Ion mobility and mass spectrometry techniques are coupled with a temperature-controlled electrospray ionization source to follow the structural transitions of ubiquitin in aqueous solution (pH = 3) ...at elevated solution temperatures (T = 26–96 °C). Changes in the charge state distribution are consistent with a two-state, cooperative unfolding transition having a melting temperature of T m = 71 ± 2 °C, in agreement with prior measurements Wintrode, P. L. ; Makhatadze, G. I. ; Privalov, P. L. Proteins, 1994, 18, 246−253 . However, analysis of ion mobility distributions reveals the two-state transition is a composite of transitions involving at least nine unique species: three native or native-like structures; two that appear to be equilibrium intermediates (i.e., populations of new conformers that form at elevated temperatures but subsequently disappear at higher temperatures); and four products observed at high temperatures, including the well-characterized ubiquitin A state, and two solution species that are differentiated based on a cis- or trans-configured Glu18-Pro19 peptide bond. These nine states vary in abundances by factors as large as ∼103 over the range of solution temperatures. Although experimental melting transitions are conceived as a loss of well-defined structure leading to a random distribution of unstructured, denatured forms, the results provide evidence for new conformers having at least some well-defined structural elements are stabilized as temperature is increased.
1. The challenges associated with monitoring low-density carnivores across large landscapes have limited the ability to implement and evaluate conservation and management strategies for such species. ...Non-invasive sampling techniques and advanced statistical approaches have alleviated some of these challenges and can even allow for spatially explicit estimates of density, one of the most valuable wildlife monitoring tools. 2. For some species, individual identification comes at no cost when unique attributes (e.g. pelage patterns) can be discerned with remote cameras, while other species require viable genetic material and expensive laboratory processing for individual assignment. Prohibitive costs may still force monitoring efforts to use species distribution or occupancy as a surrogate for density, which may not be appropriate under many conditions. 3. Here, we used a large-scale monitoring study of fisher Pekania pennanti to evaluate the effectiveness of occupancy as an approximation to density, particularly for informing harvest management decisions. We combined remote cameras with baited hair snares during 2013-2015 to sample across a 70 096-km² region of western New York, USA. We fit occupancy and Royle-Nichols models to species detection-non-detection data collected by cameras, and spatial capture-recapture (SCR) models to individual encounter data obtained by genotyped hair samples. Variation in the state variables within 15-km² grid cells was modelled as a function of landscape attributes known to influence fisher distribution. 4. We found a close relationship between grid cell estimates of fisher state variables from the models using detection-non-detection data and those from the SCR model, likely due to informative spatial covariates across a large landscape extent and a grid cell resolution that worked well with the movement ecology of the species. Fisher occupancy and density were both positively associated with the proportion of coniferous-mixed forest and negatively associated with road density. As a result, spatially explicit management recommendations for fisher were similar across models, though relative variation was dampened for the detection-non-detection data. 5. Synthesis and applications. Our work provides empirical evidence that models using detection-non-detection data can make similar inferences regarding relative spatial variation of the focal population to models using more expensive individual encounters when the selected spatial grain approximates or is marginally smaller than home range size. When occupancy alone is chosen as a cost-effective state variable for monitoring, simulation and sensitivity analyses should be used to understand how inferences from detection-non-detection data will be affected by aspects of study design and species ecology.
The results presented in this report are based on analyses of 16,721 days of data downloaded from 96 archival tags recovered from bigeye tuna (Thunnus obesus; 54-159 cm in length, 0.97-5.44 years of ...age) at liberty from 31 to 1,508 days in the equatorial eastern Pacific Ocean. Analyses of daily timed depth and temperature records resulted in the classification of the data into three daily behavior types: characteristic, associative (associated with floating objects), and other. There is a significant positive correlation between the proportion of time fish exhibit characteristic behavior and increasing length, and significant negative correlations between the proportion of time bigeye exhibit associative and other behavior with increasing length. For the smallest (54-80 cm) to largest (100-159 cm) length classes, the vertical habitats utilized when exhibiting non-associative behaviors were 99 and 98% of the time above the thermocline depth (60 m) during the night, at the same average depth of 34 m, and 60 and 72% of the time below the thermocline during the day at average depths of 163 and 183 m, respectively. For the same smallest to largest length classes, when exhibiting associative behavior, the average nighttime and daytime depths were 25 and 21, and 33 and 37 m, respectively. The apparent effects of the environment on the behavior of the fish are discussed.
