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Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle, and in particular to identify candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used to evaluate the genetic structure of the GWH in relation to other cattle breeds by carrying out principal components and model-based clustering analyses. Secondly, the candidate genomic regions were identified by integrating the findings from: a) a genome-wide association study using GWH, other white headed breeds (Hereford and Simmental), and breeds with a non-white headed phenotype (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel, Dutch Belted, and Holstein Friesian); b) scans for specific signatures of selection in GWH cattle by comparison with four other Dutch traditional breeds (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel and Dutch Belted) and the commercial Holstein Friesian; and c) detection of candidate genes identified via these approaches. The alignment of the filtered reads to the reference genome (ARS-UCD1.2) resulted in a mean depth of coverage of 8.7X. After variant calling, the lowest number of breed-specific variants was detected in Holstein Friesian (148,213), and the largest in Deep Red (558,909). By integrating the results, we identified five genomic regions under selection on BTA4 (70.2–71.3 Mb), BTA5 (10.0–19.7 Mb), BTA20 (10.0–19.9 and 20.0–22.7 Mb), and BTA25 (0.5–9.2 Mb). These regions contain positional and functional candidate genes associated with retinal degeneration (e.g., CWC27 and CLUAP1), ultraviolet protection (e.g., ERCC8), and pigmentation (e.g. PDE4D) which are probably associated with the GWH specific pigmentation and/or eye-protective phenotypes, e.g. Ambilateral Circumocular Pigmentation (ACOP). Our results will assist in characterizing the molecular basis of GWH phenotypes and the biological implications of its adaptation. [ABSTRACT FROM AUTHOR]

Objectives: Altitude is one of the most demanding environmental pressures for human populations. Highlanders from Asia, America and Africa have been shown to exhibit different biological adaptations, but Oceanian populations remain understudied [Woolcock et al., 1972; Cotes et al., 1974; Senn et al., 2010]. We tested the hypothesis that highlanders phenotypically differ from lowlanders in Papua New Guinea, as a result of inhabiting the highest mountains in Oceania for at least 20,000 years. Materials and methods: We collected data for 13 different phenotypes related to altitude for 162 Papua New Guineans living at high altitude (Mont Wilhelm, 2,300–2,700 m above sea level (a.s.l.) and low altitude (Daru, <100m a.s.l.). Multilinear regressions were performed to detect differences between highlanders and lowlanders for phenotypic measurements related to body proportions, pulmonary function, and the circulatory system. Results: Six phenotypes were significantly different between Papua New Guinean highlanders and lowlanders. Highlanders show shorter height (p-value = 0.001), smaller waist circumference (p-value = 0.002), larger Forced Vital Capacity (FVC) (p-value = 0.008), larger maximal (p-value = 3.20e -4) and minimal chest depth (p-value = 2.37e -5) and higher haemoglobin concentration (p-value = 3.36e -4). Discussion: Our study reports specific phenotypes in Papua New Guinean highlanders potentially related to altitude adaptation. Similar to other human groups adapted to high altitude, the evolutionary history of Papua New Guineans appears to have also followed an adaptive biological strategy for altitude. [ABSTRACT FROM AUTHOR]

Where is the visual aesthetic preference rooted from and what's its relationship with the perceptual preference that is emerging early? Do young children naturally prefer some visual stimuli or do they learn to appreciate visual stimuli for aesthetic pleasure? Here, for young preschool children who are on the age that the preferences are developing, we provide findings from a study to show that the interplay between early emerging perceptual sensitivity and perceptual exposure promotes the emergence of preschool children's aesthetic preferences for simple visual patterns. Specifically in the experiments, 4-year-old children were exposed to either symmetric or asymmetric non-figurative forms in a perceptually demanding game; the group of children who received exposure to symmetric patterns showed aesthetic preference to the exposed patterns, while no preference was found in the group that received exposure to asymmetric patterns. The following recognition test then showed that the symmetric objects were differentiated better and remembered more clearly by the children, indicating that the symmetry was perceptually encoded better. These findings suggest that the early emerging perceptual sensitivity to 'good features' such as symmetry provides the prior cognitive prerequisites, allowing visual perceptual exposure to nourish the eventual formation of aesthetic preference. Thus, the preferences for aesthetic appreciation are likely the outcome of the interplay between biological and ecological adaptation. [ABSTRACT FROM AUTHOR]

Background: Metastatic breast cancer is the leading cause of cancer death in women, but the genomics of metastasis in breast cancer are poorly studied. Methods: We explored a set of 11,616 breast tumors, including 5,034 metastases, which had undergone targeted sequencing during standard clinical care. Results: Besides the known hotspot mutations in ESR1, we observed a metastatic enrichment of previously unreported, lower-prevalence mutations in the ligand-binding domain, implying that these mutations may also be functional. Furthermore, individual ESR1 hotspots are significantly enriched in specific metastatic tissues and histologies, suggesting functional differences between these mutations. Other alterations enriched across all metastases include loss of function of the CDK4 regulator CDKN1B, and mutations in the transcription factor CTCF. Mutations enriched at specific metastatic sites generally reflect biology of the target tissue and may be adaptations to growth in the local environment. These include PTEN and ASXL1 alterations in brain metastases and NOTCH1 alterations in skin. We observed an enrichment of KRAS, KEAP1, STK11 and EGFR mutations in lung metastases. However, the patterns of other mutations in these tumors indicate that these are misdiagnosed lung primaries rather than breast metastases. Conclusions: An order-of-magnitude increase in samples relative to previous studies allowed us to detect novel genomic characteristics of metastatic cancer and to expand and clarify previous findings. [ABSTRACT FROM AUTHOR]

In distributed speech recognition applications, the front-end device that stands for any handheld electronic device like smartphones and personal digital assistants (PDAs) captures the speech signal, extracts the speech features, and then sends the speech-feature vector sequence to the back-end server for decoding. Since the front-end mobile device has limited computation capacity, battery power and bandwidth, there exists a feasible strategy of reducing the frame rate of the speech-feature vector sequence to alleviate the drawback. Previously, we proposed a method for adjusting the transition probabilities of the hidden Markov model to enable it to address the degradation of recognition accuracy caused by the frame-rate mismatch between the input and the original model. The previous model adaptation method is referred to as the adapting-then-connecting approach that adapts each model individually and then connects the adapted models to form a word network for speech recognition. We have found that this model adaption approach introduces transitions that skip too many states and increase the number of insertion errors. In this study, we propose an improved model adaptation approach denoted as the connecting-then-adapting approach that first connects the individual models to form a word network and then adapts the connected network for speech recognition. This new approach calculates the transition matrix of a connected model, adapts the transition matrix of the connected model according to the frame rate, and then creates a transition arc for each transition probability. The new approach can better align the speech feature sequence with the states in the word network and therefore reduce the number of insertion errors. We conducted experiments to investigate the effectiveness of our new approach and analyzed the results with respect to insertion, deletion, and substitution errors. The experimental results indicate that the proposed new method obtains a better recognition rate than the old method. [ABSTRACT FROM AUTHOR]

It is important to understand if, and to what extent, the pig can utilize xylose as an energy source if xylanase releases free xylose in the small intestine. The experimental objectives were to determine the effects of industry-relevant dietary xylose concentrations and adaptation time on xylose retention efficiency and metabolism, diet digestibility and energy value, nitrogen balance, and hindgut fermentation. Forty-eight pigs were housed in metabolism crates and randomly assigned to one of four treatments with increasing D-xylose levels (n = 12/treatment) in 2 replications of a 22-d experiment with 3 collection periods. The control diet was xylose-free (0%), to which either 2, 4, or 8% D-xylose was added. Adaptation effects were assessed during three fecal and urine collection periods: d 5–7, 12–14, and 19–21. On d 22, pigs from the 0 and 8% treatments were euthanized; cecal and colon digesta were collected. Dietary xylose did not affect the total tract digestibility of dry matter, gross energy, or crude protein (P>0.10). Digesta short chain fatty acids concentrations and molar proportions and cecal pH were not different (P>0.10). This experiment utilized a targeted metabolomics approach to characterize and quantify urine xylose and metabolite excretion. Xylose retention decreased from 60% to 47% to 41% when pigs were fed diets containing 2, 4, or 8% xylose, respectively. In the 4 and 8% treatments, xylose retention was greater in the 2nd and 3rd collection periods compared to the 1st. A comprehensive pathway for xylose metabolism was proposed and D-threitol was confirmed as the major urinary metabolite of xylose. In conclusion, pigs can metabolize xylose, but with considerably lower efficiency than glucose, and may be able to adapt with time to utilize xylose more efficiently. [ABSTRACT FROM AUTHOR]

