Dataset Information

Low genetic differentiation across three major ocean populations of the whale shark, Rhincodon typus.

ABSTRACT: BACKGROUND:Whale sharks are a declining species for which little biological data is available. While these animals are protected in many parts of their range, they are fished legally and illegally in some countries. Baseline biological and ecological data are needed to allow the formulation of an effective conservation plan for whale sharks. It is not known, for example, whether the whale shark is represented by a single worldwide panmictic population or by numerous, reproductively isolated populations. Genetic analysis of population structure is one essential component of the baseline data required for whale shark conservation. METHODOLOGY/PRINCIPAL FINDINGS:We have identified 8 polymorphic microsatellites in the whale shark and used these markers to assess genetic variation and population structure in a panel of whale sharks covering a broad geographic region. This is the first record of microsatellite loci in the whale shark, which displayed an average of 9 alleles per locus and mean H(o) = 0.66 and H(e) = 0.69. All but one of the eight loci meet the expectations of Hardy-Weinberg equilibrium. Analysis of these loci in whale sharks representing three major portions of their range, the Pacific (P), Caribbean (C), and Indian (I) Oceans, determined that there is little population differentiation between animals sampled in different geographic regions, indicating historical gene flow between populations. F(ST) values for inter-ocean comparisons were low (PxC = 0.0387, CxI = 0.0296 and PxI = -0.0022), and only CxI approached statistical significance (p = 0.0495). CONCLUSIONS/SIGNIFICANCE:We have shown only low levels of genetic differentiation between geographically distinct whale shark populations. Existing satellite tracking data have revealed both regional and long-range migration of whale sharks throughout their range, which supports the finding of gene flow between populations. Whale sharks traverse geographic and political boundaries during their life history and interbreed with animals from distant populations; conservation efforts must therefore target international protection for this species.

SUBMITTER: Schmidt JV

PROVIDER: S-EPMC2662413 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Low genetic differentiation across three major ocean populations of the whale shark, Rhincodon typus.

Schmidt Jennifer V JV Schmidt Claudia L CL Ozer Fusun F Ernst Robin E RE Feldheim Kevin A KA Ashley Mary V MV Levine Marie M

PloS one 20090407 4

<h4>Background</h4>Whale sharks are a declining species for which little biological data is available. While these animals are protected in many parts of their range, they are fished legally and illegally in some countries. Baseline biological and ecological data are needed to allow the formulation of an effective conservation plan for whale sharks. It is not known, for example, whether the whale shark is represented by a single worldwide panmictic population or by numerous, reproductively isola ...[more]

PMID: 19352489

Similar Datasets

Project description:BACKGROUND:The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species. Therefore, it is also the largest extant species of the paraphyletic assemblage commonly referred to as fishes. As both a phenotypic extreme and a member of the group Chondrichthyes - the sister group to the remaining gnathostomes, which includes all tetrapods and therefore also humans - its genome is of substantial comparative interest. Whale sharks are also listed as an endangered species on the International Union for Conservation of Nature's Red List of threatened species and are of growing popularity as both a target of ecotourism and as a charismatic conservation ambassador for the pelagic ecosystem. A genome map for this species would aid in defining effective conservation units and understanding global population structure. RESULTS:We characterised the nuclear genome of the whale shark using next generation sequencing (454, Illumina) and de novo assembly and annotation methods, based on material collected from the Georgia Aquarium. The data set consisted of 878,654,233 reads, which yielded a draft assembly of 1,213,200 contigs and 997,976 scaffolds. The estimated genome size was 3.44Gb. As expected, the proteome of the whale shark was most closely related to the only other complete genome of a cartilaginous fish, the holocephalan elephant shark. The whale shark contained a novel Toll-like-receptor (TLR) protein with sequence similarity to both the TLR4 and TLR13 proteins of mammals and TLR21 of teleosts. The data are publicly available on GenBank, FigShare, and from the NCBI Short Read Archive under accession number SRP044374. CONCLUSIONS:This represents the first shotgun elasmobranch genome and will aid studies of molecular systematics, biogeography, genetic differentiation, and conservation genetics in this and other shark species, as well as providing comparative data for studies of evolutionary biology and immunology across the jawed vertebrate lineages.

