Jones Geoffrey P.

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Jones
First Name
Geoffrey P.
ORCID
0000-0002-6244-1245

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  • Preprint
    Marine dispersal scales are congruent over evolutionary and ecological time
    ( 2016-10) Pinsky, Malin L. ; Saenz-Agudelo, Pablo ; Salles, Océane C. ; Almany, Glenn R. ; Bode, Michael ; Berumen, Michael L. ; Andrefouet, Serge ; Thorrold, Simon R. ; Jones, Geoffrey P. ; Planes, Serge
    The degree to which offspring remain near their parents or disperse widely is critical for understanding population dynamics, evolution, and biogeography, and for designing conservation actions. In the ocean, most estimates suggesting short-distance dispersal are based on direct ecological observations of dispersing individuals, while indirect evolutionary estimates often suggest substantially greater homogeneity among populations. Reconciling these two approaches and their seemingly competing perspectives on dispersal has been a major challenge. However, here we show for the first time that evolutionary and ecological measures of larval dispersal can closely agree by using both to estimate the distribution of dispersal distances. In orange clownfish (Amphiprion percula) populations in Kimbe Bay, Papua New Guinea, we found that evolutionary dispersal kernels were 17 [95% CI: 12–24] km wide, while an exhaustive set of direct larval dispersal observations suggested kernel widths of 27 [19–36] km or 19 [15–27] km across two years. The similarity between these two approaches suggests that ecological and evolutionary dispersal kernels can be equivalent, and that the apparent disagreement between direct and indirect measurements can be overcome. Our results suggest that carefully applied evolutionary methods, which are often less expensive, can be broadly relevant for understanding ecological dispersal across the tree of life.
  • Preprint
    Connectivity dominates larval replenishment in a coastal reef fish metapopulation
    ( 2011-01-25) Saenz-Agudelo, Pablo ; Jones, Geoffrey P. ; Thorrold, Simon R. ; Planes, Serge
    Direct estimates of larval retention and connectivity are essential to understand the structure and dynamics of marine metapopulations, and optimize the size and spacing of reserves within networks of marine protected areas (MPAs). For coral reef fishes, while there are some empirical estimates of self-recruitment at isolated populations, exchange among sub-populations has been rarely quantified. Here we used microsatellite DNA markers and a likelihood-based parentage analysis to assess the relative magnitude of self-recruitment and exchange among 8 geographically distinct sub-populations of the panda clownfish Amphiprion polymnus along 30 km of coastline near Port Moresby, Papua New Guinea. In addition, we used an assignment/exclusion test to identify immigrants arriving from genetically distinct sources. Overall, 82% of the juveniles were immigrants while 18% were progeny of parents genotyped in our focal metapopulation. Of the immigrants, only 6% were likely to be genetically distinct from the focal metapopulation, suggesting most of the connectivity is among sub-populations from a rather homogeneous genetic pool. Of the 18% that were progeny of known adults, two thirds dispersed among the 8 sub-populations and only one third settled back into natal sub- populations. Comparison of our data with previous studies suggested that variation in dispersal distances is likely to be influenced by the geographic setting and spacing of sub-populations.
  • Article
    Seascape and life-history traits do not predict self-recruitment in a coral reef fish
    (The Royal Society, 2016-08-09) Herrera, Marcela ; Nanninga, Gerrit ; Planes, Serge ; Jones, Geoffrey P. ; Thorrold, Simon R. ; Saenz-Agudelo, Pablo ; Almany, Glenn R. ; Berumen, Michael L.
    The persistence and resilience of many coral reef species are dependent on rates of connectivity among sub-populations. However, despite increasing research efforts, the spatial scale of larval dispersal remains unpredictable for most marine metapopulations. Here, we assess patterns of larval dispersal in the angelfish Centropyge bicolor in Kimbe Bay, Papua New Guinea, using parentage and sibling reconstruction analyses based on 23 microsatellite DNA loci. We found that, contrary to previous findings in this system, self-recruitment (SR) was virtually absent at both the reef (0.4–0.5% at 0.15 km2) and the lagoon scale (0.6–0.8% at approx. 700 km2). While approximately 25% of the collected juveniles were identified as potential siblings, the majority of sibling pairs were sampled from separate reefs. Integrating our findings with earlier research from the same system suggests that geographical setting and life-history traits alone are not suitable predictors of SR and that high levels of localized recruitment are not universal in coral reef fishes.