A central argument in the research on traditional knowledge, which persists in the scientific literature, is that the entrance of exotic plants in local medical systems is directly associated with acculturation. However, this logic has put an end for a long period to efforts to understand why such species have so successfully entered socio-ecological systems or even their real role in such systems. This study provides evidence that (1) in some socio-environmental contexts, exotic medicinal species usually confer greater adaptive advantages to local populations, and (2) despite their general importance, exotic species only excel in medical systems when cost-benefit ratio is favorable to them. Thus, in order to avoid the loss of knowledge about native plants and to ensure biocultural conservation, it is necessary to create strategies to amplify the advantages of these species. [ABSTRACT FROM AUTHOR]

The results of our recent study on mathematical modeling of microbial genome evolution indicate that, on average, genomes of bacteria and archaea evolve in the regime of mutation-selection balance defined by positive selection coefficients associated with gene acquisition that is counter-acted by the intrinsic deletion bias. This analysis was based on the strong assumption that parameters of genome evolution are universal across the diversity of bacteria and archaea, and yielded extremely low values of the selection coefficient. Here we further refine the modeling approach by taking into account evolutionary factors specific for individual groups of microbes using two independent fitting strategies, an ad hoc hard fitting scheme and a mixture model. The resulting estimate of the mean selection coefficient of s∼10−10 associated with the gain of one gene implies that, on average, acquisition of a gene is beneficial, and that microbial genomes typically evolve under a weak selection regime that might transition to strong selection in highly abundant organisms with large effective population sizes. The apparent selective pressure towards larger genomes is balanced by the deletion bias, which is estimated to be consistently greater than unity for all analyzed groups of microbes. The estimated values of s are more realistic than the lower values obtained previously, indicating that global and group-specific evolutionary factors synergistically affect microbial genome evolution that seems to be driven primarily by adaptation to existence in diverse niches. [ABSTRACT FROM AUTHOR]

Pregnancy and lactation are physiological periods that result in an increased metabolic demand that, if not satisfied, could provoke a threat to homeostasis. In this study changes in the values of Non-Esterified Fatty Acids (NEFA) and β-hydroxybutyrate (BHB), glucose, insulin, thyroid hormones, milk composition and yield were investigated in buffaloes during the late pregnancy and early lactation. From a total of 50 buffaloes, blood samples were collected -7±5 days before expected calving; +7±5; +30±5 and +50±5 days post-partum; milk samples were collected at the same post-partum time points. On serum samples, the values of Non-Esterified Fatty Acids (NEFA), β-hydroxybutyrate (BHB), glucose, insulin, Triiodothyronine (T3), Thyroxine (T4) and Thyroid-stimulating hormone (TSH) were evaluated. On milk, fat %, protein %, lactose %, somatic cells score (SCS), milk yield and daily milk production (DMP) were assessed. Peripartum period significantly influenced all studied parameters (P<0.05). Milk constituents and productivity statistically changed throughout monitoring period (P<0.005). Milk yield resulted positively correlated with insulin and TSH values, negatively correlated with NEFA and BHB. Insulin was negatively correlated with lactose % and positively correlated with SCS. The obtained results showed that the peripartum period and lactation are accompanied by marked changes in some biochemical variables and in the thyroid hormones values in Italian Mediterranean Buffaloes. Moreover, the relationship found between TSH values and milk yield seems to suggest a possible role of thyroid gland on the maintenance of lactogenesis. This study underlines the importance of monitoring the hormonal status of buffalo during the transition period in order to understand when adjustments of regulatory mechanisms break through physiological limits predisposing the buffalo to metabolic problems. [ABSTRACT FROM AUTHOR]

Objective: To examine the effects of socioecological factors on multiple communicable diseases across Vietnam. Methods: We used the Moran’s I tests to evaluate spatial clusters of diseases and applied multilevel negative binomial regression models using the Bayesian framework to analyse the association between socioecological factors and the diseases queried by oral, airborne, vector-borne, and animal transmission diseases. Results and significance: The study found that oral-transmission diseases were spatially distributed across the country; whereas, the airborne-transmission diseases were more clustered in the Northwest and vector-borne transmission diseases were more clustered in the South. Most of diseases were sensitive with climatic factors. For instance, a 1°C increase in average temperature is significantly associated with 0.4% (95CI, 0.3–0.5), 2.5% (95%CI, 1.4–3.6), 0.9% (95%CI, 0.6–1.4), 1.1% (95%CI), 5% (95%CI, 3-.7.4), 0.4% (95%CI, 0.2–0.7), and 2% (95%CI, 1.5–2.8) increase in risk of diarrhoea, shigellosis, mumps, influenza, dengue, malaria, and rabies respectively. The influences of socio-economic factors on risk of communicable diseases are varied by factors with the biggest influence of population density. The research findings reflect an important implication for the climate change adaptation strategies of health sectors. A development of weather-based early warning systems should be considered to strengthen communicable disease prevention in Vietnam. [ABSTRACT FROM AUTHOR]

We show that genetic recombination can be a powerful mechanism for escaping suboptimal peaks. Recent studies of empirical fitness landscapes reveal complex gene interactions and multiple peaks. However, classical work on recombination largely ignores the effect of complex gene interactions. Briefly, we restrict to fitness landscapes where the global peak is difficult to access. If the optimal genotype can be generated by shuffling genes present in the population, then recombination will produce the genotype. If, in addition, recombination is sufficiently rare, then the proportion of the genotype is expected to increase. Specifically, we consider landscapes where shuffling of suboptimal peak genotypes can produce the global peak genotype. The advantage of recombination we identify has no correspondence for 2-locus systems or for smooth landscapes. The effect of recombination indicated is sometimes extreme, also for rare recombination, in the sense that shutting off recombination could result in the organism failing to adapt. A standard question about recombination is whether the mechanism tends to accelerate or decelerate adaptation. However, we argue that extreme effects may be more important than how the majority falls. In a limited sense, our result can be considered a support for Sewall Wright’s view that adaptation sometimes works better in subdivided populations. [ABSTRACT FROM AUTHOR]

We evaluate the world terrestrial network of protected areas (PAs) for its partnership potential in responding to climate change. That is, if a PA engaged in collaborative, trans-boundary management of species, by investing in conservation partnerships with neighboring areas, what climate change adaptation benefits might accrue? We consider core tenets of conservation biology related to protecting large areas with high environmental heterogeneity and low climate change velocity and ask how a series of biodiversity adaptation indicators change across spatial scales encompassing potential PA and non-PA partners. Less than 1% of current world terrestrial PAs equal or exceed the size of established and successful conservation partnerships. Partnering at this scale would increase the biodiversity adaptation indicators by factors up to two orders of magnitude, compared to a null model in which each PA is isolated. Most partnership area surrounding PAs is comprised of non-PAs (70%), indicating the importance of looking beyond the current network of PAs when promoting climate change adaptation. Given monumental challenges with PA-based species conservation in the face of climate change, partnerships provide a logical and achievable strategy for helping areas adapt. Our findings identify where strategic partnering efforts in highly vulnerable areas of the world may prove critical in safeguarding biodiversity. [ABSTRACT FROM AUTHOR]

Phosphorus, an essential element for all living organisms, is a limiting nutrient in many regions of the ocean due to its fast recycling. Changes in phosphate (Pi) availability in aquatic systems affect diatom growth and productivity. We investigated the early adaptive mechanisms in the marine diatom Phaeodactylum tricornutum to P deprivation using a combination of transcriptomics, metabolomics, physiological and biochemical experiments. Our analysis revealed strong induction of gene expression for proteins involved in phosphate acquisition and scavenging, and down-regulation of processes such as photosynthesis, nitrogen assimilation and nucleic acid and ribosome biosynthesis. P deprivation resulted in alterations of carbon allocation through the induction of the pentose phosphate pathway and cytosolic gluconeogenesis, along with repression of the Calvin cycle. Reorganization of cellular lipids was indicated by coordinated induced expression of phospholipases, sulfolipid biosynthesis enzymes and a putative betaine lipid biosynthesis enzyme. A comparative analysis of nitrogen- and phosphorus-deprived P. tricornutum revealed both common and distinct regulation patterns in response to phosphate and nitrate stress. Regulation of central carbon metabolism and amino acid metabolism was similar, whereas unique responses were found in nitrogen assimilation and phosphorus scavenging in nitrogen-deprived and phosphorus-deprived cells, respectively. [ABSTRACT FROM AUTHOR]

