Working Group of the Global University of Queensland – World Bank – Global Environmental Facility Project, Coral Reef Target Research and Capacity Building for Management, Great Barrier Reef Marine Park Authority, and the Australian Government Department of Sustainability, Environment, Water, Population and Communities. J-P Hobbs is supported by a UWA-AIMS-CSIRO fellowship.
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- 2013
112. The status of coral reef ecology research in the Red Sea
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Berumen, Michael L., Hoey, Andrew S., Bass, W. H., Bouwmeester, J., Catania, D., Cochran, Jesse E. M., Khalil, M. T., Miyake, S., Mughal, M. R., Spaet, J. L. Y., Saenz-Agudelo, Pablo, Berumen, Michael L., Hoey, Andrew S., Bass, W. H., Bouwmeester, J., Catania, D., Cochran, Jesse E. M., Khalil, M. T., Miyake, S., Mughal, M. R., Spaet, J. L. Y., and Saenz-Agudelo, Pablo
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Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Coral Reefs 32 (2013): 737-748, doi:10.1007/s00338-013-1055-8., The Red Sea has long been recognized as a region of high biodiversity and endemism. Despite this diversity and early history of scientific work, our understanding of the ecology of coral reefs in the Red Sea has lagged behind that of other large coral reef systems. We carried out a quantitative assessment of ISI-listed research published from the Red Sea in eight specific topics (apex predators, connectivity, coral bleaching, coral reproductive biology, herbivory, marine protected areas, non-coral invertebrates and reef associated bacteria) and compared the amount of research conducted in the Red Sea to that of the Australia’s Great Barrier Reef (GBR) and the Caribbean. On average, for these eight topics, the Red Sea had 1/6th the amount of research compared to the GBR and about 1/8th the amount of the Caribbean. Further, more than 50% of the published research from the Red Sea originated from the Gulf of Aqaba, a small area (< 2% of the area of the Red Sea) in the far northern Red Sea. We summarize the general state of knowledge in these eight topics and highlight areas of future research priorities for the Red Sea region. Notably, data that could inform science-based management approaches is badly lacking in most Red Sea countries. The Red Sea, as a geologically “young” sea located in one of the warmest regions of the world, has the potential to provide insight to pressing topics such as speciation processes as well as the capacity of reef systems and organisms to adapt to global climate change. As one of the world’s most biodiverse coral reef regions, the Red Sea may yet have a significant role to play in our understanding of coral reef ecology at a global scale., 2014-06-21
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- 2013
113. Dispersal of grouper larvae drives local resource sharing in a coral reef fishery
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Almany, Glenn, Hamilton, Richard, Bode, Michael, Matawai, Manuai, Potuku, Tapas, Saenz-Agudelo, Pablo, Planes, Serge, Berumen, Michael, Rhodes, Kevin, Thorrold, Simon, Russ, Garry, Jones, Geoffrey, Almany, Glenn, Hamilton, Richard, Bode, Michael, Matawai, Manuai, Potuku, Tapas, Saenz-Agudelo, Pablo, Planes, Serge, Berumen, Michael, Rhodes, Kevin, Thorrold, Simon, Russ, Garry, and Jones, Geoffrey
- Abstract
Free to read at publisher's site. In many tropical nations, fisheries management requires a community-based approach because small customary marine tenure areas define the spatial scale of management [1]. However, the fate of larvae originating from a community's tenure is unknown, and thus the degree to which a community can expect their management actions to replenish the fisheries within their tenure is unclear [2, 3]. Furthermore, whether and how much larval dispersal links tenure areas can provide a strong basis for cooperative management [4, 5]. Using genetic parentage analysis, we measured larval dispersal from a single, managed spawning aggregation of squaretail coral grouper (Plectropomus areolatus) and determined its contribution to fisheries replenishment within five community tenure areas up to 33 km from the aggregation at Manus Island, Papua New Guinea. Within the community tenure area containing the aggregation, 17%-25% of juveniles were produced by the aggregation. In four adjacent tenure areas, 6%-17% of juveniles were from the aggregation. Larval dispersal kernels predict that 50% of larvae settled within 14 km of the aggregation. These results strongly suggest that both local and cooperative management actions can provide fisheries benefits to communities over small spatial scales.
