Complex patterns of genetic population structure in the mouthbrooding marine catfish, Bagre marinus, in the Gulf of Mexico and U.S. Atlantic.

Patterns of genetic variation reflect interactions among microevolutionary forces that vary in strength with changing demography. Here, patterns of variation within and among samples of the mouthbrooding gafftopsail catfish (Bagre marinus, Family Ariidae) captured in the U.S. Atlantic and throughout the Gulf of Mexico were analyzed using genomics to generate neutral and non-neutral SNP data sets. Because genomic resources are lacking for ariids, linkage disequilibrium network analysis was used to examine patterns of putatively adaptive variation. Finally, historical demographic parameters were estimated from site frequency spectra. The results show four differentiated groups, corresponding to the (1) U.S. Atlantic, and the (2) northeastern, (3) northwestern, and (4) southern Gulf of Mexico. The non-neutral data presented two contrasting signals of structure, one due to increases in diversity moving west to east and north to south, and another to increased heterozygosity in the Atlantic. Demographic analysis suggested that recently reduced long-term effective population size in the Atlantic is likely an important driver of patterns of genetic variation and is consistent with a known reduction in population size potentially due to an epizootic. Overall, patterns of genetic variation resemble that of other fishes that use the same estuarine habitats as nurseries, regardless of the presence/absence of a larval phase, supporting the idea that adult/juvenile behavior and habitat are important predictors of contemporary patterns of genetic structure.

Philopatry influences the genetic population structure of the blacktip shark (Carcharhinus limbatus) at multiple spatial scales.

Understanding how interactions among microevolutionary forces generate genetic population structure of exploited species is vital to the implementation of management policies that facilitate persistence. Philopatry displayed by many coastal shark species can impact gene flow and facilitate selection, and has direct implications for the spatial scales of management. Here, genetic structure of the blacktip shark (Carcharhinus limbatus) was examined using a mixed-marker approach employing mitochondrial control region sequences and 4339 SNP-containing loci generated using ddRAD-Seq. Genetic variation was assessed among young-of-the-year sampled in 11 sites in waters of the United States in the western North Atlantic Ocean, including the Gulf of Mexico. Spatial and environmental analyses detected 68 nuclear loci putatively under selection, enabling separate assessments of neutral and adaptive genetic structure. Both mitochondrial and neutral SNP data indicated three genetically distinct units-the Atlantic, eastern Gulf, and western Gulf-that align with regional stocks and suggest regional philopatry by males and females. Heterogeneity at loci putatively under selection, associated with temperature and salinity, was observed among sites within Gulf units, suggesting local adaptation. Furthermore, five pairs of siblings were identified in the same site across timescales corresponding with female reproductive cycles. This indicates that females re-used a site for parturition, which has the potential to facilitate the sorting of adaptive variation among neighbouring sites. The results demonstrate differential impacts of microevolutionary forces at varying spatial scales and highlight the importance of conserving essential habitats to maintain sources of adaptive variation that may buffer species against environmental change.

Escaped bait: Bull shark Carcharhinus leucas with an intentionally attached harness rig.

A 193 cm total length female bull shark Carcharhinus leucas was captured in Florida bearing intentionally attached materials which resembled a harness. Harness-type live bait rigs are commonly used for small baitfish; some anglers use such devices with small sharks when targeting large sharks and bony fish. Biofouling on the apparatus and the extent of the injuries indicated the material had likely been on the shark for several years. This case highlights the dangers of using these types of devices on juveniles of long-lived species that attain a large body size.

Environmental DNA detection tracks established seasonal occurrence of blacktip sharks (Carcharhinus limbatus) in a semi-enclosed subtropical bay.