Rubisco (Ribulose-1, 5-biphosphate carboxylase/oxygenase) is the most important enzyme on earth, catalyzing the first step of photosynthetic CO2 fixation. So, without it, there would be no storing of the sun’s energy in plants. Molecular adaptation of Rubisco to C4 photosynthetic pathway has attracted a lot of attention. C4 plants, which comprise less than 5% of land plants, have evolved more efficient photosynthesis compared to C3 plants. Interestingly, a large number of independent transitions from C3 to C4 phenotype have occurred. Each time, the Rubisco enzyme has been subject to similar changes in selective pressure, thus providing an excellent model for convergent evolution at the molecular level. Molecular adaptation is often identified with positive selection and is typically characterized by an elevated ratio of non-synonymous to synonymous substitution rate (dN/dS). However, convergent adaptation is expected to leave a different molecular signature, taking the form of repeated transitions toward identical or similar amino acids. Here, we used a previously introduced codon-based differential-selection model to detect and quantify consistent patterns of convergent adaptation in Rubisco in eudicots. We further contrasted our results with those obtained by classical codon models based on the estimation of dN/dS. We found that the two classes of models tend to select distinct, although overlapping, sets of positions. This discrepancy in the results illustrates the conceptual difference between these models while emphasizing the need to better discriminate between qualitatively different selective regimes, by using a broader class of codon models than those currently considered in molecular evolutionary studies. [ABSTRACT FROM AUTHOR]

Butana and Kenana are two types of zebu cattle found in Sudan. They are unique amongst African indigenous zebu cattle because of their high milk production. Aiming to understand their genome structure, we genotyped 25 individuals from each breed using the Illumina BovineHD Genotyping BeadChip. Genetic structure analysis shows that both breeds have an admixed genome composed of an even proportion of indicine (0.75 ± 0.03 in Butana, 0.76 ± 0.006 in Kenana) and taurine (0.23 ± 0.009 in Butana, 0.24 ± 0.006 in Kenana) ancestries. We also observe a proportion of 0.02 to 0.12 of European taurine ancestry in ten individuals of Butana that were sampled from cattle herds in Tamboul area suggesting local crossbreeding with exotic breeds. Signatures of selection analyses (iHS and Rsb) reveal 87 and 61 candidate positive selection regions in Butana and Kenana, respectively. These regions span genes and quantitative trait loci (QTL) associated with biological pathways that are important for adaptation to marginal environments (e.g., immunity, reproduction and heat tolerance). Trypanotolerance QTL are intersecting candidate regions in Kenana cattle indicating selection pressure acting on them, which might be associated with an unexplored level of trypanotolerance in this cattle breed. Several dairy traits QTL are overlapping the identified candidate regions in these two zebu cattle breeds. Our findings underline the potential to improve dairy production in the semi-arid pastoral areas of Africa through breeding improvement strategy of indigenous local breeds. [ABSTRACT FROM AUTHOR]

Species may become invasive after introduction to a new range because phenotypic traits pre-adapt them to spread and become dominant. In addition, adaptation to novel selection pressures in the introduced range may further increase their potential to become invasive. The diploid Leucanthemum vulgare and the tetraploid L. ircutianum are native to Eurasia and have been introduced to North America, but only L. vulgare has become invasive. To investigate whether phenotypic differences between the two species in Eurasia could explain the higher abundance of L. vulgare in North America and whether rapid evolution in the introduced range may have contributed to its invasion success, we grew 20 L. vulgare and 21 L. ircutianum populations from Eurasia and 21 L. vulgare populations from North America under standardized conditions and recorded performance and functional traits. In addition, we recorded morphological traits to investigate whether the two closely related species can be clearly distinguished by morphological means and to what extent morphological traits have changed in L. vulgare post-introduction. We found pronounced phenotypic differences between L. vulgare and L. ircutianum from the native range as well as between L. vulgare from the native and introduced ranges. The two species differed significantly in morphology but only moderately in functional or performance traits that could have explained the higher invasion success of L. vulgare in North America. In contrast, leaf morphology was similar between L. vulgare from the native and introduced range, but plants from North America flowered later, were larger and had more and larger flower heads than those from Eurasia. In summary, we found litte evidence that specific traits of L. vulgare may have pre-adapted this species to become more invasive than L. ircutianum, but our results indicate that rapid evolution in the introduced range likely contributed to the invasion success of L. vulgare. [ABSTRACT FROM AUTHOR]

Nothosaurs form a subclade of the secondarily marine Sauropterygia that was well represented in late Early to early Late Triassic marine ecosystems. Here we present and discuss the internal skull anatomy of the small piscivorous nothosaur Nothosaurus marchicus from coastal to shallow marine Lower Muschelkalk deposits (Anisian) of Winterswijk, The Netherlands, which represents the oldest sauropterygian endocast visualized to date. The cranial endocast is only partially encapsulated by ossified braincase elements. Cranial flattening and lateral constriction by hypertrophied temporal musculature grant the brain a straight, tubular geometry that lacks particularly well-developed cerebral lobes but does potentially involve distinguishable optic lobes, suggesting vision may have represented an important sense during life. Despite large orbit size, the circuitous muscular pathway linking the basisphenoidal and orbital regions indicates poor oculomotor performance. This suggests a rather fixed ocular orientation, although eye placement and neck manoeuvrability could have enabled binocular if not stereoscopic vision. The proportionally large dorsal projection of the braincase endocast towards the well-developed pineal foramen advocates substantial dependence on the corresponding pineal system in vivo. Structures corroborating keen olfactory or acoustic senses were not identified. The likely atrophied vomeronasal organ argues against the presence of a forked tongue in Nothosaurus, and the relative positioning of external and internal nares contrasts respiratory configurations proposed for pistosauroid sauropterygians. The antorbital domain furthermore accommodates a putative rostral sensory plexus and pronounced lateral nasal glands that were likely exapted as salt glands. Previously proposed nothosaurian ‘foramina eustachii’ arose from architectural constraints on braincase development rather than representing functional foramina. Several modifications to brain shape and accessory organs were achieved through heterochronic development of the cranium, particularly the braincase. In summary, the cranium of Nothosaurus marchicus reflects important physiological and neurosensory adaptations that enabled the group’s explosive invasion of shallow marine habitats in the late Early Triassic. [ABSTRACT FROM AUTHOR]

Adenylation domains CcbC and LmbC control the specific incorporation of amino acid precursors in the biosynthesis of lincosamide antibiotics celesticetin and lincomycin. Both proteins originate from a common L-proline-specific ancestor, but LmbC was evolutionary adapted to use an unusual substrate, (2S,4R)-4-propyl-proline (PPL). Using site-directed mutagenesis of the LmbC substrate binding pocket and an ATP-[32P]PPi exchange assay, three residues, G308, A207 and L246, were identified as crucial for the PPL activation, presumably forming together a channel of a proper size, shape and hydrophobicity to accommodate the propyl side chain of PPL. Subsequently, we experimentally simulated the molecular evolution leading from L-proline-specific substrate binding pocket to the PPL-specific LmbC. The mere change of three amino acid residues in originally strictly L-proline-specific CcbC switched its substrate specificity to prefer PPL and even synthetic alkyl-L-proline derivatives with prolonged side chain. This is the first time that such a comparative study provided an evidence of the evolutionary relevant adaptation of the adenylation domain substrate binding pocket to a new sterically different substrate by a few point mutations. The herein experimentally simulated rearrangement of the substrate binding pocket seems to be the general principle of the de novo genesis of adenylation domains’ unusual substrate specificities. However, to keep the overall natural catalytic efficiency of the enzyme, a more comprehensive rearrangement of the whole protein would probably be employed within natural evolution process. [ABSTRACT FROM AUTHOR]

A warming climate increases thermal inputs to lakes with potential implications for water quality and aquatic ecosystems. In a previous study, we used a dynamic water column temperature and mixing simulation model to simulate chronic (7-day average) maximum temperatures under a range of potential future climate projections at selected sites representative of different U.S. regions. Here, to extend results to lakes where dynamic models have not been developed, we apply a novel machine learning approach that uses Gaussian Process regression to describe the model response surface as a function of simplified lake characteristics (depth, surface area, water clarity) and climate forcing (winter and summer air temperatures and potential evapotranspiration). We use this approach to extrapolate predictions from the simulation model to the statistical sample of U.S. lakes in the National Lakes Assessment (NLA) database. Results provide a national-scale scoping assessment of the potential thermal risk to lake water quality and ecosystems across the U.S. We suggest a small fraction of lakes will experience less risk of summer thermal stress events due to changes in stratification and mixing dynamics, but most will experience increases. The percentage of lakes in the NLA with simulated 7-day average maximum water temperatures in excess of 30°C is projected to increase from less than 2% to approximately 22% by the end of the 21st century, which could significantly reduce the number of lakes that can support cold water fisheries. Site-specific analysis of the full range of factors that influence thermal profiles in individual lakes is needed to develop appropriate adaptation strategies. [ABSTRACT FROM AUTHOR]