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- 2013
114. On minimizing assignment errors and the trade-off between false positives and negatives in parentage analysis
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Harrison, Hugo B., primary, Saenz-Agudelo, Pablo, additional, Planes, Serge, additional, Jones, Geoffrey P., additional, and Berumen, Michael L., additional
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- 2013
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115. Persistence of self-recruitment and patterns of larval connectivity in a marine protected area network
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Berumen, Michael L., Almany, Glenn R, Planes, Serge, Jones, Geoffrey P, Saenz-Agudelo, Pablo, Thorrold, Simon R, Berumen, Michael L., Almany, Glenn R, Planes, Serge, Jones, Geoffrey P, Saenz-Agudelo, Pablo, and Thorrold, Simon R
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The use of marine protected area (MPA) networks to sustain fisheries and conserve biodiversity is predicated on two critical yet rarely tested assumptions. Individual MPAs must produce sufficient larvae that settle within that reserve's boundaries to maintain local populations while simultaneously supplying larvae to other MPA nodes in the network that might otherwise suffer local extinction. Here, we use genetic parentage analysis to demonstrate that patterns of self-recruitment of two reef fishes (Amphiprion percula and Chaetodon vagabundus) in an MPA in Kimbe Bay, Papua New Guinea, were remarkably consistent over several years. However, dispersal from this reserve to two other nodes in an MPA network varied between species and through time. The stability of our estimates of self-recruitment suggests that even small MPAs may be self-sustaining. However, our results caution against applying optimization strategies to MPA network design without accounting for variable connectivity among species and over time. 2012 The Authors.
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- 2012
116. Estimating connectivity in marine populations : an empirical evaluation of assignment tests and parentage analysis under different gene flow scenarios
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Saenz-Agudelo, Pablo, Jones, Geoffrey P., Thorrold, Simon R., Planes, Serge, Saenz-Agudelo, Pablo, Jones, Geoffrey P., Thorrold, Simon R., and Planes, Serge
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Author Posting. © Blackwell Publishing, 2009. This is the author's version of the work. It is posted here by permission of Blackwell Publishing for personal use, not for redistribution. The definitive version was published in Molecular Ecology 18 (2009): 1765-1776, doi:10.1111/j.1365-294X.2009.04109.x., The application of spatially explicit models of population dynamics to fisheries management and the design marine reserves network systems has been limited due to a lack of empirical estimates of larval dispersal. Here we compared assignment tests and parentage analysis for examining larval retention and connectivity under two different gene flow scenarios using panda clownfish (Amphiprion polymnus) in Papua New Guinea. A metapopulation of panda clownfish in Bootless Bay with little or no genetic differentiation among 5 spatially discrete locations separated by 2-6km provided the high gene flow scenario. The low gene flow scenario compared the Bootless Bay metapopulation with a genetically distinct population (Fst = 0.1) located at Schumann Island, New Britain, 1,500km to the north-east. We used assignment tests and parentage analysis based on microsatellite DNA data to identify natal origins of 177 juveniles in Bootless Bay and 73 juveniles at Schumann Island. At low rates of gene flow, assignment tests correctly classified juveniles to their source population. On the other hand, parentage analysis led to an overestimate of self-recruitment within the two populations due to the significant deviation from panmixia when both populations were pooled. At high gene flow (within Bootless Bay), assignment tests underestimated self-recruitment and connectivity among subpopulations, and grossly overestimated self-recruitment within the overall metapopulation. However, the assignment tests did identify immigrants from distant (genetically distinct) populations. Parentage analysis clearly provided the most accurate estimates of connectivity in situations of high gene flow., We thank ARC Centre of Excellence, the National Science Foundation (OCE 0424688), the Coral Reef Initiatives for the Pacific (CRISP), the TOTAL Foundation, Populations Fractionées et Insulaires (PPF EPHE) and GEF/World bank’s CRTR program (Connectivity working group) for financial support.