Abstract
In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The ...reaction takes place in photosystem II, where the Mn
4
CaO
5
cluster first stores four oxidizing equivalents, the S
0
to S
4
intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O–O bond formation chemistry
1–3
. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok’s photosynthetic water oxidation cycle, the S
3
→S
4
→S
0
transition where O
2
is formed and Kok’s water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn
4
CaO
5
cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom O
x
, which was introduced as a bridging ligand between Ca and Mn1 during the S
2
→S
3
transition
4–6
, disappears or relocates in parallel with Y
z
reduction starting at approximately 700 μs after the third flash. The onset of O
2
evolution, as indicated by the shortening of the Mn1–Mn4 distance, occurs at around 1,200 μs, signifying the presence of a reduced intermediate, possibly a bound peroxide.
A total of 1522 yellowfin tuna, Thunnus albacares, were captured, tagged, and released with surgically implanted archival tags (ATs), in six discrete areas of the eastern and central Pacific Ocean, ...during 2002 through 2019. Of 483 ATs returned (31.7%), 227 ATs from yellowfin (48–147 cm in fork length) at liberty from 32 to 1846 d (
x¯ = 300.1 d) provided suitable data sets which were processed using an unscented Kalman filter model with sea‐surface temperature measurements integrated (UKFsst) in order to obtain most probable tracks and movement parameters. Although some differences were observed in the movement patterns for fish from within and among the six release areas, 99% of the 227 fish remained within 1000 M of their release locations, indicating limited dispersion and fidelity to release locations. The median movement parameter D, which defines dispersion from the UKFsst model, for the fish released in the offshore equatorial areas showed much greater dispersion rates compared to those for the fish released along the coast or around islands. The rates of mixing of yellowfin among the release areas were found to be dependent on the distances between release areas, with, in general, the greatest mixing occurring among areas in closest proximity, whereas for the two areas offshore Mexico and the two offshore equatorial areas, the rates of mixing were nonexistent or negligible.
Oxygen minimum zones in the open ocean are predicted to significantly increase in volume over the coming decades as a result of anthropogenic climatic warming. The resulting reduction in dissolved ...oxygen (DO) in the pelagic realm is likely to have detrimental impacts on water-breathing organisms, particularly those with higher metabolic rates, such as billfish, tunas, and sharks. However, little is known about how free-living fish respond to low DO environments, and therefore, the effect increasing OMZs will have cannot be predicted reliably. Here, we compare the responses of two active predators (bigeye tuna
Thunnus obesus
and yellowfin tuna
Thunnus albacares
) to DO at depth throughout the eastern Pacific Ocean. Using time-series data from 267 tagged tunas (59,910 days) and 3D maps of modelled DO, we find that yellowfin tuna respond to low DO at depth by spending more time in shallower, more oxygenated waters. By contrast, bigeye tuna, which forage at deeper depths well below the thermocline, show fewer changes in their use of the water column. However, we find that bigeye tuna increased the frequency of brief upward vertical excursions they performed by four times when DO at depth was lower, but with no concomitant significant difference in temperature, suggesting that this behaviour is driven in part by the need to re-oxygenate following time spent in hypoxic waters. These findings suggest that increasing OMZs will impact the behaviour of these commercially important species, and it is therefore likely that other water-breathing predators with higher metabolic rates will face similar pressures. A more comprehensive understanding of the effect of shoaling OMZs on pelagic fish vertical habitat use, which may increase their vulnerability to surface fisheries, will be important to obtain if these effects are to be mitigated by future management actions.
Accelerating declines of an increasing number of animal populations worldwide necessitate methods to reliably and efficiently estimate demographic parameters such as population density and ...trajectory. Standard methods for estimating demographic parameters from noninvasive genetic samples are inefficient because lower-quality samples cannot be used, and they assume individuals are identified without error. We introduce the genotype spatial partial identity model (gSPIM), which integrates a genetic classification model with a spatial population model to combine both spatial and genetic information, thus reducing genotype uncertainty and increasing the precision of demographic parameter estimates. We apply this model to data from a study of fishers (Pekania pennanti) in which 37% of hair samples were originally discarded because of uncertainty in individual identity. The gSPIM density estimate using all collected samples was 25% more precise than the original density estimate, and the model identified and corrected three errors in the original individual identity assignments. A simulation study demonstrated that our model increased the accuracy and precision of density estimates 63 and 42%, respectively, using three replicated assignments (e.g., PCRs for microsatellites) per genetic sample. Further, the simulations showed that the gSPIM model parameters are identifiable with only one replicated assignment per sample and that accuracy and precision are relatively insensitive to the number of replicated assignments for high-quality samples. Current genotyping protocols devote the majority of resources to replicating and confirming high-quality samples, but when using the gSPIM, genotyping protocols could be more efficient by devoting more resources to low-quality samples.