Anthropogenic threats to natural systems can be exacerbated due to connectivity between marine, freshwater, and terrestrial ecosystems, complicating the already daunting task of governance across the land-sea interface. Globalization, including new access to markets, can change social-ecological, land-sea linkages via livelihood responses and adaptations by local people. As a first step in understanding these trans-ecosystem effects, we examined exit and entry decisions of artisanal fishers and smallholder farmers on the rapidly globalizing Caribbean coast of Nicaragua. We found that exit and entry decisions demonstrated clear temporal and spatial patterns and that these decisions differed by livelihood. In addition to household characteristics, livelihood exit and entry decisions were strongly affected by new access to regional and global markets. The natural resource implications of these livelihood decisions are potentially profound as they provide novel linkages and spatially-explicit feedbacks between terrestrial and marine ecosystems. Our findings support the need for more scientific inquiry in understanding trans-ecosystem tradeoffs due to linked-livelihood transitions as well as the need for a trans-ecosystem approach to natural resource management and development policy in rapidly changing coastal regions. [ABSTRACT FROM AUTHOR]

Opuntia plants grow naturally in areas where temperatures are extreme and highly variable in the day during the entire year. These plants survive through different adaptations to respond to adverse environmental conditions. Despite this capability, it is unknown how CAM photosynthetic activity and growth in Opuntia plantlets is affected by constant heat or cold. Therefore, the main objective of this research was to evaluate the short-term effect of high (40°C) and low (4°C) continuous temperatures on the photosynthetic efficiency, the organic acid content (malic acid) and the relative growth rate (RGR) in seven-month-old Opuntia streptacantha plantlets during 5, 10, and 15 days. Chlorophyll fluorescence analysis allowed us to determine that high temperatures negatively impact the photosynthetic efficiency of O. streptacantha plantlets, which exhibited the lowest values of maximum quantum efficiency of the photosystem II (Fv/Fm = 52%, Fv/F0 = 85%), operational quantum yield of PS (ΦPSII = 65%) and relative electron transport rate (rETR = 65%), as well as highest values of basal fluorescence (F0 = 226%) during 15 days of treatment. Similarly, low temperatures decreased Fv/Fm (16%), Fv/F0 (50%), ΦPSII and rETR (16%). High temperatures also decreased nocturnal acidification in approximately 34–50%, whereas low temperatures increased it by 30–36%. Additionally, both continuous temperatures affected drastically diurnal consumption of malic acid, which was related to a significant RGR inhibition, where the specific photosynthetic structure area component was the most affected. Our results allowed determining that, despite the high tolerance to extreme temperatures described for Opuntia plants, young individuals of O. streptacantha suffered photosynthetic impairment that led to the inhibition of their growth. Thus, the main findings reported in this study can help to predict the potential impact of climatic change on the establishment and survival of succulent species of arid and semiarid regions of Mexico. [ABSTRACT FROM AUTHOR]

Freezing is a defensive response to acute stress that is associated with coping and alterations in attentional processing. However, it remains unclear whether individuals in high risk professions, who are skilled at making rapid decisions in emergency situations, show altered threat-induced freezing. Here we investigated the effect of incident experience in a high risk profession on freezing. Additionally, we explored whether any effect of incident experience on freezing would be different for profession-related and -unrelated threat. Forty experienced and inexperienced firefighters were presented neutral, pleasant, related-unpleasant, and unrelated-unpleasant pictures in a passive viewing task. Postural sway and heart rate were assessed to determine freezing. Both postural and heart rate data evidenced reduced freezing upon unpleasant pictures in the experienced versus the inexperienced group. Relatedness of the unpleasant pictures did not modulate these effects. These findings indicate that higher incident experience relates to decreased threat-induced freezing, at least in a passive task context. This might suggest that primary defense responses are malleable through experience. Finally, these findings demonstrate the potential of using animal to human translational approaches to investigate defensive behaviors in relation to incident experience in high risk professions and stimulate future research on the role of freezing in resilience and coping. [ABSTRACT FROM AUTHOR]

Phylogenetic analysis by maximum likelihood (PAML) has become the standard approach to study positive selection at the molecular level, but other methods may provide complementary ways to identify amino acid replacements associated with particular conditions. Here, we compare results of the decision tree (DT) model method with ones of PAML using the key photosynthetic enzyme RuBisCO as a model system to study molecular adaptation to particular ecological conditions in oaks (Quercus). We sequenced the chloroplast rbcL gene encoding RuBisCO large subunit in 158 Quercus species, covering about a third of the global genus diversity. It has been hypothesized that RuBisCO has evolved differentially depending on the environmental conditions and leaf traits governing internal gas diffusion patterns. Here, we show, using PAML, that amino acid replacements at the residue positions 95, 145, 251, 262 and 328 of the RuBisCO large subunit have been the subject of positive selection along particular Quercus lineages associated with the leaf traits and climate characteristics. In parallel, the DT model identified amino acid replacements at sites 95, 219, 262 and 328 being associated with the leaf traits and climate characteristics, exhibiting partial overlap with the results obtained using PAML. [ABSTRACT FROM AUTHOR]

The brain constantly adjusts perceived duration based on the recent event history. One such lab phenomenon is subjective time expansion induced in an oddball paradigm (“oddball chronostasis”), where the duration of a distinct item (oddball) appears subjectively longer when embedded in a series of other repeated items (standards). Three hypotheses have been separately proposed but it remains unresolved which or all of them are true: 1) attention prolongs oddball duration, 2) repetition suppression reduces standards duration, and 3) accumulative temporal preparation (anticipation) expedites the perceived item onset so as to lengthen its duration. We thus conducted critical systematic experiments to dissociate the relative contribution of all hypotheses, by orthogonally manipulating sequences types (repeated, ordered, or random) and target serial positions. Participants’ task was to judge whether a target lasts shorter or longer than its reference. The main finding was that a random item sequence still elicited significant chronostasis even though each item was odd. That is, simply being a target draws top-down attention and induces chronostasis. In Experiments 1 (digits) and 2 (orientations), top-down attention explained about half of the effect while saliency/adaptation explained the other half. Additionally, for non-repeated (ordered and random) sequence types, a target with later serial position still elicited stronger chronostasis, favoring a temporal preparation over a repetition suppression account. By contrast, in Experiment 3 (colors), top-down attention was likely the sole factor. Consequently, top-down attention is necessary and sometimes sufficient to explain oddball chronostasis; saliency/adaptation and temporal preparation are contingent factors. These critical boundary conditions revealed in our study serve as quantitative constraints for neural models of duration perception. [ABSTRACT FROM AUTHOR]

Erythrocyte-binding antigens (EBAs) and P. falciparum reticulocyte-binding homologue proteins (PfRhs) are two important protein families that can vary in expression and utilization by P. falciparum to evade inhibitory antibodies. We evaluated antibodies at repeated time-points among individuals living in an endemic region in Nigeria over almost one year against these vaccine candidates. Antibody levels against EBA140, EBA175, EBA181, PfRh2, PfRh4, and MSP2, were measured by ELISA. We also used parasites with disrupted EBA140, EBA175 and EBA181 genes to show that all these were targets of invasion inhibitory antibodies. However, antigenic targets of inhibitory antibodies were not stable and changed substantially over time in most individuals, independent of age. Antibodies levels measured by ELISA also varied within and between individuals over time and the antibodies against EBA181, PfRh2 and MSP2 declined more rapidly in younger individuals (≤15 years) compared with older (>15). The breadth of high antibody responses over time was more influenced by age than by the frequency of infection. High antibody levels were associated with a more stable invasion inhibitory response, which could indicate that during the long process of formation of immunity, many changes not only in levels but also in functional responses are needed. This is an important finding in understanding natural immunity against malaria, which is essential for making an efficacious vaccine. [ABSTRACT FROM AUTHOR]

