Isolation and Characterization of Polymorphic Microsatellite Markers from a Globally Distributed Marine Apex Predator, the Tiger Shark (Galeocerdo cuvier)

High levels of fishing have resulted in declines among many of the oceans top predators, including the globally distributed tiger shark (Galeocerdo cuvier). Overexploitation of this species has led to declines in parts of its distribution, which may have important ecological consequences given the tiger shark’s trophic position as a large bodied, generalist predator. To assess the population genetics of this species, an enrichment protocol was used to isolate a suite of nine di- and tetra-nucleotide microsatellite loci within the tiger shark, which were subsequently characterized using genomic DNA derived from 40 individuals sampled from Hawaiian waters. The number of alleles per locus ranged from 3 to 23, and the average expected heterozygosities across loci ranged from 0.30 to 0.93. Analyses suggested a low frequency of null alleles across markers, and all loci conformed to both Hardy–Weinberg and linkage equilibrium at P \u3e 0.01

Development and Characterization of 11 Novel Microsatellite Loci for the Roundscale Spearfish Tetrapturus georgii and Their Cross-Species Amplification Among Other Istiophorid Species

Eleven novel polymorphic microsatellite loci were developed and characterized for the recently validated roundscale spearfish Tetrapturus georgii. Characterization of these markers, based on 35 roundscale spearfish from the western North Atlantic, revealed two to 21 alleles per locus with an average expected heterozygosity (HE) of 0·09–0·94, and all loci conformed to Hardy–Weinberg expectations. Cross-amplification of these 11 loci against all other eight known istiophorid species indicates promising prospects for the utility of these markers for istiophorids in general

Isolation of 11 Polymorphic Tri- and Tetranucleotide Microsatellite Loci in a North American Sedge (\u3ci\u3eCarex scoparia\u3c/i\u3e: Cyperaceae) and Cross-Species Amplification in Three Additional \u3ci\u3eCarex\u3c/i\u3e Species

We report on the isolation and evaluation of 11 microsatellites from a widespread eastern North American wetland sedge, Carex scoparia. Loci exhibit 3–9 alleles over five populations and significant FIS (0.204–0.717) in most populations. All primers cross-amplify in at least two other species, and 10 cross-amplify in the more distantly related C. stipata. These markers will be used to examine population genetics and patterns of chromosomal diversification in this ecologically important sedge species and its relatives

Population Structure and Dispersal of the Coral-Excavating Sponge Cliona delitrix

Some excavating sponges of the genus Cliona compete with live reef corals, often killing and bioeroding entire colonies. Important aspects affecting distribution of these species, such as dispersal capability and population structure, remain largely unknown. Thus, the aim of this study was to determine levels of genetic connectivity and dispersal of Cliona delitrix across the Greater Caribbean (Caribbean Sea, Bahamas and Florida), to understand current patterns and possible future trends in their distribution and effects on coral reefs. Using ten species-specific microsatellite markers, we found high levels of genetic differentiation between six genetically distinct populations: one in the Atlantic (Florida-Bahamas), one specific to Florida and four in the South Caribbean Sea. In Florida, two independent breeding populations are likely separated by depth. Gene flow and ecological dispersal occur among other populations in the Florida reef tract, and between some Florida locations and the Bahamas. Similarly, gene flow occurs between populations in the South Caribbean Sea, but appears restricted between the Caribbean Sea and the Atlantic (Florida-Bahamas). Dispersal of C. delitrix was farther than expected for a marine sponge and favoured in areas where currents are strong enough to transport sponge eggs or larvae over longer distances. Our results support the influence of ocean current patterns on genetic connectivity, and constitute a baseline to monitor future C. delitrix trends under climate change

Anthropogenic disturbance and evolutionary parameters: a lemon shark population experiencing habitat loss

The level of genetic variation in natural populations influences evolutionary potential, and may therefore influence responses to selection in the face of future environmental changes. By combining long-term monitoring of marked individuals with genetic pedigree reconstruction, we assessed whether habitat loss influenced genetic variation in a lemon shark (Negaprion brevirostris) population at an isolated nursery lagoon (Bimini, Bahamas). We also tracked changes in the strength and direction of natural selection. Contrary to initial expectations, we found that after the habitat loss neutral genetic variation increased, as did additive genetic variance for juvenile morphological traits (body length and mass). We hypothesize that these effects might result from philopatric behavior in females coupled with a possible influx of male genotypes from other nursery sites. We also found changes in the strength of selection on morphological traits, which weakened considerably after the disturbance; habitat loss therefore changed the phenotypes favored by natural selection. Because such human-induced shifts in the adaptive landscape may be common, we suggest that conservation biologists should not simply focus on neutral genetic variation per se, but also on assessing and preserving evolutionary parameters, such as additive genetic variation and selection

Contrasting Patterns of Population Structure and Dispersal for the Giant Barrel Sponge (Xestospongia muta) within the Florida Reef Tract and Caribbean

Sponges are one of the dominant fauna on Florida and Caribbean reefs, with species diversity often exceeding that of scleractinian corals. Despite their importance as structural components and habitat providers on reefs, their dispersal dynamics are little understood. We utilized eight microsatellite markers to study the population structure and migration patterns of the giant barrel sponge (Xestospongia muta), a widespread species throughout Florida and the Caribbean. Bayesian multilocus genotype analyses clustered 157 samples from the Bahamas, Honduras, and the US Virgin Islands into three distinct groups. 159 samples from nine locations within 284 km of the Florida reef tract (Key Largo to the Dry Tortugas) formed a fourth group. Population structure among the four groups was high (FST = 0.155; P = 0.001), with no recent migration among the groups. In contrast, high levels of migration were detected within the Florida reef tract. Reefs in the Upper Keys (Long Key) appear to be sources of larvae to reefs in the north (Key Largo) and also to reefs in the south (Key West and the Dry Tortugas). This pattern of migration closely matches current pathways within the South Florida recirculation system, suggesting that currents play an important role in dispersing X. muta larvae within the Florida reef tract. Although there was an overall lack of isolation by distance among the four groups, a significant correlation between genetic and geographic distance was found among the Florida sampling sites indicating that mating within the reef tract is not random. Asexual reproduction appears not to be the cause as only 1.3% of individuals in Florida shared the same genotype (1.6% overall). Rather, limited larval dispersal along the reef tract and among Caribbean locations has probably led to inbreeding within reefs, explaining the significant deficit in heterozygosity detected (FIS = 0.219; P = 0.001)

Comparative Population Genetics and Evolutionary History of Two Commonly Misidentified Billfishes of Management and Conservation Concern

Background: Misidentifications between exploited species may lead to inaccuracies in population assessments, with potentially irreversible conservation ramifications if overexploitation of either species is occurring. A notable showcase is provided by the realization that the roundscale spearfish (Tetrapturus georgii), a recently validated species, has been historically misidentified as the morphologically very similar and severely overfished white marlin (Kajikia albida) (IUCN listing: Vulnerable). In effect, no information exists on the population status and evolutionary history of the enigmatic roundscale spearfish, a large, highly vagile and broadly distributed pelagic species. We provide the first population genetic evaluation of the roundscale spearfish, utilizing nuclear microsatellite and mitochondrial DNA sequence markers. Furthermore, we re-evaluated existing white marlin mitochondrial genetic data and present our findings in a comparative context to the roundscale spearfish. Results: Microsatellite and mitochondrial (control region) DNA markers provided mixed evidence for roundscale spearfish population differentiation between the western north and south Atlantic regions, depending on marker-statistical analysis combination used. Mitochondrial DNA analyses provided strong signals of historical population growth for both white marlin and roundscale spearfish, but higher genetic diversity and effective female population size (1.5-1.9X) for white marlin. Conclusions: The equivocal indications of roundscale spearfish population structure, combined with a smaller effective female population size compared to the white marlin, already a species of concern, suggests that a species-specific and precautionary management strategy recognizing two management units is prudent for this newly validated billfish

The Behavioural and Genetic Mating System of the Sand Tiger Shark, Carcharias taurus, an Intrauterine Cannibal

Sand tiger sharks (Carcharias taurus) have an unusual mode of reproduction, whereby the first embryos in each of the paired uteri to reach a certain size (‘hatchlings’) consume all of their smaller siblings during gestation (‘embryonic cannibalism’ or EC). If females commonly mate with multiple males (‘behavioural polyandry’) then litters could initially have multiple sires. It is possible, however, that EC could exclude of all but one of these sires from producing offspring thus influencing the species genetic mating system (‘genetic monogamy’). Here, we use microsatellite DNA profiling of mothers and their litters (n = 15, from two to nine embryos per litter) to quantify the frequency of behavioural and genetic polyandry in this system. We conservatively estimate that nine of the females we examined (60%) were behaviourally polyandrous. The genetic mating system was characterized by assessing sibling relationships between hatchlings and revealed only 40 per cent genetic polyandry (i.e. hatchlings were full siblings in 60% of litters). The discrepancy stemmed from three females that were initially fertilized by multiple males but only produced hatchlings with one of them. This reveals that males can be excluded even after fertilizing ova and that some instances of genetic monogamy in this population arise from the reduction in litter size by EC. More research is needed on how cryptic post-copulatory and post-zygotic processes contribute to determining paternity and bridging the behavioural and genetic mating systems of viviparous species

Low Genetic Differentiation across Three Major Ocean Populations of the Whale Shark, Rhincodon typus

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

Long-term site fidelity of endangered smalltooth sawfish (Pristis pectinata) from different mothers

Understanding how endangered species use nursery habitats is vital for recovery planning. Research on the smalltooth sawfish (Pristis pectinata) has shown that areas of estuarine nurseries, called hotspots, are used consistently. The objectives of our study were 1) to determine whether 10 young-of-the-year smalltooth sawfish in an artificial, non-main-stem portion (i.e., a seawall canal system) of a hotspot were descended from one or different mothers and 2) to document long-term habitat use by these individuals. At least 4 mothers contributed to the group, which comprised siblings, half-siblings, and unrelated individuals. Young sawfish exhibited site fidelity to their capture location, spending 61% of their time there. Continuous residency lasted as long as 86 days, but these fish made small-scale diel