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- 2009
117. Taxonomic, Spatial and Temporal Patterns of Bleaching in Anemones Inhabited by Anemonefishes
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Hobbs, Jean-Paul A., primary, Frisch, Ashley J., additional, Ford, Benjamin M., additional, Thums, Michele, additional, Saenz-Agudelo, Pablo, additional, Furby, Kathryn A., additional, and Berumen, Michael L., additional
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- 2013
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118. Dispersal of Grouper Larvae Drives Local Resource Sharing in a Coral Reef Fishery
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Almany, Glenn R., primary, Hamilton, Richard J., additional, Bode, Michael, additional, Matawai, Manuai, additional, Potuku, Tapas, additional, Saenz-Agudelo, Pablo, additional, Planes, Serge, additional, Berumen, Michael L., additional, Rhodes, Kevin L., additional, Thorrold, Simon R., additional, Russ, Garry R., additional, and Jones, Geoffrey P., additional
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- 2013
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119. Relative accuracy of three common methods of parentage analysis in natural populations
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Harrison, Hugo B., primary, Saenz‐Agudelo, Pablo, additional, Planes, Serge, additional, Jones, Geoffrey P., additional, and Berumen, Michael L., additional
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- 2012
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120. Development of 35 novel microsatellite markers for the two-band anemonefish Amphiprion bicinctus
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Nanninga, Gerrit, primary, Mughal, Mehreen, additional, Saenz-Agudelo, Pablo, additional, Bayer, Till, additional, and Berumen, Michael, additional
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- 2012
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121. Patterns and persistence of larval retention and connectivity in a marine fish metapopulation
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Saenz‐Agudelo, Pablo, primary, Jones, Geoffrey P., additional, Thorrold, Simon R., additional, and Planes, Serge, additional
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- 2012
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122. Connectivity dominates larval replenishment in a coastal reef fish metapopulation
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Saenz-Agudelo, Pablo, primary, Jones, Geoffrey P., additional, Thorrold, Simon R., additional, and Planes, Serge, additional
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- 2011
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123. Relative accuracy of three common methods of parentage analysis in natural populations.
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Harrison, Hugo B., Saenz‐Agudelo, Pablo, Planes, Serge, Jones, Geoffrey P., and Berumen, Michael L.
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POPULATION genetics , *MOLECULAR ecology , *BIODIVERSITY , *MICROSATELLITE repeats , *BIOMARKERS - Abstract
Parentage studies and family reconstructions have become increasingly popular for investigating a range of evolutionary, ecological and behavioural processes in natural populations. However, a number of different assignment methods have emerged in common use and the accuracy of each may differ in relation to the number of loci examined, allelic diversity, incomplete sampling of all candidate parents and the presence of genotyping errors. Here, we examine how these factors affect the accuracy of three popular parentage inference methods ( colony, famoz and an exclusion- Bayes' theorem approach by Christie ( Molecular Ecology Resources, 2010a, 10, 115) to resolve true parent-offspring pairs using simulated data. Our findings demonstrate that accuracy increases with the number and diversity of loci. These were clearly the most important factors in obtaining accurate assignments explaining 75-90% of variance in overall accuracy across 60 simulated scenarios. Furthermore, the proportion of candidate parents sampled had a small but significant impact on the susceptibility of each method to either false-positive or false-negative assignments. Within the range of values simulated, colony outperformed Fa Moz, which outperformed the exclusion- Bayes' theorem method. However, with 20 or more highly polymorphic loci, all methods could be applied with confidence. Our results show that for parentage inference in natural populations, careful consideration of the number and quality of markers will increase the accuracy of assignments and mitigate the effects of incomplete sampling of parental populations. [ABSTRACT FROM AUTHOR]
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- 2013
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124. Oceanographical-driven dispersal and environmental variation explain genetic structure in an upwelling coastal ecosystem.