When laboratory dogs are rehomed into private households, they experience an extreme change in their life situation. They leave their familiar, limited environment in the research facility and encounter a multitude of animate and inanimate stimuli in their new home. Although literature reports have described the experiences with rehoming as being mostly positive, scientific observations of the dogs in everyday situations have not been done. Hence, we conducted an observational test with 74 laboratory beagles 6 weeks after adoption in their new homes. This test included standardized tasks and elements; the dogs were observed during specific interactions with their new owners and during a walk. Furthermore, the owners of these 74 and of 71 additional dogs participated in standardized phone interviews 1 and 12 weeks after adoption, during which they answered questions about the dogs’ behavior in everyday situations. In the observational test, the dogs behaved mostly friendly towards humans and dogs, were tolerant during manipulations by the owner and were relaxed during the walk, even in traffic. Eighty percent (of n = 71) of the dogs walked well behaved on the leash without pulling. According to the interviews, the majority of the dogs showed desired, friendly and relaxed behavior, and the survey results reflected the bonding between dog and owner. The analysis of a possible influence of various factors (age, sex, origin, etc.) using mixed regression models confirmed the results from two previous behavior tests and interviews. Specifically, dogs that had been bred in the research facility scored significantly better than dogs that the research facility had purchased from commercial laboratory dog breeders (p = 0.0113). The results of this study demonstrate a successful adaptation of the rehomed beagles to their new life situation. [ABSTRACT FROM AUTHOR]

Objective: To determine the effects of exogenous glucagon-like peptide-2 (GLP-2), with or without massive distal bowel resection, on adaptation of jejunal mucosa, enteric neurons, gut hormones and tissue reserves in rats. Background: GLP-2 is a gut hormone known to be trophic for small bowel mucosa, and to mimic intestinal adaptation in short bowel syndrome (SBS). However, the effects of exogenous GLP-2 and SBS on enteric neurons are unclear. Methods: Sprague Dawley rats were randomized to four treatments: Transected Bowel (TB) (n = 8), TB + GLP-2 (2.5 nmol/kg/h, n = 8), SBS (n = 5), or SBS + GLP-2 (2.5 nmol/kg/h, n = 9). SBS groups underwent a 60% jejunoileal resection with cecectomy and jejunocolic anastomosis. All rats were maintained on parenteral nutrition for 7 d. Parameters measured included gut morphometry, qPCR for hexose transporter (SGLT-1, GLUT-2, GLUT-5) and GLP-2 receptor mRNA, whole mount immunohistochemistry for neurons (HuC/D, VIP, nNOS), plasma glucose, gut hormones, and body composition. Results: Resection increased the proportion of nNOS immunopositive myenteric neurons, intestinal muscularis propria thickness and crypt cell proliferation, which were not recapitulated by GLP-2 therapy. Exogenous GLP-2 increased jejunal mucosal surface area without affecting enteric VIP or nNOS neuronal immunopositivity, attenuated resection-induced reductions in jejunal hexose transporter abundance (SGLT-1, GLUT-2), increased plasma amylin and decreased peptide YY concentrations. Exogenous GLP-2 attenuated resection-induced increases in blood glucose and body fat loss. Conclusions: Exogenous GLP-2 stimulates jejunal adaptation independent of enteric neuronal VIP or nNOS changes, and has divergent effects on plasma amylin and peptide YY concentrations. The novel ability of exogenous GLP-2 to modulate resection-induced changes in peripheral glucose and lipid reserves may be important in understanding the whole-body response following intestinal resection, and is worthy of further study. [ABSTRACT FROM AUTHOR]

Rhizocephala, a group of parasitic castrators of other crustaceans, shows remarkable morphological adaptations to their lifestyle. The adult female parasite consists of a body that can be differentiated into two distinct regions: a sac-like structure containing the reproductive organs (the externa), and a trophic, root like system situated inside the hosts body (the interna). Parasitism results in the castration of their hosts, achieved by absorbing the entire reproductive energy of the host. Thus, the ratio of the host and parasite sizes is crucial for the understanding of the parasite’s energetic cost. Using advanced imaging methods (micro-CT in conjunction with 3D modeling), we measured the volume of parasitic structures (externa, interna, egg mass, egg number, visceral mass) and the volume of the entire host. Our results show positive correlations between the volume of (1) entire rhizocephalan (externa + interna) and host body, (2) rhizocephalan externa and host body, (3) rhizocephalan visceral mass and rhizocephalan body, (4) egg mass and rhizocephalan externa, (5) rhizocephalan egg mass and their egg number. Comparing the rhizocephalan Sylon hippolytes, a parasite of caridean shrimps, and representatives of Peltogaster, parasites of hermit crabs, we could match their different traits on a reconstructed relationship. With this study we add new and significant information to our global understanding of the evolution of parasitic castrators, of interactions between a parasitic castrator and its host and of different parasitic strategies within parasitic castrators exemplified by rhizocephalans. [ABSTRACT FROM AUTHOR]

Although the “adaptive” strategy used by Escherichia coli has dominated our understanding of bacterial chemotaxis, the environmental conditions under which this strategy emerged is still poorly understood. In this work, we study the performance of various chemotactic strategies under a range of stochastic time- and space-varying attractant distributions in silico. We describe a novel “speculator” response in which the bacterium compare the current attractant concentration to the long-term average; if it is higher then they tumble persistently, while if it is lower than the average, bacteria swim away in search of more favorable conditions. We demonstrate how this response explains the experimental behavior of aerobically-grown Rhodobacter sphaeroides and that under spatially complex but slowly-changing nutrient conditions the speculator response is as effective as the adaptive strategy of E. coli. [ABSTRACT FROM AUTHOR]

It has been proposed that Antarctic environments select microorganisms with unique biochemical adaptations, based on the tenet ‘Everything is everywhere, but, the environment selects’ by Baas-Becking. However, this is a hypothesis that has not been extensively evaluated. This study evaluated the fundamental prediction contained in this hypothesis—in the sense that species are structured in the landscape according to their local habitats-, using as study model the phylogenetic diversity of the culturable bacteria of Fildes Peninsula (King George Island, Antarctica). Eighty bacterial strains isolated from 10 different locations in the area, were recovered. Based on phylogenetic analysis of 16S rRNA gene sequences, the isolates were grouped into twenty-six phylotypes distributed in three main clades, of which only six are exclusive to Antarctica. Results showed that phylotypes do not group significantly by habitat type; however, local habitat types had phylogenetic signal, which support the phylogenetic niche conservatism hypothesis and not a selective role of the environment like the Baas-Becking hypothesis suggests. We propose that, more than habitat selection resulting in new local adaptations and diversity, local historical colonization and species sorting (i.e. differences in speciation and extinction rates that arise by interaction of species level traits with the environment) play a fundamental role on the culturable bacterial diversity in Antarctica. [ABSTRACT FROM AUTHOR]

Hibernators have a distinctive ability to adapt to seasonal changes of body temperature in a range between 37°C and near freezing, exhibiting, among other features, a unique reversibility of cardiac contractility. The adaptation of myocardial contractility in hibernation state relies on alterations of excitation contraction coupling, which becomes less-dependent from extracellular Ca2+ entry and is predominantly controlled by Ca2+ release from sarcoplasmic reticulum, replenished by the Ca2+-ATPase (SERCA). We found that the specific SERCA inhibitor cyclopiazonic acid (CPA), in contrast to its effect in papillary muscles (PM) from rat hearts, did not reduce but rather potentiated contractility of PM from hibernating ground squirrels (GS). In GS ventricles we identified drastically elevated, compared to rats, expression of Orai1, Stim1 and Trpc1/3/4/5/6/7 mRNAs, putative components of store operated Ca2+ channels (SOC). Trpc3 protein levels were found increased in winter compared to summer GS, yet levels of Trpc5, Trpc6 or Trpc7 remained unchanged. Under suppressed voltage-dependent K+, Na+ and Ca2+ currents, the SOC inhibitor 2-aminoethyl diphenylborinate (2-APB) diminished whole-cell membrane currents in isolated cardiomyocytes from hibernating GS, but not from rats. During cooling-reheating cycles (30°C–7°C–30°C) of ground squirrel PM, 2-APB did not affect typical CPA-sensitive elevation of contractile force at low temperatures, but precluded the contractility at 30°C before and after the cooling. Wash-out of 2-APB reversed PM contractility to control values. Thus, we suggest that SOC play a pivotal role in governing the ability of hibernator hearts to maintain their function during the transition in and out of hibernating states. [ABSTRACT FROM AUTHOR]