  • Preprint
    Otolith geochemistry does not reflect dispersal history of clownfish larvae
    ( 2010-06) Berumen, Michael L. ; Walsh, Harvey J. ; Raventos, N. ; Planes, Serge ; Jones, Geoffrey P. ; Starczak, Victoria R. ; Thorrold, Simon R.
    Natural geochemical signatures in calcified structures are commonly employed to retrospectively estimate dispersal pathways of larval fish and invertebrates. However, the accuracy of the approach is generally untested due to the absence of individuals with known dispersal histories. We used genetic parentage analysis (genotyping) to divide 110 new recruits of the orange clownfish, Amphiprion percula, from Kimbe Island, Papua New Guinea, into two groups: “self-recruiters” spawned by parents on Kimbe Island and “immigrants” that had dispersed from distant reefs (>10km away). Analysis of daily increments in sagittal otoliths found no significant difference in PLDs or otolith growth rates between self-recruiting and immigrant larvae. We also quantified otolith Sr/Ca and Ba/Ca ratios during the larval phase using laser ablation inductively coupled plasma mass spectrometry. Again, we found no significant differences in larval profiles of either element between self-recruits and immigrants. Our results highlight the need for caution when interpreting otolith dispersal histories based on natural geochemical tags in the absence of water chemistry data or known-origin larvae with which to test the discriminatory ability of natural tags.
  • Preprint
    First genealogy for a wild marine fish population reveals multi-generational philopatry
    ( 2016-10) Salles, Océane C. ; Pujol, Benoit ; Maynard, Jeffrey A. ; Almany, Glenn R. ; Berumen, Michael L. ; Jones, Geoffrey P. ; Saenz-Agudelo, Pablo ; Srinivasan, Maya ; Thorrold, Simon R. ; Planes, Serge
    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 may also increase the probability of inbreeding that can compromise persistence. While 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 multi-generational pedigrees that are currently lacking for marine fishes. Here we present the first multi-generational 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) over a 10-year 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 multi-generational pedigrees over a relatively short time period, as we present here, provides a framework for assessing the ability of marine populations to persist and adapt to accelerating climate change.
  • Preprint
    Coral reef fish populations can persist without immigration
    ( 2015-10) Salles, Océane C. ; Maynard, Jeffrey A. ; Joannides, Marc ; Barbu, Corentin M. ; Saenz-Agudelo, Pablo ; Almany, Glenn R. ; Berumen, Michael L. ; Thorrold, Simon R. ; Jones, Geoffrey P. ; Planes, Serge
    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 parameterize 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.
  • Preprint
    On minimising assignment errors and the trade‐off between false positives and negatives in parentage analysis
    ( 2013-05) Harrison, Hugo B. ; Saenz-Agudelo, Pablo ; Planes, Serge ; Jones, Geoffrey P. ; Berumen, Michael L.
    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.
  • Preprint
    Homogeneity of coral reef communities across 8 degrees of latitude in the Saudi Arabian Red Sea
    ( 2015-11) Roberts, May B. ; Jones, Geoffrey P. ; McCormick, Mark I. ; Munday, Philip L. ; Neale, Stephen ; Thorrold, Simon R. ; Robitzch, Vanessa S. N. ; Berumen, Michael L.
    Coral reef communities between 26.8°N and 18.6°N latitude in the Saudi Arabian Red Sea were surveyed to provide baseline data and an assessment of fine-scale biogeography of communities in this region. Forty reefs along 1100 km of coastline were surveyed using depth-stratified visual transects of fish and benthic communities. Fish abundance and benthic cover data were analyzed using multivariate approaches to investigate whether coral reef communities differed with latitude. A total of 215 fish species and 90 benthic categories were recorded on the surveys. There were no significant differences among locations in fish abundance, species richness, or among several diversity indices. Despite known environmental gradients within the Red Sea, the communities remained surprisingly similar. The communities do, however, exhibit subtle changes across this span of reefs that likely reflect the constrained distributions of several species of reef fish and benthic fauna.