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Peluso, Lívia, Faúndez, Juan, Navarrete, Sergio A., Broitman, Bernardo R., Aiken, Christopher M., and Saenz-Agudelo, Pablo
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The seascape comprises multiple environmental variables that interact with species biology to determine patterns of spatial genetic variation. The environment imposes spatially variable selective forces together with homogenizing and diverging drivers that facilitate or restrict dispersal, which is a complex, time-dependent process. Understanding how the seascape influences spatial patterns of genetic variation remains elusive, particularly in coastal upwelling systems. Here, we combine genome-wide SNP data, Lagrangian larval dispersal simulated over a hydrodynamic model, and ocean environmental information to quantify the relative contribution of ocean circulation and environmental heterogeneity as drivers of the spatial genetic structure of two congeneric intertidal limpets, Scurria scurra and S. araucana, along the central coast of Chile. We find that a genetic break observed in both limpet species coincides with a break in connectivity shown by the Lagrangian dispersal, suggesting that mean ocean circulation is an important seascape feature, in particular for S. scurra. For S. araucana, environmental variation appears as a better predictor of genetic structure than ocean circulation. Overall, our study shows broad patterns of seascape forcing on genetic diversity and contributes to our understanding of the complex ecological and evolutionary interactions along coastal upwelling systems. [ABSTRACT FROM AUTHOR]
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- 2024
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125. Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus).
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Payet, Samuel D., Pratchett, Morgan S., Saenz‐Agudelo, Pablo, Berumen, Michael L., DiBattista, Joseph D., and Harrison, Hugo B.
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CORAL trout , *CORAL reef fishes , *GEODESY , *GROUPERS , *CORALS - Abstract
Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology since they reveal how diversity is generated and how it may respond to future environmental change. Here, we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (Plectropomus leopardus [Lacépède 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (~100 km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred ~190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50% smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that P. leopardus in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (~10–120 kya) and may be vulnerable to localized disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of the Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories. [ABSTRACT FROM AUTHOR]
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- 2022
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126. Strong habitat and weak genetic effects shape the lifetime reproductive success in a wild clownfish population
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Salles, Océane C., Almany, Glenn R., Berumen, Michael L., Jones, Geoffrey P., Saenz-Agudelo, Pablo, Srinivasan, Maya, Thorrold, Simon R., Pujol, Benoit, and Planes, Serge
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multi-generational pedigree, additive genetic variation, maternal effects, environmental effects, adaptation, selection, heritability, evolvability ,14. Life underwater - Abstract
Lifetime reproductive success (LRS), the number of offspring an individual contributes to the next generation, is of fundamental importance in ecology and evolutionary biology. LRS may be influenced by environmental, maternal and additive genetic factors, and the relative contributions of each are critical in determining whether species can adapt to rapid environmental change. However, studies quantifying LRS across multiple generations in wild populations are extremely rare, and to date, non-existent for marine species. Here we use pedigrees of up to 5 generations resolved from a 10-year data-set for a wild orange clownfish population from Kimbe Island (PNG) to assess the contribution of every breeder to the local population. We quantified the additive genetic, maternal and environmental contributions to variation in LRS for the self-recruiting portion of the population using a genetic linear mixed model approach. We found that the habitat of the breeder, including the anemone species and geographic location, made the greatest contribution to LRS, explaining ~97% of the variation. There were low to negligible contributions of genetic (1.3%) and maternal factors (1.9%) equating with low heritability and evolvability. Our findings imply our population will be extremely susceptible to short-term, small-scale changes in habitat structure and may have limited capacity to adapt to these changes., Response to reviewers, Preprint, Supplementary information, metadata, R code (txt format) and R.data files
127. Comparative population genetics of congeneric limpets across a biogeographic transition zone reveals common patterns of genetic structure and demographic history.