Many studies on the microbiome of animals have been reported but a comprehensive analysis is lacking. Here we present a meta-analysis on the microbiomes of arthropods and their terrestrial habitat, focusing on the functional profile of bacterial communities derived from metabolic traits that are essential for microbial life. We report a detailed analysis of probably the largest set of biochemically defined functional traits ever examined in microbiome studies. This work deals with the phylum proteobacteria, which is usually dominant in marine and terrestrial environments and covers all functions associated with microbiomes. The considerable variation in the distribution and abundance of proteobacteria in microbiomes has remained fundamentally unexplained. This analysis reveals discrete functional groups characteristic for adaptation to anaerobic conditions, which appear to be defined by environmental filtering of taxonomically related taxa. The biochemical diversification of the functional groups suggests an evolutionary trajectory in the structure of arthropods’ microbiome, from metabolically versatile to specialized proteobacterial organisms that are adapted to complex environments such as the gut of social insects. Bacterial distribution in arthropods’ microbiomes also shows taxonomic clusters that do not correspond to functional groups and may derive from other factors, including common contaminants of soil and reagents. [ABSTRACT FROM AUTHOR]

The detection of genomic regions involved in local adaptation is an important topic in current population genetics. There are several detection strategies available depending on the kind of genetic and demographic information at hand. A common drawback is the high risk of false positives. In this study we introduce two complementary methods for the detection of divergent selection from populations connected by migration. Both methods have been developed with the aim of being robust to false positives. The first method combines haplotype information with inter-population differentiation (FST). Evidence of divergent selection is concluded only when both the haplotype pattern and the FST value support it. The second method is developed for independently segregating markers i.e. there is no haplotype information. In this case, the power to detect selection is attained by developing a new outlier test based on detecting a bimodal distribution. The test computes the FST outliers and then assumes that those of interest would have a different mode. We demonstrate the utility of the two methods through simulations and the analysis of real data. The simulation results showed power ranging from 60–95% in several of the scenarios whilst the false positive rate was controlled below the nominal level. The analysis of real samples consisted of phased data from the HapMap project and unphased data from intertidal marine snail ecotypes. The results illustrate that the proposed methods could be useful for detecting locally adapted polymorphisms. The software HacDivSel implements the methods explained in this manuscript. [ABSTRACT FROM AUTHOR]

Complex foldings of the vaginal wall are unique to some cetaceans and artiodactyls and are of unknown function(s). The patterns of vaginal length and cumulative vaginal fold length were assessed in relation to body length and to each other in a phylogenetic context to derive insights into functionality. The reproductive tracts of 59 female cetaceans (20 species, 6 families) were dissected. Phylogenetically-controlled reduced major axis regressions were used to establish a scaling trend for the female genitalia of cetaceans. An unparalleled level of vaginal diversity within a mammalian order was found. Vaginal folds varied in number and size across species, and vaginal fold length was positively allometric with body length. Vaginal length was not a significant predictor of vaginal fold length. Functional hypotheses regarding the role of vaginal folds and the potential selection pressures that could lead to evolution of these structures are discussed. Vaginal folds may present physical barriers, which obscure the pathway of seawater and/or sperm travelling through the vagina. This study contributes broad insights to the evolution of reproductive morphology and aquatic adaptations and lays the foundation for future functional morphology analyses. [ABSTRACT FROM AUTHOR]

High altitude flight in rarefied, extremely cold and hypoxic air is a very challenging activity. Only a few species of birds can achieve it. Hitherto, the structure of the lungs of such birds has not been studied. This is because of the rarity of such species and the challenges of preparing well-fixed lung tissue. Here, it was posited that in addition to the now proven physiological adaptations, high altitude flying birds will also have acquired pulmonary structural adaptations that enable them to obtain the large amounts of oxygen (O2) needed for flight at high elevation, an environment where O2 levels are very low. The Andean goose (Chloephaga melanoptera) normally resides at altitudes above 3000 meters and flies to elevations as high as 6000 meters where O2 becomes limiting. In this study, its lung was morphologically- and morphometrically investigated. It was found that structurally the lungs are exceptionally specialized for gas exchange. Atypically, the infundibulae are well-vascularized. The mass-specific volume of the lung (42.8 cm3.kg-1), the mass-specific respiratory surface area of the blood-gas (tissue) barrier (96.5 cm2.g-1) and the mass-specific volume of the pulmonary capillary blood (7.44 cm3.kg-1) were some of the highest values so far reported in birds. The pulmonary structural specializations have generated a mass-specific total (overall) pulmonary morphometric diffusing capacity of the lung for oxygen (DLo2) of 0.119 mlO2.sec-1.mbar-1.kg-1, a value that is among some of the highest ones in birds that have been studied. The adaptations of the lung of the Andean goose possibly produce the high O2 conductance needed to live and fly at high altitude. [ABSTRACT FROM AUTHOR]

The Bemisia tabaci Mediterranean (MED) cryptic species has been rapidly invading to most parts of the world owing to its strong ecological adaptability, which is considered as a model insect for stress tolerance studies under rapidly changing environments. Selection of a suitable reference gene for quantitative stress-responsive gene expression analysis based on qRT-PCR is critical for elaborating the molecular mechanisms of thermotolerance. To obtain accurate and reliable normalization data in MED, eight candidate reference genes (β-act, GAPDH, β-tub, EF1-α, GST, 18S, RPL13A and α-tub) were examined under various thermal stresses for varied time periods by using geNorm, NormFinder and BestKeeper algorithms, respectively. Our results revealed that β-tub and EF1-α were the best reference genes across all sample sets. On the other hand, 18S and GADPH showed the least stability for all the samples studied. β-act was proved to be highly stable only in case of short-term thermal stresses. To our knowledge this was the first comprehensive report on validation of reference genes under varying temperature stresses in MED. The study could expedite particular discovery of thermotolerance genes in MED. Further, the present results can form the basis of further research on suitable reference genes in this invasive insect and will facilitate transcript profiling in other invasive insects. [ABSTRACT FROM AUTHOR]

The relationship between the coral genotype and the environment is an important area of research in degraded coral reef ecosystems. We used a reciprocal outplanting experiment with 930 corals representing ten genotypes on each of eight reefs to investigate the influence of genotype and the environment on growth and survivorship in the threatened Caribbean staghorn coral, Acropora cervicornis. Coral genotype and site were strong drivers of coral growth and individual genotypes exhibited flexible, non-conserved reaction norms, complemented by ten-fold differences in growth between specific G-E combinations. Growth plasticity may diminish the influence of local adaptation, where foreign corals grew faster than native corals at their home sites. Novel combinations of environment and genotype also significantly affected disturbance response during and after the 2015 bleaching event, where these factors acted synergistically to drive variation in bleaching and recovery. Importantly, small differences in temperature stress elicit variable patterns of survivorship based on genotype and illustrate the importance of novel combinations of coral genetics and small differences between sites representing habitat refugia. In this context, acclimatization and flexibility is especially important given the long lifespan of corals coping with complex environmental change. The combined influence of site and genotype creates short-term differences in growth and survivorship, contributing to the standing genetic variation needed for adaptation to occur over longer timescales and the recovery of degraded reefs through natural mechanisms. [ABSTRACT FROM AUTHOR]

Adaptation of agents through learning or evolution is an important component of the resilience of Complex Adaptive Systems (CAS). Without adaptation, the flexibility of such systems to cope with outside pressures would be much lower. To study the capabilities of CAS to adapt, social simulations with agent-based models (ABMs) provide a helpful tool. However, the value of ABMs for studying adaptation depends on the availability of methodologies for sensitivity analysis that can quantify resilience and adaptation in ABMs. In this paper we propose a sensitivity analysis methodology that is based on comparing time-dependent probability density functions of output of ABMs with and without agent adaptation. The differences between the probability density functions are quantified by the so-called earth-mover’s distance. We use this sensitivity analysis methodology to quantify the probability of occurrence of critical transitions and other long-term effects of agent adaptation. To test the potential of this new approach, it is used to analyse the resilience of an ABM of adaptive agents competing for a common-pool resource. Adaptation is shown to contribute positively to the resilience of this ABM. If adaptation proceeds sufficiently fast, it may delay or avert the collapse of this system. [ABSTRACT FROM AUTHOR]

Salinity is the primary driver of osmoregulatory evolution in decapods, and may have influenced their diversification into different osmotic niches. In semi-terrestrial crabs, hyper-osmoregulatory ability favors sojourns into burrows and dilute media, and provides a safeguard against hemolymph dilution; hypo-osmoregulatory ability underlies emersion capability and a life more removed from water sources. However, most comparative studies have neglected the roles of the phylogenetic and environmental components of inter-specific physiological variation, hindering evaluation of phylogenetic patterns and the adaptive nature of osmoregulatory evolution. Semi-terrestrial fiddler crabs (Uca) inhabit fresh to hyper-saline waters, with species from the Americas occupying higher intertidal habitats than Indo-west Pacific species mainly found in the low intertidal zone. Here, we characterize numerous osmoregulatory traits in all ten fiddler crabs found along the Atlantic coast of Brazil, and we employ phylogenetic comparative methods using 24 species to test for: (i) similarities of osmoregulatory ability among closely related species; (ii) salinity as a driver of osmoregulatory evolution; (iii) correlation between salt uptake and secretion; and (iv) adaptive peaks in osmoregulatory ability in the high intertidal American lineages. Our findings reveal that osmoregulation in Uca exhibits strong phylogenetic patterns in salt uptake traits. Salinity does not correlate with hyper/hypo-regulatory abilities, but drives hemolymph osmolality at ambient salinities. Osmoregulatory traits have evolved towards three adaptive peaks, revealing a significant contribution of hyper/hypo-regulatory ability in the American clades. Thus, during the evolutionary history of fiddler crabs, salinity has driven some of the osmoregulatory transformations that underpin habitat diversification, although others are apparently constrained phylogenetically. [ABSTRACT FROM AUTHOR]

Fertilization sensitivity to heat in rice is a major issue within climate change scenarios in the tropics. A panel of 167 indica landraces and improved varieties was phenotyped for spikelet sterility (SPKST) under 38°C during anthesis and for several secondary traits potentially affecting panicle micro-climate and thus the fertilization process. The panel was genotyped with an average density of one marker per 29 kb using genotyping by sequencing. Genome-wide association analyses (GWAS) were conducted using three methods based on single marker regression, haplotype regression and simultaneous fitting of all markers, respectively. Fourteen loci significantly associated with SPKST under at least two GWAS methods were detected. A large number of associations was also detected for the secondary traits. Analysis of co-localization of SPKST associated loci with QTLs detected in progenies of bi-parental crosses reported in the literature allowed to narrow -down the position of eight of those QTLs, including the most documented one, qHTSF4.1. Gene families underlying loci associated with SPKST corresponded to functions ranging from sensing abiotic stresses and regulating plant response, such as wall-associated kinases and heat shock proteins, to cell division and gametophyte development. Analysis of diversity at the vicinity of loci associated with SPKST within the rice three thousand genomes, revealed widespread distribution of the favourable alleles across O. sativa genetic groups. However, few accessions assembled the favourable alleles at all loci. Effective donors included the heat tolerant variety N22 and some Indian and Taiwanese varieties. These results provide a basis for breeding for heat tolerance during anthesis and for functional validation of major loci governing this trait. [ABSTRACT FROM AUTHOR]

Tardigrades belong to the most radiation tolerant animals on Earth, as documented by a number of studies using both low-LET and high-LET ionizing radiation. Previous studies have focused on semi-terrestrial species, which are also very tolerant to desiccation. The predominant view on the reason for the high radiation tolerance among these semi-terrestrial species is that it relies on molecular mechanisms that evolved as adaptations for surviving dehydration. In this study we report the first study on radiation tolerance in a marine tardigrade, Echiniscoides sigismundi. Adult specimens in the hydrated active state were exposed to doses of gamma radiation from 100 to 5000 Gy. The results showed little effect of radiation at 100 and 500 Gy but a clear decline in activity at 1000 Gy and higher. The highest dose survived was 4000 Gy, at which ca. 8% of the tardigrades were active 7 days after irradiation. LD50 in the first 7 days after irradiation was in the range of 1100–1600 Gy. Compared to previous studies on radiation tolerance in semi-terrestrial and limnic tardigrades, Echiniscoides sigismundi seems to have a lower tolerance. However, the species still fits into the category of tardigrades that have high tolerance to both desiccation and radiation, supporting the hypothesis that radiation tolerance is a by-product of adaptive mechanisms to survive desiccation. More studies on radiation tolerance in tardigrade species adapted to permanently wet conditions, both marine and freshwater, are needed to obtain a more comprehensive picture of the patterns of radiation tolerance. [ABSTRACT FROM AUTHOR]

Recent human adaptations have shaped population differentiation in genomic regions containing putative functional variants, mostly located in predicted regulatory elements. However, their actual functionalities and the underlying mechanism of recent adaptation remain poorly understood. In the current study, regions of genes and repeats were investigated for functionality depending on the degree of population differentiation, FST or ΔDAF (a difference in derived allele frequency). The high FST in the 5´ or 3´ untranslated regions (UTRs), in particular, confirmed that population differences arose mainly from differences in regulation. Expression quantitative trait loci (eQTL) analyses using lymphoblastoid cell lines indicated that the majority of the highly population-specific regions represented cis- and/or trans-eQTL. However, groups having the highest ΔDAFs did not necessarily have higher proportions of eQTL variants; in these groups, the patterns were complex, indicating recent intricate adaptations. The results indicated that East Asian (EAS) and European populations (EUR) experienced mutual selection pressures. The mean derived allele frequency of the high ΔDAF groups suggested that EAS and EUR underwent strong adaptation; however, the African population in Africa (AFR) experienced slight, yet broad, adaptation. The DAF distributions of variants in the gene regions showed clear selective pressure in each population, which implies the existence of more recent regulatory adaptations in cells other than lymphoblastoid cell lines. In-depth analysis of population-differentiated regions indicated that the coding gene, RNF135, represented a trans-regulation hotspot via cis-regulation by the population-specific variants in the region of selective sweep. Together, the results provide strong evidence of actual intricate adaptation of human populations via regulatory manipulation. [ABSTRACT FROM AUTHOR]

Tibetan pigs have survived at high altitude for millennia and they have a suite of adaptive features to tolerate the hypoxic environment. However, the molecular mechanisms underlying the regulation of hypoxia-adaptive phenotypes have not been completely elucidated. In this study, we analyzed differentially expressed genes (DEGs), biological pathways and constructed co-expression regulation networks using whole-transcriptome microarrays from lung tissues of Tibetan and Duroc pigs both at high and low altitude. A total of 3,066 DEGs were identified and this list was over-represented for the ontology terms including metabolic process, catalytic activity, and KEGG pathway including metabolic pathway and PI3K-Akt signaling pathway. The regulatory (RIF) and phenotypic (PIF) impact factor analysis identified several known and several potentially novel regulators of hypoxia adaption, including: IKBKG, KLF6 and RBPJ (RIF1), SF3B1, EFEMP1, HOXB6 and ATF6 (RIF2). These findings provide new details of the regulatory architecture of hypoxia-adaptive genes and also insight into which genes may undergo epigenetic modification for further study in the high-altitude adaptation. [ABSTRACT FROM AUTHOR]

Patterns of connectivity and self-recruitment are recognized as key factors shaping the dynamics of marine populations. Connectivity is also essential for maintaining and restoring natural ecological processes with genetic diversity contributing to the adaptation and persistence of any species in the face of global disturbances. Estimates of connectivity are crucial to inform the design of both marine protected areas (MPAs) and MPA networks. Among several approaches, genetic structure is frequently used as a proxy for patterns of connectivity. Using 8 microsatellite loci, we investigated genetic structure of the two-banded sea bream Diplodus vulgaris, a coastal fish that is both commercially and ecologically important. Adults were sampled in 7 locations (stretches of coastline approximately 8 km long) and juveniles in 14 sites (~100 to 200 m of coastline) along 200 km of the Apulian Adriatic coast (SW Adriatic Sea), within and outside an MPA (Torre Guaceto MPA, Italy). Our study found similar genetic diversity indices for both the MPA and the surrounding fished areas. An overall lack of genetic structure among samples suggests high gene flow (i.e. connectivity) across a scale of at least 200 km. However, some local genetic divergences found in two locations demonstrate some heterogeneity in processes renewing the population along the Apulian Adriatic coast. Furthermore, two sites appeared genetically divergent, reinforcing our observations within the genetic makeup of adults and confirming heterogeneity in early stage genetics that can come from either different supply populations or from chaotic genetic patchiness occurring under temporal variation in recruitment and in the reproductive success. While the specific role of the MPA is not entirely known in this case, these results confirm the presence of regional processes and the key role of connectivity in maintaining the local population supply. [ABSTRACT FROM AUTHOR]

Evidence indicates that hormones modulate the intensity of maternal care. Oxytocin is known for its positive influence on maternal behavior and its important role for childbirth. In contrast, testosterone promotes egocentric choices and reduces empathy. Further, testosterone decreases during parenthood which could be an adaptation to increased parental investment. The present study investigated the interaction between testosterone and oxytocin in attentional control and their influence on attention to baby schema in women. Higher endogenous testosterone was expected to decrease selective attention to child portraits in a face-in-the-crowd-paradigm, while oxytocin was expected to counteract this effect. As predicted, women with higher salivary testosterone were slower in orienting attention to infant targets in the context of adult distractors. Interestingly, reaction times to infant and adult stimuli decreased after oxytocin administration, but only in women with high endogenous testosterone. These results suggest that oxytocin may counteract the adverse effects of testosterone on a central aspect of social behavior and maternal caretaking. [ABSTRACT FROM AUTHOR]

The ribosome is an ancient machine, performing the same function across organisms. Although functionally unitary, recent experiments suggest specialized roles for some ribosomal proteins. Our central thesis is that ribosomal proteins function in a modular fashion to decode genetic information in a context dependent manner. We show through large data analyses that although many ribosomal proteins are essential with consistent effect on growth in different conditions in yeast and similar expression across cell and tissue types in mice and humans, some ribosomal proteins are used in an environment specific manner. The latter set of variable ribosomal proteins further function in a coordinated manner forming modules, which are adapted to different environmental cues in different organisms. We show that these environment specific modules of ribosomal proteins in yeast have differential genetic interactions with other pathways and their 5’UTRs show differential signatures of selection in yeast strains, presumably to facilitate adaptation. Similarly, we show that in higher metazoans such as mice and humans, different modules of ribosomal proteins are expressed in different cell types and tissues. A clear example is nervous tissue that uses a ribosomal protein module distinct from the rest of the tissues in both mice and humans. Our results suggest a novel stratification of ribosomal proteins that could have played a role in adaptation, presumably to optimize translation for adaptation to diverse ecological niches and tissue microenvironments. [ABSTRACT FROM AUTHOR]

Feeding adaptation, social behaviour, and interspecific interactions related to sexual dimorphism and allometric growth are particularly challenging to be investigated in the high sexual monomorphic Delphinidae. We used geometric morphometrics to extensively explore sexual dimorphism and ontogenetic allometry of different projections of the skull and the mandible of the bottlenose dolphin Tursiops truncatus. Two-dimensional landmarks were recorded on the dorsal, ventral, lateral, and occipital views of the skull, and on the lateral view of the left and the right mandible of 104 specimens from the Mediterranean and the North Seas, differing environmental condition and degree of interspecific associations. Landmark configurations were transformed, standardized and superimposed through a Generalized Procrustes Analysis. Size and shape differences between adult males and females were respectively evaluated through ANOVA on centroid size, Procrustes ANOVA on Procrustes distances, and MANOVA on Procrustes coordinates. Ontogenetic allometry was investigated by multivariate regression of shape coordinates on centroid size in the largest homogenous sample from the North Sea. Results evidenced sexual dimorphic asymmetric traits only detected in the adults of the North Sea bottlenose dolphins living in monospecific associations, with females bearing a marked incision of the cavity hosting the left tympanic bulla. These differences were related to a more refined echolocalization system that likely enhances the exploitation of local resources by philopatric females. Distinct shape in immature versus mature stages and asymmetric changes in postnatal allometry of dorsal and occipital traits, suggest that differences between males and females are established early during growth. Allometric growth trajectories differed between males and females for the ventral view of the skull. Allometric trajectories differed among projections of skull and mandible, and were related to dietary shifts experienced by subadults and adults. [ABSTRACT FROM AUTHOR]

Increased understanding of the molecular components involved in reproduction may assist in understanding the evolutionary adaptations used by animals, including hermaphrodites, to produce offspring and retain a continuation of their lineage. In this study, we focus on the Mediterranean snail, Theba pisana, a hermaphroditic land snail that has become a highly invasive pest species within agricultural areas throughout the world. Our analysis of T. pisana CNS tissue has revealed gene transcripts encoding molluscan reproduction-associated proteins including APGWamide, gonadotropin-releasing hormone (GnRH) and an egg-laying hormone (ELH). ELH isoform 1 (ELH1) is known to be a potent reproductive peptide hormone involved in ovulation and egg-laying in some aquatic molluscs. Two other non-CNS ELH isoforms were also present in T. pisana (Tpi-ELH2 and Tpi-ELH3) within the snail dart sac and mucous glands. Bioactivity of a synthetic ELH1 on sexually mature T. pisana was confirmed through bioassay, with snails showing ELH1-induced egg-laying behaviours, including soil burrowing and oviposition. In summary, this study presents a detailed molecular analysis of reproductive neuropeptide genes in a land snail and provides a foundation for understanding ELH function. [ABSTRACT FROM AUTHOR]

Hfq is a global regulator that is involved in environmental adaptation of bacteria and in pathogenicity. To gain insight into the role of Hfq in Vibrio alginolyticus, an hfq deletion mutant was constructed in V. alginolyticus ZJ-T strain and phenotypically characterized. Deletion of hfq led to an alteration of colony morphology and reduced extracellular polysaccharide production, a general impairment of growth in both rich medium and minimal media with different carbon sources or amino acids, enhanced sensitivity to oxidative stress and to several antibiotics. Furthermore, a differential transcriptomic analysis showed significant changes of transcript abundance for 306 protein coding genes, with 179 genes being up regulated and 127 down-regulated. Several of these changes could be related to the observed phenotypes of the mutant. Transcriptomic data also provided evidence for the induction of the extracytoplasmic stress response in absence of Hfq. Altogether, these findings point to broad regulatory functions for Hfq in V. alginolyticus cells, likely to underlie an important role in pathogenicity. [ABSTRACT FROM AUTHOR]

The present study aims to identify the heat responsive genes and biological pathways in heat stressed buffalo mammary epithelial cells (MECs). The primary mammary epithelial cells of riverine buffalo were exposed to thermal stress at 42°C for one hour. The cells were subsequently allowed to recover at 37°C and harvested at different time intervals (30 min to 48 h) along with control samples (un-stressed). In order to assess the impact of heat stress in buffalo MECs, several in-vitro cellular parameters (lactate dehydrogenase activity, cell proliferation assay, cellular viability, cell death and apoptosis) and transcriptional studies were conducted. The heat stress resulted in overall decrease in cell viability and cell proliferation of MECs while induction of cellular apoptosis and necrosis. The transcriptomic profile of heat stressed MECs was generated using Agilent 44 K bovine oligonucleotide array and at cutoff criteria of ≥3-or ≤3 fold change, a total of 153 genes were observed to be upregulated while 8 genes were down regulated across all time points post heat stress. The genes that were specifically up-regulated or down-regulated were identified as heat responsive genes. The upregulated genes in heat stressed MECs belonged to heat shock family viz., HSPA6, HSPB8, DNAJB2, HSPA1A. Along with HSPs, genes like BOLA, MRPL55, PFKFB3, PSMC2, ENDODD1, ARID5A, and SENP3 were also upregulated. Microarray data revealed that the heat responsive genes belonged to different functional classes viz., chaperons; immune responsive; cell proliferation and metabolism related. Gene ontology analysis revealed enrichment of several biological processes like; cellular process, metabolic process, response to stimulus, biological regulation, immune system processes and signaling. The transcriptome analysis data was further validated by RT-qPCR studies. Several HSP (HSP40, HSP60, HSP70, HSP90, and HSPB1), apoptotic (Bax and Bcl2), immune (IL6, TNFα and NF-kβ) and oxidative stress (GPX1 and DUSP1) related genes showed differential expression profile at different time points post heat stress. The transcriptional data strongly indicated the induction of survival/apoptotic mechanism in heat stressed buffalo MECs. The overrepresented pathways across all time points were; electron transport chain, cytochrome P450, apoptosis, MAPK, FAS and stress induction of HSP regulation, delta Notch signaling, apoptosis modulation by HSP70, EGFR1 signaling, cytokines and inflammatory response, oxidative stress, TNF-alpha and NF- kB signaling pathway. The study thus identified several genes from different functional classes and biological pathways that could be termed as heat responsive in buffalo MEC. The responsiveness of buffalo MECs to heat stress in the present study clearly suggested its suitability as a model to understand the modulation of buffalo mammary gland expression signature in response to environmental heat load. [ABSTRACT FROM AUTHOR]