The integration of eDNA analysis into the population assessment and monitoring of sharks could greatly improve temporal and spatial data used for management purposes. This study aimed to compare eDNA detection against well-established seasonal changes in blacktip shark (Carcharhinus limbatus) abundance in Terra Ceia Bay (FL, USA). We used a species-specific real-time PCR approach to detect C. limbatus eDNA in the bay on a near monthly basis from spring through mid-fall in 2018 and 2019. Previous studies have shown that C. limbatus give birth in the bay in early summer and immature sharks occur there until late fall, when decreasing water temperatures cause them to move offshore and southwards. Water samples (2 L) were collected (4-6 per month) and filtered in the field, with each then being subjected to real-time PCR. Carcharhinus limbatus 'positive' filters were significantly more commonly collected during the April-July sampling period than during the August-October sampling period. While following the predicted pattern, eDNA concentration was generally too low for accurate quantification. Our results show that C. limbatus eDNA detection follows known seasonal residency patterns consistently over 2 years of monitoring. Species-specific eDNA analysis using real-time PCR could therefore represent a cost-effective, scalable sampling tool to facilitate improved shark population monitoring in semi-enclosed marine habitats.

Complete mitochondrial genome of the Critically Endangered Smalltooth Sawfish Pristis pectinata (Rajiformes: Pristidae).

In this study we describe the first complete mitochondrial sequence of the Critically Endangered Smalltooth Sawfish Pristis pectinata. It is 16,802 bp in length and contains all 37 genes found in typical vertebrate mitogenomes. The nucleotide composition of the coding strand is 31.1% A, 26.0% C, 13.1% G and 28.9% T. There are 29 bp overlaps and 38 short intergenic spaces dispersed in the mitogenome. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) were found in the protein-coding genes. The length of the 22 tRNA genes range from 67 bp (tRNA(Ser2)) to 75 bp (tRNA(Leu1)). The control region is 1102 bp in length with high A + T (62.0%) and poor G (13.5%) content.

Genetic diversity despite population collapse in a critically endangered marine fish: the smalltooth sawfish (Pristis pectinata).

Sawfish (family Pristidae) are among the most critically endangered marine fish in the world, yet very little is known about how genetic bottlenecks, genetic drift, and inbreeding depression may be affecting these elasmobranchs. In the US Atlantic, the smalltooth sawfish (Pristis pectinata) has declined to 1-5% of its abundance in the 1900s, and its core distribution has contracted to southwest Florida. We used 8 polymorphic microsatellite markers to show that this remnant population still exhibits high genetic diversity in terms of average allelic richness (18.23), average alleles per locus (18.75, standard deviation [SD] 6.6) and observed heterozygosity (0.43-0.98). Inbreeding is rare (mean individual internal relatedness = -0.02, SD 0.14; F(IS) = -0.011, 95% confidence interval [CI] = -0.039 to 0.011), even though the estimated effective population size (N(e)) is modest (250-350, 95% CI = 142-955). Simulations suggest that the remnant smalltooth sawfish population will probably retain >90% of its current genetic diversity over the next century even at the lower estimate of N(e). There is no evidence of a genetic bottleneck accompanying last century's demographic bottleneck, and we discuss hypotheses that could explain this. We also discuss features of elasmobranch life history and population biology that could make them less vulnerable than other large marine vertebrates to genetic change associated with reduced population size.

Environmental influences on the spatial ecology of juvenile smalltooth sawfish (Pristis pectinata): results from acoustic monitoring.

To aid recovery efforts of smalltooth sawfish (Pristis pectinata) populations in U.S. waters a research project was developed to assess how changes in environmental conditions within estuarine areas affected the presence, movements, and activity space of this endangered species. Forty juvenile P. pectinata were fitted with acoustic tags and monitored within the lower 27 km of the Caloosahatchee River estuary, Florida, between 2005 and 2007. Sawfish were monitored within the study site from 1 to 473 days, and the number of consecutive days present ranged from 1 to 125. Residency index values for individuals varied considerably, with annual means highest in 2005 (0.95) and lowest in 2007 (0.73) when several P. pectinata moved upriver beyond detection range during drier conditions. Mean daily activity space was 1.42 km of river distance. The distance between 30-minute centers of activity was typically <0.1 km, suggesting limited movement over short time scales. Salinity electivity analysis demonstrated an affinity for salinities between 18 and at least 24 psu, suggesting movements are likely made in part, to remain within this range. Thus, freshwater flow from Lake Okeechobee (and its effect on salinity) affects the location of individuals within the estuary, although it remains unclear whether or not these movements are threatening recovery.