Harvest data are often used by wildlife managers when setting harvest regulations for species because the data are regularly collected and do not require implementation of logistically and ...financially challenging studies to obtain the data. However, when harvest data are not available because an area had not previously supported a harvest season, alternative approaches are required to help inform management decision making. When distribution or density data are required across large areas, occupancy modeling is a useful approach, and under certain conditions, can be used as a surrogate for density. We collaborated with the New York State Department of Environmental Conservation (NYSDEC) to conduct a camera trapping study across a 70,096-km2 region of southern New York in areas that were currently open to fisher (Pekania Martes pennanti) harvest and those that had been closed to harvest for approximately 65 years. We used detection–nondetection data at 826 sites to model occupancy as a function of site-level landscape characteristics while accounting for sampling variation. Fisher occupancy was influenced positively by the proportion of conifer and mixed-wood forest within a 15-km2 grid cell and negatively associated with road density and the proportion of agriculture. Model-averaged predictions indicated high occupancy probabilities (>0.90) when road densities were low (<1 km/km2) and coniferous and mixed forest proportions were high (>0.50). Predicted occupancy ranged 0.41–0.67 in wildlife management units (WMUs) currently open to trapping, which could be used to guide a minimum occupancy threshold for opening new areas to trapping seasons. There were 5 WMUs that had been closed to trapping but had an average predicted occupancy of 0.52 (0.07 SE), and above the threshold of 0.41. These areas are currently under consideration by NYSDEC for opening a conservative harvest season. We demonstrate the use of occupancy modeling as an aid to management decision making when harvest-related data are unavailable and when budgetary constraints do not allow for capture–recapture studies to directly estimate density.
An optimal search theory, the so-called Lévy-flight foraging hypothesis, predicts that predators should adopt search strategies known as Lévy flights where prey is sparse and distributed ...unpredictably, but that Brownian movement is sufficiently efficient for locating abundant prey. Empirical studies have generated controversy because the accuracy of statistical methods that have been used to identify Lévy behaviour has recently been questioned. Consequently, whether foragers exhibit Lévy flights in the wild remains unclear. Crucially, moreover, it has not been tested whether observed movement patterns across natural landscapes having different expected resource distributions conform to the theory’s central predictions. Here we use maximum-likelihood methods to test for Lévy patterns in relation to environmental gradients in the largest animal movement data set assembled for this purpose. Strong support was found for Lévy search patterns across 14 species of open-ocean predatory fish (sharks, tuna, billfish and ocean sunfish), with some individuals switching between Lévy and Brownian movement as they traversed different habitat types. We tested the spatial occurrence of these two principal patterns and found Lévy behaviour to be associated with less productive waters (sparser prey) and Brownian movements to be associated with productive shelf or convergence-front habitats (abundant prey). These results are consistent with the Lévy-flight foraging hypothesis, supporting the contention that organism search strategies naturally evolved in such a way that they exploit optimal Lévy patterns.
Endothermy in vertebrates has been postulated to confer physiological and ecological advantages. In endothermic fish, niche expansion into cooler waters is correlated with specific physiological ...traits and is hypothesized to lead to greater foraging success and increased fitness. Using the seasonal co-occurrence of three tuna species in the eastern Pacific Ocean as a model system, we used cardiac gene expression data (as a proxy for thermal tolerance to low temperatures), archival tag data, and diet analyses to examine the vertical niche expansion hypothesis for endothermy in situ. Yellowfin, albacore, and Pacific bluefin tuna (PBFT) in the California Current system used more surface, mesopelagic, and deep waters, respectively. Expression of cardiac genes for calcium cycling increased in PBFT and coincided with broader vertical and thermal niche utilization. However, the PBFT diet was less diverse and focused on energy-rich forage fishes but did not show the greatest energy gains. Ecosystem-based management strategies for tunas should thus consider species-specific differences in physiology and foraging specialization.
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