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Peluso, Lívia, Broitman, Bernardo R., Lardies, Marco A., Nespolo, Roberto F., and Saenz‐Agudelo, Pablo
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COMPARATIVE genetics , *LIFE zones , *LIMPETS , *GENETIC variation , *DEMOGRAPHY , *POPULATION genetics - Abstract
The distribution of genetic diversity is often heterogeneous in space, and it usually correlates with environmental transitions or historical processes that affect demography. The coast of Chile encompasses two biogeographic provinces and spans a broad environmental gradient together with oceanographic processes linked to coastal topography that can affect species' genetic diversity. Here, we evaluated the genetic connectivity and historical demography of four Scurria limpets, S. scurra, S. variabilis, S. ceciliana and S. araucana, between ca. 19° S and 53° S in the Chilean coast using genome‐wide SNPs markers. Genetic structure varied among species which was evidenced by species‐specific breaks together with two shared breaks. One of the shared breaks was located at 22–25° S and was observed in S. araucana and S. variabilis, while the second break around 31–34° S was shared by three Scurria species. Interestingly, the identified genetic breaks are also shared with other low‐disperser invertebrates. Demographic histories show bottlenecks in S. scurra and S. araucana populations and recent population expansion in all species. The shared genetic breaks can be linked to oceanographic features acting as soft barriers to dispersal and also to historical climate, evidencing the utility of comparing multiple and sympatric species to understand the influence of a particular seascape on genetic diversity. [ABSTRACT FROM AUTHOR]
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- 2023
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128. Pre‐domestication bottlenecks of the cultivated seaweed Gracilaria chilensis.
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Huanel, Oscar R., Quesada‐Calderón, Suany, Ríos Molina, Cristian, Morales‐González, Sarai, Saenz‐Agudelo, Pablo, Nelson, Wendy A., Arakaki, Natalia, Mauger, Stéphane, Faugeron, Sylvain, and Guillemin, Marie‐Laure
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GRACILARIA , *LAST Glacial Maximum , *SINGLE nucleotide polymorphisms , *OCEAN currents , *COLONIZATION (Ecology) - Abstract
Gracilaria chilensis is the main cultivated seaweed in Chile. The low genetic diversity observed in the Chilean populations has been associated with the over‐exploitation of natural beds and/or the founder effect that occurred during post‐glacial colonization from New Zealand. How these processes have affected its evolutionary trajectory before farming and incipient domestication is poorly understood. In this study, we used 2232 single nucleotide polymorphisms (SNPs) to assess how the species' evolutionary history in New Zealand (its region of origin), the founder effect linked to transoceanic dispersion and colonization of South America, and the recent over‐exploitation of natural populations have influenced the genetic architecture of G. chilensis in Chile. The contrasting patterns of genetic diversity and structure observed between the two main islands in New Zealand attest to the important effects of Quaternary glacial cycles on G. chilensis. Approximate Bayesian Computation (ABC) analyses indicated that Chatham Island and South America were colonized independently near the end of the Last Glacial Maximum and emphasized the importance of coastal and oceanic currents during that period. Furthermore, ABC analyses inferred the existence of a recent and strong genetic bottleneck in Chile, matching the period of over‐exploitation of the natural beds during the 1970s, followed by rapid demographic expansion linked to active clonal propagation used in farming. Recurrent genetic bottlenecks strongly eroded the genetic diversity of G. chilensis prior to its cultivation, raising important challenges for the management of genetic resources in this incipiently domesticated species. [ABSTRACT FROM AUTHOR]
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- 2022
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129. First genealogy for a wild marine fish population reveals multigenerational philopatry.
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Salles, Océane C., Almany, Glenn R., Planes, Serge, Maynard, Jeffrey A., Pujol, Benoit, Berumen, Michael L., Jones, Geoffrey P., Srinivasan, Maya, Saenz-Agudelo, Pablo, and Thorrold, Simon R.
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MARINE fishes , *PHILOPATRY , *CLOWN anemonefish , *INBREEDING , *CORAL reef fishes - Abstract
Natal philopatry, the return of individuals to their natal area for reproduction, has advantages and disadvantages for animal populations. Natal philopatry may generate local genetic adaptation, but it may also increase the probability of inbreeding that can compromise persistence. Although natal philopatry is well documented in anadromous fishes, marine fish may also return to their birth site to spawn. How philopatry shapes wild fish populations is, however, unclear because it requires constructing multigenerational pedigrees that are currently lacking for marine fishes. Here we present the first multigenerational pedigree for a marine fish population by repeatedly genotyping all individuals in a population of the orange clownfish (Amphiprion percula) at Kimbe Island (Papua New Guinea) during a 10-y period. Based on 2927 individuals, our pedigree analysis revealed that longitudinal philopatry was recurrent over five generations. Progeny tended to settle close to their parents, with related individuals often sharing the same colony. However, successful inbreeding was rare, and genetic diversity remained high, suggesting occasional inbreeding does not impair local population persistence. Local reproductive success was dependent on the habitat larvae settled into, rather than the habitat they came from. Our study suggests that longitudinal philopatry can influence both population replenishment and local adaptation of marine fishes. Resolving multigenerational pedigrees during a relatively short period, as we present here, provides a framework for assessing the ability of marine populations to persist and adapt to accelerating climate change. [ABSTRACT FROM AUTHOR]
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- 2016
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130. A review of contemporary patterns of endemism for shallow water reef fauna in the Red Sea.
