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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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Trophic position and niche width are fundamental components of a species' ecology, reflecting resource use, and influencing key demographic parameters such as somatic growth, maturation, and survival. Concepts about a species' trophic niche space have important implications for local management and habitat protection, and can shed light about resilience to changing climate for species occurring over broad spatial scales. For elusive marine animals such as sea turtles, trophic niche is challenging to study, and researchers often rely on other metrics, such as isotopic niche, as a proxy. Here, stable isotope analysis (δ13C and δ15N values) was conducted on bulk skin tissue of 718 green turtles (Chelonia mydas) distributed among 16 foraging areas in the eastern Pacific from the USA to Chile, a range spanning ~10,000 km. Compound‐specific nitrogen isotope analysis of amino acids (CSIA‐AA) was applied to 21 turtles among seven sites. Isotopic niche space was determined via Bayesian ellipse area (BEA) and convex hull area (CHA) analyses of bulk isotope values, which were also used along with amino acid δ15N values to determine trophic position (TP). Substantial variability in bulk tissue δ13C and δ15N values was found within and among sites, and amino acid δ15N values confirmed this was largely due to spatial differences in baseline nitrogen isotopic compositions, but also to a lesser extent from TP differences among the green turtle foraging populations. Isotope niche space varied among sites, influenced by the diversity of prey types and relative input of terrestrial‐ vs. marine‐derived nutrients; BEAs were the most suitable measurement of isotopic niche space due to the larger influence of outlying values with the CHA approach. Amino acid isotope‐derived TP estimates that accounted for local habitat conditions (e.g., mixed seagrass/macroalgae diet) performed the best among several approaches; TP ranged from 2.3 to 3.6, which indicates an omnivorous diet for most populations. In addition to providing additional spatial resolution for δ13C and δ15N isoscapes in the eastern Pacific, especially in coastal habitats, this study further establishes CSIA‐AA as an effective tool to study the trophic ecology of sea turtles across a variety of food webs and habitats. [ABSTRACT FROM AUTHOR]

Capacity to cope with warming temperatures is a key determining factor of species' persistence under global climate change. Many successful invasive species have heightened thermal tolerance relative to their native counterparts, which may provide competitive advantages for habitat utilization and resource acquisition under warming scenarios, ultimately contributing to radically altered community composition. Enhanced transcriptional plasticity may be an important factor conferring superior abilities to cope with environmental stress, but the molecular mechanisms driving key differences of organismal traits in invasive versus native species are not well known. Although it is predicted that established invaders will evolve canalized phenotypes well‐adapted to new environments, it is not clear whether the same expectations are true for invaders of variable thermal environments or under climate warming scenarios where abilities to cope with fluctuating and increasing temperatures may provide fitness advantages. Here, we compare a highly successful invasive fish and a sympatric endangered native fish living in a dynamic estuarine environment that is projected to warm under climate change. We linked organismal physiological limits with global transcriptional responses at multiple common relative and absolute temperature thresholds and determined that heightened thermal tolerance of invasive Inland Silversides (Menidia beryllina) is associated with transcriptional changes that are greater both in the number of genes and the magnitude of response relative to native Delta Smelt (Hypomesus transpacificus). Modulated genes contributed to the enrichment of biological processes that differed between species and generally increased with temperature. These results are in concordance with the hypothesis that transcriptional plasticity may play a key role in determining population persistence, species interactions, and shaping community assemblages under climate change. Future studies encompassing a wider range of species and taxa are needed to determine whether this is a general pattern found between native and invasive species more broadly. [ABSTRACT FROM AUTHOR]

Advances in high‐throughput sequencing (HTS) technologies coupled with increased interdisciplinary collaboration are rapidly expanding capacity in the scope and scale of wildlife genetic studies. While existing HTS methods can be directly applied to address some evolutionary and ecological questions, certain research goals necessitate tailoring methods to specific study organisms, such as high‐throughput genotyping of the same loci that are comparable over large spatial and temporal scales. These needs are particularly common for studies of highly mobile species of conservation concern like marine turtles, where life history traits, limited financial resources and other constraints require affordable, adaptable methods for HTS genotyping to meet a variety of study goals. Here, we present a versatile marine turtle HTS targeted enrichment platform adapted from the recently developed Rapture (RAD‐Capture) method specifically designed to meet these research needs. Our results demonstrate consistent enrichment of targeted regions throughout the genome and discovery of candidate variants in all species examined for use in various conservation genetics applications. Accurate species identification confirmed the ability of our platform to genotype over 1,000 multiplexed samples and identified areas for future methodological improvement such as optimization for low initial concentration samples. Finally, analyses within green turtles supported the ability of this platform to identify informative SNPs for stock structure, population assignment and other applications over a broad geographic range of interest to management. This platform provides an additional tool for marine turtle genetic studies and broadens capacity for future large‐scale initiatives such as collaborative global marine turtle genetic databases. [ABSTRACT FROM AUTHOR]