Project description:BackgroundMeasuring coastal-pelagic prey fields at scales relevant to the movements of marine predators is challenging due to the dynamic and ephemeral nature of these environments. Whale sharks (Rhincodon typus) are thought to aggregate in nearshore tropical waters due to seasonally enhanced foraging opportunities. This implies that the three-dimensional movements of these animals may be associated with bio-physical properties that enhance prey availability. To date, few studies have tested this hypothesis.MethodsHere, we conducted ship-based acoustic surveys, net tows and water column profiling (salinity, temperature, chlorophyll fluorescence) to determine the volumetric density, distribution and community composition of mesozooplankton (predominantly euphausiids and copepods) and oceanographic properties of the water column in the vicinity of whale sharks that were tracked simultaneously using satellite-linked tags at Ningaloo Reef, Western Australia. Generalised linear mixed effect models were used to explore relationships between the 3-dimensional movement behaviours of tracked sharks and surrounding prey fields at a spatial scale of ~ 1 km.ResultsWe identified prey density as a significant driver of horizontal space use, with sharks occupying areas along the reef edge where densities were highest. These areas were characterised by complex bathymetry such as reef gutters and pinnacles. Temperature and salinity profiles revealed a well-mixed water column above the height of the bathymetry (top 40 m of the water column). Regions of stronger stratification were associated with reef gutters and pinnacles that concentrated prey near the seabed, and entrained productivity at local scales (~ 1 km). We found no quantitative relationship between the depth use of sharks and vertical distributions of horizontally averaged prey density. Whale sharks repeatedly dove to depths where spatially averaged prey concentration was highest but did not extend the time spent at these depth layers.ConclusionsOur work reveals previously unrecognized complexity in interactions between whale sharks and their zooplankton prey.

Project description:Satellite tracking of 27 whale sharks in the eastern tropical Pacific, examined in relation to environmental data, indicates preferential occupancy of thermo-biological frontal systems. In these systems, thermal gradients are caused by wind-forced circulation and mixing, and biological gradients are caused by associated nutrient enrichment and enhanced primary productivity. Two of the frontal systems result from upwelling, driven by divergence in the current systems along the equator and the west coast of South America; the third results from wind jet dynamics off Central America. All whale sharks were tagged near Darwin Island, Galápagos, within the equatorial Pacific upwelling system. Occupancy of frontal habitat is pronounced in synoptic patterns of shark locations in relation to serpentine, temporally varying thermal fronts across a zonal expanse > 4000 km. 80% of shark positions in northern equatorial upwelling habitat and 100% of positions in eastern boundary upwelling habitat were located within the upwelling front. Analysis of equatorial shark locations relative to thermal gradients reveals occupancy of a transition point in environmental stability. Equatorial subsurface tag data show residence in shallow, warm (>22°C) water 94% of the time. Surface zonal current speeds for all equatorial tracking explain only 16% of the variance in shark zonal movement speeds, indicating that passive drifting is not a primary determinant of movement patterns. Movement from equatorial to eastern boundary frontal zones occurred during boreal winter, when equatorial upwelling weakens seasonally. Off Peru sharks tracked upwelling frontal positions within ~100-350 km from the coast. Off Central America, the largest tagged shark (12.8 m TL) occupied an oceanic front along the periphery of the Panama wind jet. Seasonal movement from waning equatorial upwelling to productive eastern boundary habitat is consistent with underlying trophic dynamics. Persistent shallow residence in thermo-biological frontal zones suggests the role of physical-biological interactions that concentrate food resources.

Dataset Information

Low genetic differentiation across three major ocean populations of the whale shark, Rhincodon typus.

Publications

Low genetic differentiation across three major ocean populations of the whale shark, Rhincodon typus.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets