Population genetics

Gopher Tortoises are an imperiled terrestrial tortoise considered ecosystem engineers, as their burrows support over 350 species of “commensals”. Due to extensive anthropogenic habitat destruction and fragmentation, tortoise populations have significantly declined over the past 100 years. This isolation is leading to a premature loss of genetic variation, further precipitating the decline of this species. Understanding the genetic structure of this species can aid management decisions through intentionally relocating animals based on genetic units and historic gene flow, to preserve adaptive diversity and evolutionary potential on a large scale. I investigated whether Southeast Florida has a genetically distinct subpopulation of Gopher Tortoises in the unexamined southeasternmost extent of their range, from Palm Beach to Miami-Dade counties, using 9 microsatellite loci previously characterized for this species (Schwartz et al 2003) and found that our populations are only modestly differentiated from each other, and have greater genetic diversity than other populations.

Coral reefs worldwide are experiencing unprecedented and rapid declines. However, deeper, mesophotic coral ecosystems (MCEs; 30–150 m) may act as refuges for coral species, providing larvae to recolonize degraded shallow reefs. This study assessed the genetic connectivity of shallow and mesophotic Montastraea cavernosa populations on the Belize Barrier Reef and the community structure of their endosymbiotic algae (Family Symbiodiniaceae) across a fine-scale depth gradient (10, 16, 25, 35 m). Evaluation of nine polymorphic microsatellite markers demonstrated that relatively shallow (10 and 16 m) M. cavernosa populations were genetically distinct from relatively deep (25 and 35 m) populations. High throughput sequencing of ribosomal coding DNA from Symbiodiniaceae communities of M. cavernosa revealed differences in community structure across depth, with shallow-specialist and depth-generalist community profiles. This research provides important information for the management of distinct deep and adds to the body of research on the understudied MCEs of the Mesoamerican Reef.

The wahoo, Acanthocyhium solandri, is a pelagic marine fish which inhabits tropical,
subtropical, and warm temperate waters worldwide. Despite being highly mobile and
economically important over most of their range, there is little scientific data
concerning population structure, movement patterns, or environmental preferences of
wahoo. In this study I investigate wahoo genetic population structure and
phytogeography on a global scale, and deploy pop-up satellite archival tags (PSA T's)
in the western Atlantic Ocean to determine movement patterns and environmental
preferences of wahoo.
Wahoo population genetic structure was examined across their entire global range
with intron six of lactate dehydrogenase-A (ldhA6, 10 locations, N = 213) and
mtDNA cytochrome h (Cyth, 13 locations, N = 322). Results show extensive sharing ofhaplotypes and no significant structure between all locations (mtDNA ~ST <
0.0001, P = 0.634; nuclear FsT = 0.0125, P = 0.1 06). Overall nuclear heterozygosity
(H = 0.714) and mtDNA haplotype diversity (h = 0.918) are both high, while overall
mtDNA nucleotide diversity (n = 0.006) and nuclear nucleotide diversity (n = 0.004)
are uniformly low. Coalescence indicates an effective female population size CNeF) at
- 816,000, and a population bottleneck - 690,000 years ago.
Movement patterns and environmental preferences were investigated by
deploying PSA T's onto four individual wahoo in the western Atlantic Ocean.
Tagging success rate (75%) validates the deployment protocol developed for this
project. Results indicate that wahoo in the western Atlantic ocean spend the greatest
portion of their time between 0 and 20 meters of depth, and between temperatures of
20oC and 26°C. More time was spent near the deeper extremes of their range during
the nocturnal period, and daily visits to the surface were observed. Wahoo were
observed traveling north in Fall and Winter, contrary to previous notions concerning
the migratory movements of this species.
The genetic results indicate a worldwide stock for wahoo, which reinforces the
mandate for international cooperation on fisheries issues. The PSA T results
demonstrate the value of the acquired data to the investigation of important life
history parameters in pelagic species. The information generated from this project
will benefit fisheries managers, marine biologists, evolutionary biologists, and both
commercial and recreational fishing interests.

The cues used by marine turtles to locate foraging areas in the open ocean are largely
unknown though some species (especially the green turtle [Chelonia mydas], the
loggerhead [Caretta caretta], and the leatherback [Dermochelys coriacea]) somehow
locate areas of high productivity. Loggerheads can detect airborne odors, but a capacity
to orient has not yet been investigated. In this comparative study, tethered loggerheads
and leatherbacks were exposed to dimethyl sulfide (DMS) or food odors in a laminar
flow of air. Turtles did not orient into the air current. Free-swimming loggerheads and
green turtles were also exposed to air- or waterborne food (squid) odor plus a neutral
visual stimulus. Both species showed increases in swimming activity and biting behavior
to both stimuli. These results suggest that airborne odors are likely not used to locate
distant areas, but that they are used in localized food searching efforts.

This study investigated a resident community of Atlantic spotted dolphins (Stenella frontalis) on Little Bahama Bank (LBB) in the Bahamas utilizing a noninvasive molecular approach. Genetic template material was collected and extracted from fecal material of S. frontalis. Fine-scale population structure was found within LBB according to mitochondrial DNA (mtDNA) and microsatellites (Fst = 0.25317, P < 0.0001 and Fst = 0.04491, P < 0.0001, respectively). Three main social clusters (North, Central, South/Roam) exist on LBB and all clusters were found to be genetically distinct according to microsatellite analyses. Mitochondrial haplotypes revealed North and South/Roam were not differentiated, but Central was different from both. When separated by sex, males were less genetically structured than females. Males showed no evidence of structure according to Ost or Rst.

The Major Histocompatibility Complex (MHC) encodes proteins critical to the vertebrate immune response; therefore MHC diversity is an indicator of population health. I have (1) Isolated exon 2 of the class II gene DQA in Tursiops truncatus in the North Indian River Lagoon (IRL) (n=17), South IRL (n=29) and adjacent Atlantic waters (n=20), (2) assessed genetic variability between groups, (3) developed a method to genotype individuals, (4) typed 11 unique alleles in 66 individuals, (5) detected geographic patterns of diversity between estuarine and coastal individuals (FST=0.1255, p<0.05), (6) found evidence of positive selection centered in the binding pockets P1, P6 and P9 of the peptide binding region (w=2.08), (7) found that patterns of polymorphism did not closely match patterns of diversity in neutral markers, (8) performed a pilot study with Orcinus orca. The initial findings highlight the need for further comparative work and suggest that silent mutations are not neutral.

Persistent, anthropogenic contaminants collectively known as endocrine-disrupting chemicals (EDCs), are considered to be potential threats to wildlife reproductive fitness (Wingfield, 2002). The modes by which EDCs act on the reproductive system, and establishment of steroid profiles in wildlife, are important areas of study. Two means of performing an endocrine snapshot profile from dolphin tissues (serum and urine) were tested on samples, comparing a novel high performance liquid chromatography method to newly-validated enzyme-linked immunoassays (ELISAs). Serum and urine samples were obtained from two marine parks, and from free-ranging dolphins in the Indian River Lagoon (IRL) and Charleston Harbor (CHS) systems. Relative binding affinities of steroids versus putative EDCs to steroid receptors were compared in dolphin reproductive tissues, obtained by the Georgia Aquarium's Dolphin Conservation Field Station (GADCFS) from strained bottlenose dolphins (four male, three female) during 2010 and 20ll.........I conclude that endocrine disruptors are tissue and receptor specific, and both legacy and emerging contaminants are of concern to dolphin stocks, particularly those facing other significant environmental stressors.

Demographic changes, through immigration/emigration (or death) can affect the social and community structure of a population. This study reports on the effects of demographic changes following 2 intense hurricanes on two sympatric delphinid species: Atlantic bottlenose dolphins, Tursiops truncatus, and Atlantic spotted dolphins Stenella frontalis. Thirty percent of the bottlenose population was lost after the hurricanes, with an influx of roughly the same number of immigrants. The stable community split into two cohesive units. Preferences in association in relation to reproductive status and sex remained. Immigrants assimilated well into the population, especially males. There is a conflict of interest between resident males and females in accepting immigrants and often females find more resistance than males. Long-term analysis of spotted dolphins revealed a community structure defined by long-term site fidelity, natal philopatry of both sexes and three social clusters.