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DiBattista, Joseph D., Roberts, May B., Bouwmeester, Jessica, Bowen, Brian W., Coker, Darren J., Lozano‐Cortés, Diego F., Howard Choat, J., Gaither, Michelle R., Hobbs, Jean‐Paul A., Khalil, Maha T., Kochzius, Marc, Myers, Robert F., Paulay, Gustav, Robitzch, Vanessa S. N., Saenz‐Agudelo, Pablo, Salas, Eva, Sinclair‐Taylor, Tane H., Toonen, Robert J., Westneat, Mark W., and Williams, Suzanne T.
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REEF animals , *BIOGEOGRAPHY , *ANIMAL communities , *MARINE biodiversity ,RED Sea environmental conditions - Abstract
Aim The Red Sea is characterised by a unique fauna and historical periods of desiccation, hypersalinity and intermittent isolation. The origin and contemporary composition of reef-associated taxa in this region can illuminate biogeographical principles about vicariance and the establishment (or local extirpation) of existing species. Here we aim to: (1) outline the distribution of shallow water fauna between the Red Sea and adjacent regions, (2) explore mechanisms for maintaining these distributions and (3) propose hypotheses to test these mechanisms. Location Red Sea, Gulf of Aden, Arabian Sea, Arabian Gulf and Indian Ocean. Methods Updated checklists for scleractinian corals, fishes and non-coral invertebrates were used to determine species richness in the Red Sea and the rest of the Arabian Peninsula and assess levels of endemism. Fine-scale diversity and abundance of reef fishes within the Red Sea were explored using ecological survey data. Results Within the Red Sea, we recorded 346 zooxanthellate and azooxanthellate scleractinian coral species of which 19 are endemic (5.5%). Currently 635 species of polychaetes, 211 echinoderms and 79 ascidians have been documented, with endemism rates of 12.6%, 8.1% and 16.5% respectively. A preliminary compilation of 231 species of crustaceans and 137 species of molluscs include 10.0% and 6.6% endemism respectively. We documented 1071 shallow fish species, with 12.9% endemic in the entire Red Sea and 14.1% endemic in the Red Sea and Gulf of Aden. Based on ecological survey data of endemic fishes, there were no major changes in species richness or abundance across 1100 km of Saudi Arabian coastline. Main conclusions The Red Sea biota appears resilient to major environmental fluctuations and is characterized by high rates of endemism with variable degrees of incursion into the Gulf of Aden. The nearby Omani and Arabian Gulfs also have variable environments and high levels of endemism, but these are not consistently distinct across taxa. The presence of physical barriers does not appear to explain species distributions, which are more likely determined by ecological plasticity and genetic diversity. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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131. Linking local retention, self-recruitment, and persistence in marine metapopulations.
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Lett, Christophe, Nguyen-Huu, Tri, Cuif, Marion, Saenz-Agudelo, Pablo, and Kaplan, David M.
