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18 results for “Larval connectivity”
Larval dispersal histogram data used for ATLAS deliverable D1.6: Biologically realistic Lagrangian dispersal and connectivity
<p>Larval dispersal histogram data for ATLAS deliverable D1.6 "Biologically realistic Lagrangian connectivity" (https://www.eu-atlas.org/resources/atlas-partners-document-area/atlas-deliverables/455-d1-6-biologically-realistic-lagrangian-connectivity/file). Tar archive files are ordered by ATLAS case study source region and with folders by larval behaviour type. The numbered behaviour types are described in deliverable D1.6. Each netcdf histogram file, e.g. hists_age_21.nc, contains the histogram for larvae of a single age in 5-day steps, from 00 (0 days) to 37 (185 days).</p> <p>Within each file histogram file, particle counts in each Viking20 model grid-cell are contained in a 4-d array with dimensions (launch month, lauch year, model gridsquare y index, model gridsquare x index). The Viking20 grid in the North Atlantic is the ORCA tripolar grid. Details of the model mesh are in the included file viking20_mesh_mask.tgz</p> <p>Histograms are in netcdf files:</p> <p>============================</p> <p>$ ncdump -h hists_age_00.nc<br> netcdf hists_age_00 {<br> dimensions:<br> coordinate = 4 ;<br> coordinate_1 = 50 ;<br> coordinate_2 = 1719 ;<br> coordinate_3 = 1784 ;<br> variables:<br> int64 coordinate(coordinate) ;<br> coordinate:units = "month" ;<br> coordinate:long_name = "Launch month" ;<br> int64 coordinate_1(coordinate_1) ;<br> coordinate_1:units = "year" ;<br> coordinate_1:long_name = "Launch year" ;<br> int64 coordinate_2(coordinate_2) ;<br> coordinate_2:units = "index" ;<br> coordinate_2:long_name = "J index" ;<br> int64 coordinate_3(coordinate_3) ;<br> coordinate_3:units = "index" ;<br> coordinate_3:long_name = "I index" ;<br> int64 data(coordinate, coordinate_1, coordinate_2, coordinate_3) ;<br> data :long_name = "particle count" ;</p> <p>// global attributes:<br> :Conventions = "CF-1.6" ;<br> }</p> <p>==========================================</p> <p> </p> <p> </p>
Larval dispersal patterns and connectivity of Acropora on Florida's Coral Reef and its implications for restoration
Since the 1980s, populations of Acropora cervicornis and A. palmata have experienced severe declines due to disease and anthropogenic stressors; resulting in their listing as threatened, and their need for restoration. In this study, larval survival and competency data were collected and used to calibrate a very high-resolution hydrodynamic model (up to 100m) to determine the dispersal patterns of Acropora species along the Florida's Coral Reef. The resulting connectivity matrices was incorporated into a metapopulation model to compare strategies for restoring Acropora populations. This study found that Florida's Coral Reef was historically a well-connected system, and that spatially selective restoration may be able to stimulate natural recovery. Acropora larvae are predominantly transported northward along the Florida's Coral Reef, however southward transport also occurs, driven by tides and baroclinic eddies. Local retention and self-recruitment processes were strong for a broadcast spawner with a long pelagic larval duration. Model simulations demonstrate that it is beneficial to spread restoration effort across more reefs, rather than focusing on a few reefs. Differences in population patchiness between the Acropora cervicornis and A. palmata drive the need for different approaches to their management plans. This model can be used as a tool to address the species-specific management to restore genotypically diverse Acropora populations on the Florida's Coral Reef, and its methods could be expanded to other vulnerable populations.