Climate change is predicted to intensify the impacts of invasive species by enhancing their performance relative to their native counterparts. However, few studies have compared the performance of invasive predators and native prey, despite the fact that non-native predators are well known to disrupt native communities., The 'trophic sensitivity hypothesis' suggests that predators are less tolerant of increasing environmental stress than their prey, whereas the 'tolerant invaders hypothesis' suggests that invaders are more tolerant than native species due to selection during the introduction process. It is therefore unclear how invasive predators will respond to increasing climate stressors., We coupled physiological measurements (thermal tolerance, thermal optima, salinity tolerance, predation rate) with environmental time-series data to assess the effects of warming and extreme low salinity events on non-native predators (gastropods) and native prey (oysters) from a coastal ecosystem., In general support of the trophic sensitivity hypothesis, we found that both non-native predators exhibited lower thermal optima relative to native prey, lower salinity tolerance and one predator was less tolerant of warming. However, because warming tolerance was extremely high (i.e. habitat temperature is 7·9-21 °C below thermal tolerance), near-term warming may first increase predator performance (consumption and growth rates), with negative effects on prey. Low salinity will likely produce heterogeneous effects on predator-prey interactions due to varying watershed sizes among estuaries that control the duration of low salinity events., The trophic sensitivity hypothesis may be a useful framework for understanding community responses to extreme climate change, which portends a decoupling of predator-prey interactions. However, we conclude that this hypothesis must be evaluated in environmental context and that coupling physiological metrics with in situ environmental data offers the best predictive power of near-term climate change impacts on invaded communities. Within our study system, warming is likely to intensify the impacts of both invasive predators, which may greatly reduce the abundance of the native oyster, a species of conservation and restoration focus. [ABSTRACT FROM AUTHOR]

As global change alters multiple environmental conditions, predicting species' responses can be challenging without understanding how each environmental factor influences organismal performance. Approaches quantifying mechanistic relationships can greatly complement correlative field data, strengthening our abilities to forecast global change impacts. Substantial salinity increases are projected in the San Francisco Estuary, California, due to anthropogenic water diversion and climatic changes, where the critically endangered delta smelt ( Hypomesus transpacificus) largely occurs in a low-salinity zone ( LSZ), despite their ability to tolerate a much broader salinity range. In this study, we combined molecular and organismal measures to quantify the physiological mechanisms and sublethal responses involved in coping with salinity changes. Delta smelt utilize a suite of conserved molecular mechanisms to rapidly adjust their osmoregulatory physiology in response to salinity changes in estuarine environments. However, these responses can be energetically expensive, and delta smelt body condition was reduced at high salinities. Thus, acclimating to salinities outside the LSZ could impose energetic costs that constrain delta smelt's ability to exploit these habitats. By integrating data across biological levels, we provide key insight into the mechanistic relationships contributing to phenotypic plasticity and distribution limitations and advance the understanding of the molecular osmoregulatory responses in nonmodel estuarine fishes. [ABSTRACT FROM AUTHOR]

Forecasting species' responses to climate change requires understanding the underlying mechanisms governing environmental stress tolerance, including acclimation capacity and acute stress responses. Current knowledge of these physiological processes in aquatic ectotherms is largely drawn from eurythermal or extreme stenothermal species. Yet many species of conservation concern exhibit tolerance windows and acclimation capacities in between these extremes. We linked transcriptome profiles to organismal tolerance in a mesothermal endangered fish, the delta smelt (Hypomesus transpacificus), to quantify the cellular processes, sublethal thresholds and effects of thermal acclimation on acute stress responses. Delta smelt initiated rapid molecular changes in line with expectations of theoretical thermal limitation models, but also exhibited diminished capacity to modify the expression of some genes and cellular mechanisms key to coping with acute thermal stress found in eurytherms. Sublethal critical thresholds occurred 4-6 °C below their upper tolerance limits, and thermal acclimation shifted the onset of acute thermal stress and tolerance as predicted. However, we found evidence that delta smelt's limited thermal plasticity may be partially due to an inability of individuals to effectively make physiological adjustments to truly achieve new homoeostasis under heightened temperatures, resulting in chronic thermal stress. These findings provide insight into the physiological basis of the diverse patterns of thermal tolerances observed in nature. Moreover, understanding how underlying molecular mechanisms shape thermal acclimation capacity, acute stress responses and ultimately differential phenotypes contributes to a predictive framework to deduce species' responses in situ to changes in selective pressures due to climate change. [ABSTRACT FROM AUTHOR]

ABSTRACT Invasive species with native ranges spanning strong environmental gradients are well suited for examining the roles of selection and population history in rapid adaptation to new habitats, providing insight into potential evolutionary responses to climate change. The Atlantic oyster drill (Urosalpinx cinerea) is a marine snail whose native range spans the strongest coastal latitudinal temperature gradient in the world, with invasive populations established on the US Pacific coast. Here, we leverage this system using genome‐wide SNPs and environmental data to examine invasion history and identify genotype–environment associations indicative of local adaptation across the native range, and then assess evidence for allelic frequency shifts that would signal rapid adaptation within invasive populations. We demonstrate strong genetic structuring among native regions which aligns with life history expectations, identifying southern New England as the source of invasive populations. Then, we identify putatively thermally adaptive loci across the native range but find no evidence of allele frequency shifts in invasive populations that suggest rapid adaptation to new environments. Our results indicate that while these loci may underpin local thermal adaptation in their native range, selection is relaxed in invasive populations, perhaps due to complex polygenic architecture underlying thermal traits and/or standing capacity for phenotypic plasticity. Given the prolific invasion of Urosalpinx, our study suggests population success in new environments is influenced by factors other than selection on standing genetic variation that underlies local adaptation in the native range and highlights the importance of considering population history and environmental selection pressures when evaluating adaptive capacity. [ABSTRACT FROM AUTHOR]