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MARINE ecology , *AGRICULTURAL egg production , *LARVAL dispersal , *SURVIVAL analysis (Biometry) , *METAMORPHOSIS - Abstract
Three indices of larval retention have been used in the literature to assess the tendency for self-maintenance of local marine populations: local retention (LR), selfrecruitment (SR), and relative local retention (RLR). Only one of these, LR, defined as the ratio of locally produced settlement to local egg production, has a clear relationship to selfpersistence of individual sites. However, SR, the ratio of locally produced settlement to settlement of all origins at a site, is generally easier to measure experimentally. We use theoretical, simulation, and empirical approaches to bridge the gap between these different indices, and demonstrate that there is a proportional relationship between SR and LR for metapopulations close to a stable state and with lifetime egg production (LEP) approximately uniform over space. Similarly, for systems where larval mortality rates are a relatively uniform function of release site, RLR (defined as the ratio of locally produced settlement to all settlement of local origin) and LR will also be proportional. Therefore, SR and RLR provide information on relative rates of LR for systems satisfying these conditions. Furthermore, the ratio between LR and SR can be used to evaluate global persistence of metapopulations, and therefore provides valuable information not necessarily available if only LR is considered. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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132. Local adaptation of Dromiciops marsupials (Microbiotheriidae) from southern South America: Implications for species management facing climate change.
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Quintero-Galvis JF, Saenz-Agudelo P, D'Elía G, and Nespolo RF
- Abstract
The two species of the microbiotheriid marsupial genus Dromiciops ( Dromiciops bozinovici : "Panchos's monito del monte" and Dromiciops gliroides : "monito del monte") exhibit a marked latitudinal genetic differentiation. Nevertheless, it is unclear whether this differentiation results from neutral processes or can be explained, to some extent, by local adaptation to different environmental conditions. Here, we used an SNP panel gathered by Rad-seq and searched for footprints of local adaptation (putative loci under selection) by exploring genetic associations with environmental variables in the two species of Dromiciops in Chilean and Argentinean populations. We applied three methods for detecting outlier SNPs and two genotype-environment associations approaches to quantify associations between allelic frequencies and environmental variables. Both species display strong genetic structure. D . bozinovici exhibited three distinct genetic groups, marking the first report of such structuring in this species using SNPs. In contrast, D . gliroides displayed four genetic clusters, consistent with previous studies. Both species exhibited an association of their genetic structure with environmental variables. D . bozinovici exhibited significant associations of allelic frequencies with elevation, precipitation during the warmest periods, and seasonality in the thermal regime. For D . gliroides , genetic variation appeared to be associated with more variables than D . bozinovici , including precipitation and temperature-related variables, isothermality, and elevation. All the outlier SNPs were mapped to the D . gliroides reference genome to explore if they fell within functionally known genes. These results represent a necessary first step toward identifying the genome regions that harbor genes associated with climate adaptations in Dromiciops . Notably, we identified genes involved in various functions, including carbohydrate synthesis (ALG8), muscle and neuronal regulation (MEF2D), and stress responses (PTGES3). Ultimately, this study contributes valuable insights that can inform targeted conservation strategies aimed at preserving the genetic diversity of Dromiciops in the face of environmental challenges., Competing Interests: The authors declare no competing interests., (© 2024 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)
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- 2024
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133. Environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: Toward a baseline for biodiversity monitoring of unexplored marine habitats.
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Saenz-Agudelo P, Ramirez P, Beldade R, Campoy AN, Garmendia V, Search FV, Fernández M, Wieters EA, Navarrete SA, Landaeta MF, and Pérez-Matus A
- Abstract
Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding the importance of TMREs as habitats, biodiversity reservoirs and their connections with better-studied shallow reefs. Here, we use environmental DNA (eDNA) from water samples to characterize the community composition of TMREs on the central Chilean coast, generating the first baseline for monitoring the biodiversity of these habitats. We analyzed samples from two depths (30 and 60 m) over four seasons (spring, summer, autumn, and winter) and at two locations approximately 16 km apart. We used a panel of three metabarcodes, two that target all eukaryotes (18S rRNA and mitochondrial COI) and one specifically targeting fishes (16S rRNA). All panels combined encompassed eDNA assigned to 42 phyla, 90 classes, 237 orders, and 402 families. The highest family richness was found for the phyla Arthropoda, Bacillariophyta, and Chordata. Overall, family richness was similar between depths but decreased during summer, a pattern consistent at both locations. Our results indicate that the structure (composition) of the mesophotic communities varied predominantly with seasons. We analyzed further the better-resolved fish assemblage and compared eDNA with other visual methods at the same locations and depths. We recovered eDNA from 19 genera of fish, six of these have also been observed on towed underwater videos, while 13 were unique to eDNA. We discuss the potential drivers of seasonal differences in community composition and richness. Our results suggest that eDNA can provide valuable insights for monitoring TMRE communities but highlight the necessity of completing reference DNA databases available for this region., Competing Interests: The authors declare that they have no conflict of interest., (© 2024 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)
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- 2024
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134. Population genomic analyses reveal hybridization and marked differences in genetic structure of Scurria limpet sister species with parapatric distributions across the South Eastern Pacific.