Larval dispersal patterns and connectivity of Acropora on Florida’s Coral Reef and its implications for restoration
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Biophysical larval dispersal models of observed bonefish (Albula vulpes) spawning events in Abaco, The Bahamas: An assessment of population connectivity and ocean dynamics
<p>Biophysical models are a powerful tool for assessing population connectivity of marine organisms that broadcast spawn. <em>Albula</em> <em>vulpes</em> is a species of bonefish that is an economically and culturally important sportfish found throughout the Caribbean and that exhibits genetic connectivity among geographically distant populations. We created ontogenetically relevant biophysical models for bonefish larval dispersal based upon multiple observed spawning events in Abaco, The Bahamas in 2013, 2018, and 2019. Biological parameterizations were informed through active acoustic telemetry, CTD casts, captive larval rearing, and field collections of related albulids and anguillids. Ocean conditions were derived from the Regional Navy Coastal Ocean Model American Seas dataset. Each spawning event was simulated 100 times using the program Ichthyop. Ten thousand particles were released at observed and putative spawning locations and were allowed to disperse for the full 71-day pelagic larval duration for <em>A</em>. <em>vulpes</em>. Settlement densities in defined settlement zones were assessed along with interactions with oceanographic features. The prevailing Northern dispersal paradigm exhibited strong connectivity with Grand Bahama, the Berry Islands, Andros, and self-recruitment to lower and upper Abaco. Ephemeral gyres and flow direction within Northwest and Northeast Providence Channels were shown to have important roles in larval retention to the Bahamian Archipelago. Larval development environments for larvae settling upon different islands showed few differences and dispersal was closely associated with the thermocline. Settlement patterns informed the suggestion for expansion of conservation parks in Grand Bahama, Abaco, and Andros, and the creation of a park in Eleuthera and the Berry Islands to protect fisheries. Further observation of spawning events and the creation of biophysical models will help to maximize protection for bonefish spawning locations and nursery habitat, and may help to predict year-class strength for bonefish stocks throughout the Greater Caribbean.</p>
Biophysical larval dispersal models of observed bonefish (Albula vulpes) spawning events in Abaco, The Bahamas: An assessment of population connectivity and ocean dynamics
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Data from: On-shelf larval retention limits population connectivity in a coastal broadcast spawner
Broadcast-spawning marine organisms with long pelagic larval duration are often expected to be genetically homogeneous throughout their ranges. When genetic structure is found in such taxa, it may be in the form of chaotic genetic patchiness: i.e. patterns that might seem independent of any underlying environmental variation. The joint analysis of population genetic data and marine environmental data can elucidate factors driving such spatial genetic diversity patterns. Using meso-scale sampling (at a scale of 10s to 100s of km), microsatellite data and advection connectivity simulations, we studied the effect of temperate southern Australian ocean circulation on the genetic structure of the snail Nerita atramentosa. This species has a long pelagic larval duration and is represented as a single metapopulation throughout its ~3000 km range, but even so, we found that its dispersal potential is lower than expected. Connectivity simulations indicate that this is a result of the larvae that remain on the continental shelf (where currents are erratic and often shoreward) returning to the coast in much larger numbers than larvae that become entrained in the region's shelf-edge boundary currents. Our study contributes to the growing evidence that departures from the expectations of panmixia along continuous and environmentally homogeneous coastlines are not limited to low-dispersal species, and it identifies on-shelf larval retention as an important factor limiting dispersal.
Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species
<p>Gene flow shapes spatial genetic structure as well as the potential for local adaptation of populations. Among marine animals with non-migratory adults, the presence or absence of a pelagic larval stage is thought to be a key determinant in shaping gene flow and the genetic structure of populations. In addition, the spatial distribution of suitable habitats will influence the distribution of biological populations and their pattern of gene flow. We used whole genome sequencing to study demographic history and reduced representation (ddRAD) sequencing data to analyze spatial genetic structure in the broadnosed pipefish (<em>Syngnathus typhle</em>). Its main habitat are seagrass meadows, which along the study coast (SW Norway) have a patchy distribution. Combining the results from several analyses including scans for selection, suggests that stochastic genetic drift has shaped the observed population structure largely due to its patchy habitat distribution. The restricted gene flow is further driven by life history traits such as the presence of parental care combined with no pelagic life stages, resulting in a clear isolation-by-distance pattern spanning 100s of kilometers.