Accounting for unobserved population dynamics and aging error in close-kin mark-recapture assessments.

Obtaining robust estimates of population abundance is a central challenge hindering the conservation and management of many threatened and exploited species. Close-kin mark-recapture (CKMR) is a genetics-based approach that has strong potential to improve the monitoring of data-limited species by enabling estimates of abundance, survival, and other parameters for populations that are challenging to assess. However, CKMR models have received limited sensitivity testing under realistic population dynamics and sampling scenarios, impeding the application of the method in population monitoring programs and stock assessments. Here, we use individual-based simulation to examine how unmodeled population dynamics and aging uncertainty affect the accuracy and precision of CKMR parameter estimates under different sampling strategies. We then present adapted models that correct the biases that arise from model misspecification. Our results demonstrate that a simple base-case CKMR model produces robust estimates of population abundance with stable populations that breed annually; however, if a population trend or non-annual breeding dynamics are present, or if year-specific estimates of abundance are desired, a more complex CKMR model must be constructed. In addition, we show that CKMR can generate reliable abundance estimates for adults from a variety of sampling strategies, including juvenile-focused sampling where adults are never directly observed (and aging error is minimal). Finally, we apply a CKMR model that has been adapted for population growth and intermittent breeding to two decades of genetic data from juvenile lemon sharks (Negaprion brevirostris) in Bimini, Bahamas, to demonstrate how application of CKMR to samples drawn solely from juveniles can contribute to monitoring efforts for highly mobile populations. Overall, this study expands our understanding of the biological factors and sampling decisions that cause bias in CKMR models, identifies key areas for future inquiry, and provides recommendations that can aid biologists in planning and implementing an effective CKMR study, particularly for long-lived data-limited species.

Smaller body size under warming is not due to gill-oxygen limitation in a cold-water salmonid.

Declining body size in fishes and other aquatic ectotherms associated with anthropogenic climate warming has significant implications for future fisheries yields, stock assessments and aquatic ecosystem stability. One proposed mechanism seeking to explain such body-size reductions, known as the gill oxygen limitation (GOL) hypothesis, has recently been used to model future impacts of climate warming on fisheries but has not been robustly empirically tested. We used brook trout (Salvelinus fontinalis), a fast-growing, cold-water salmonid species of broad economic, conservation and ecological value, to examine the GOL hypothesis in a long-term experiment quantifying effects of temperature on growth, resting metabolic rate (RMR), maximum metabolic rate (MMR) and gill surface area (GSA). Despite significantly reduced growth and body size at an elevated temperature, allometric slopes of GSA were not significantly different than 1.0 and were above those for RMR and MMR at both temperature treatments (15°C and 20°C), contrary to GOL expectations. We also found that the effect of temperature on RMR was time-dependent, contradicting the prediction that heightened temperatures increase metabolic rates and reinforcing the importance of longer-term exposures (e.g. >6 months) to fully understand the influence of acclimation on temperature-metabolic rate relationships. Our results indicate that although oxygen limitation may be important in some aspects of temperature-body size relationships and constraints on metabolic supply may contribute to reduced growth in some cases, it is unlikely that GOL is a universal mechanism explaining temperature-body size relationships in aquatic ectotherms. We suggest future research focus on alternative mechanisms underlying temperature-body size relationships, and that projections of climate change impacts on fisheries yields using models based on GOL assumptions be interpreted with caution.

Sources of bias in applying close-kin mark-recapture to terrestrial game species with different life histories.

Close-kin mark-recapture (CKMR) is a method analogous to traditional mark-recapture but without requiring recapture of individuals. Instead, multilocus genotypes (genetic marks) are used to identify related individuals in one or more sampling occasions, which enables the opportunistic use of samples from harvested wildlife. To apply the method accurately, it is important to build appropriate CKMR models that do not violate assumptions linked to the species' and population's biology and sampling methods. In this study, we evaluated the implications of fitting overly simplistic CKMR models to populations with complex reproductive success dynamics or selective sampling. We used forward-in-time, individual-based simulations to evaluate the accuracy and precision of CKMR abundance and survival estimates in species with different longevities, mating systems, and sampling strategies. Simulated populations approximated a range of life histories among game species of North America with lethal sampling to evaluate the potential of using harvested samples to estimate population size. Our simulations show that CKMR can yield nontrivial biases in both survival and abundance estimates, unless influential life history traits and selective sampling are explicitly accounted for in the modeling framework. The number of kin pairs observed in the sample, in combination with the type of kinship used in the model (parent-offspring pairs and/or half-sibling pairs), can affect the precision and/or accuracy of the estimates. CKMR is a promising method that will likely see an increasing number of applications in the field as costs of genetic analysis continue to decline. Our work highlights the importance of applying population-specific CKMR models that consider relevant demographic parameters, individual covariates, and the protocol through which individuals were sampled.

Genetic evidence supports a range extension for the Brazilian cownose ray Rhinoptera brasiliensis in the western North Atlantic.

We report 24 new records of the Brazilian cownose ray Rhinoptera brasiliensis outside its accepted geographic range. Sequencing of a 442-base pair portion of the mitochondrial NADH dehydrogenase subunit 2 gene for 282 Rhinoptera samples revealed eight records off the east coast of the USA and 16 from the eastern Gulf of Mexico. Both sexes of all life stages were documented in all seasons over multiple years in the Indian River and Lake Worth lagoons, Florida, indicating that their range extends further in the western North Atlantic than previously described.

The evolution of underwater flight: The redistribution of pectoral fin rays, in manta rays and their relatives (Myliobatidae).

Batoids are a diverse clade of flat cartilaginous fishes that occur primarily in benthic marine habitats. The skates and rays typically use their flexible pectoral fins for feeding and propulsion via undulatory swimming. However, two groups of rays have adopted a pelagic or bentho-pelagic lifestyle and utilize oscillatory swimming-the Myliobatidae and Gymnuridae. The myliobatids have evolved cephalic lobes, anteriorly extended appendages that are optimized for feeding, while their pectoral fins exhibit several modifications that likely arose in association with functional optimization of pelagic cruising via oscillatory flight. Here, we examine variation in fin ray distribution and ontogenetic timing of fin ray development in batoid pectoral fins in an evolutionary context using the following methods: radiography, computed tomography, dissections, and cleared and stained specimens. We propose an index for characterizing variation in the distribution of pectoral fin rays. While undulatory swimmers exhibit symmetry or slight anterior bias, we found a posterior shift in the distribution of fin rays that arose in two distinct lineages in association with oscillatory swimming. Undulatory and oscillatory swimmers occupy nonoverlapping morphospace with respect to fin ray distribution illustrating significant remodeling of pectoral fins in oscillatory swimmers. Further, we describe a derived skeletal feature in anterior pectoral fins of the Myliobatidae that is likely associated with optimization of oscillatory swimming. By examining the distribution of fin rays with clearly defined articulation points, we were able to infer evolutionary trends and body plan remodeling associated with invasion of the pelagic environment. Finally, we found that the number and distribution of fin rays is set early in development in the little skate, round stingray, and cownose ray, suggesting that fin ray counts from specimens after birth or hatching are representative of adults and therefore comparable among species.