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Saenz-Agudelo P, Peluso L, Nespolo R, Broitman BR, Haye PA, and Lardies MA
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The study of sister species that occur in parapatry around biogeographic transition zones can help understand the evolutionary processes that underlie the changes in species composition across biogeographic transition zones. The South Eastern Pacific (SEP) coast is a highly productive coastal system that exhibits a broad biogeographic transition zone around 30-35°S. Here, we present a comparative genome-wide analysis of the sister species Scurria viridula and Scurria zebrina , that occur in parapatry and whose poleward and equatorward range edges intersect in the 30-35°S SEP biogeographic transition zone. We sampled 118 specimens sourced from nine sites from Tocopilla (22°S) to Chiloé (41°S) including one site where both species overlap and analyzed over 8000 biallelic single nucleotide polymorphisms. We found evidence of hybridization between these species in the contact zone and found significant but contrasting population structures for both species. Our results indicate that the genetic structure in S . viridula , which is currently expanding its range poleward, follows a simple isolation by distance model with no traces of natural selection (no evidence of outlier loci). In contrast, S . zebrina , which has its equatorward range edge at the transition zone, displayed a pronounced genetic break approximately at 32-34°S, along a region of marked environmental heterogeneity in association with a semi-permanent coastal upwelling regime. For S . zebrina we also found 43 outlier loci associated with this genetic break, with a significant proportion of them clustering in a single linkage group. This marked difference in the presence of outlier loci between species suggests that they could be responding differently to local environmental challenges found at their overlapping geographic range edges, thus providing important new insights about genomic changes around biogeographic transition zones in sister species and the forces that shape genetic diversity in intertidal marine species., Competing Interests: The authors declare no conflict of interests., (© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)
- Published
- 2022
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135. Coral reef fish populations can persist without immigration.
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Salles OC, Maynard JA, Joannides M, Barbu CM, Saenz-Agudelo P, Almany GR, Berumen ML, Thorrold SR, Jones GP, and Planes S
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- Animals, DNA analysis, Female, Male, Models, Biological, Papua New Guinea, Perciformes genetics, Population Dynamics, Reproduction, Animal Migration, Coral Reefs, Perciformes physiology
- Abstract
Determining the conditions under which populations may persist requires accurate estimates of demographic parameters, including immigration, local reproductive success, and mortality rates. In marine populations, empirical estimates of these parameters are rare, due at least in part to the pelagic dispersal stage common to most marine organisms. Here, we evaluate population persistence and turnover for a population of orange clownfish, Amphiprion percula, at Kimbe Island in Papua New Guinea. All fish in the population were sampled and genotyped on five occasions at 2-year intervals spanning eight years. The genetic data enabled estimates of reproductive success retained in the same population (reproductive success to self-recruitment), reproductive success exported to other subpopulations (reproductive success to local connectivity), and immigration and mortality rates of sub-adults and adults. Approximately 50% of the recruits were assigned to parents from the Kimbe Island population and this was stable through the sampling period. Stability in the proportion of local and immigrant settlers is likely due to: low annual mortality rates and stable egg production rates, and the short larval stages and sensory capacities of reef fish larvae. Biannual mortality rates ranged from 0.09 to 0.55 and varied significantly spatially. We used these data to parametrize a model that estimated the probability of the Kimbe Island population persisting in the absence of immigration. The Kimbe Island population was found to persist without significant immigration. Model results suggest the island population persists because the largest of the subpopulations are maintained due to having low mortality and high self-recruitment rates. Our results enable managers to appropriately target and scale actions to maximize persistence likelihood as disturbance frequencies increase., (© 2015 The Author(s).)
- Published
- 2015
- Full Text
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