</p> <p>The spatial scale of demographic connectivity was inferred from long-term (~30 year) census population counts that uncovered a sharp decline in spatial correlations in abundance with distance (37% decorrelation over 2 km). These findings were contrasted with data from two other fish species sampled along the same coastline, both having pelagic larval stages lasting ~20 days (corkwing wrasse, <em>Symphodus melops</em>, and black goby, <em>Gobus niger</em>) where the population structure is not that evident. For these species, we found a wider spatial scale of demographic connectivity (decorrelation distances of 14 and 28 km, respectively), and weaker isolation-by-distance except at one point along the coast where both species revealed a strong barrier to gene flow, seemingly due to a lack of suitable habitat. Combined, these findings suggest that habitat fragmentation and absence of a pelagic larval stage in pipefish strongly increases geographic structuring, while the pelagic larvae of wrasse and goby increase genetic and demographic connectivity, except over extensive habitat shifts.</p>
Data from: Influence of the larval phase on connectivity: strong differences in the genetic structure of brooders and broadcasters in the Ophioderma longicauda species complex
Closely related species with divergent life-history traits are excellent models to infer the role of such traits in genetic diversity and connectivity. Ophioderma longicauda is a brittle star species complex composed of different genetic clusters, including brooders and broadcasters. These species diverged very recently and some of them are sympatric and ecologically syntopic, making them particularly suitable to study the consequences of their trait differences. At the scale of the geographic distribution of the broadcasters (Mediterranean Sea and north-eastern Atlantic), we sequenced the mitochondrial marker COI and genotyped an intron (i51) for 788 individuals. In addition, we sequenced 10 nuclear loci newly developed from transcriptome sequences, for six sympatric populations of brooders and broadcasters from Greece. At the large scale we found a high genetic structure within the brooders (COI: 0.07
Data for the publication by Mouchi et al "A step towards measuring connectivity in the deep-sea: elemental fingerprints of mollusk larval shells discriminate hydrothermal vent sites"
<p>This is the elemental data collected by fsLA-ICP-MS-MS on 600 individual larval shells of the hydrothermal-vent limpet Shinkailepas tollmanni from 14 sites in the Southwest Pacific Ocean.</p> <p>The first column indicates the sample ID corresponding to onship sample during the scientific cruise CHUBACARC (Hourdez & Jollivet, 2019).</p> <p>The second column indicates the S. tollmanni sample ID from the publication of Mouchi et al.</p> <p>Columns 3 to 15 correspond to elemental abundances measured.</p> <p>Column 16 to 18 correspond to the region, area and hydrothermal sites, respectively, for each larval shell.</p> <p> </p> <p>Hourdez, S., Jollivet, D., 2019. CHUBACARC cruise, <em>L’Atalante R/V</em>. doi: 10.17600/18001111.</p>
Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species
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Data from: Large-scale, multi-directional larval connectivity among coral reef fish populations in the Great Barrier Reef Marine Park
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Data from: Influence of the larval phase on connectivity: strong differences in the genetic structure of brooders and broadcasters in the Ophioderma longicauda species complex
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Data from: Population genomics meet Lagrangian simulations: oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas
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Data from: Patterns and persistence of larval retention and connectivity in a marine fish metapopulation
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Data from: On-shelf larval retention limits population connectivity in a coastal broadcast spawner
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Data from: Stretched to the limit; can a short pelagic larval duration connect adult populations of an Indo-Pacific diadromous fish (Kuhlia rupestris)?
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Code and data used in "Designing marine reserve networks to mitigate larval dispersal volatility with the connectivity portfolio effect"
<p>This repository contains the code and data used in "Designing marine reserve networks to mitigate larval dispersal volatility with the connectivity portfolio effect".</p> <p>The files have been placed inside a .rar to maintain the file structure necessary to run Marxan correctly.</p> <p>The main file to run the analyses is "Comparing spatial conservation prioritisation run.R" which uses functions from "Comparing spatial conservation prioritisation functions.R".</p> <p>The main input files are located in data01.Rdata, data02.Rdata, and data03.Rdata, which contain 1. a data frame of planning unit centroids, sizes, and amount of reef habitat, 2. a subset of planning unit data as a matrix, 3-14. migration, probability, and flow larval dispersal matrices, 15-18. larval release dates, 19-34 indices of Oceanic nino index (ONI), El Nino Modoki index (MOD), Dipole Mode Index (DMI), and Pacific Decadal Oscillation (PDO) of coral trout, snapper, rabbitfish, and octopus.</p> <p> </p>
Designing marine reserve networks to mitigate larval dispersal volatility with the connectivity portfolio effect - DATA
<p>Underlying data for "Designing marine reserve networks to mitigate larval dispersal volatility with the connectivity portfolio effect" found at</p> <p>.mat files are annual larval dispersal connectivity matrices for coral trout, snapper, rabbitfish, and octopus, in the province of Southeast Sulawesi, from biophysical dispersal models.</p>
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