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The European paper wasp, Polistes dominulus Christ, is an abundant wasp species in South and Central Europe which dispersed to the north in recent times. Polistes dominulus exhibits an energy-extensive mode of life, spending much time resting at the nest, which should be reflected in adaptations regarding gas exchange and standard metabolism. We analysed the resting metabolism (CO2 emission) of Polistes dominulus workers in the ambient temperature range an individual may be exposed to during a breeding season (Ta = 2.4–40.6 °C) via flow through respirometry. Behaviour and endothermic activity were assessed by infrared thermography. With rising Ta, CO2 release followed an exponential increase from 27 to 149 and 802 nl g−1 min−1 at Ta = 3, 20 and 35 °C, respectively. Measurements of the thermal regime at the nest showed that resting P. dominulus are most of the time in the lower range of their standard metabolic curve. A comparison with a “highly energetic” wasp like Vespula sp. revealed that Polistes dominulus not only optimises behaviour but also reduces metabolism to save energy. The CO2 emission patterns changed with ambient temperature, from discontinuous (≤25 °C) to cyclic (25–36 °C) and continuous gas exchange at higher temperatures. A pronounced break appeared in the data progression regarding cycle frequency and CO2 emission per gas exchange cycle between 15 and 10 °C. This striking change in gas exchange features indicates a physiological adaptation to special respiratory requirements at low temperatures. Electronic supplementary material The online version of this article (doi:10.1007/s00360-015-0915-7) contains supplementary material, which is available to authorised users.

Understanding intraspecific geographic variation in animal signals poses a challenging evolutionary problem. Studies addressing geographic variation typically focus on signals used in mate-choice, however, geographic variation in intrasexual signals involved in competition is also known to occur. In Polistes dominulus paper wasps, females have black facial spots that signal dominance: individuals wasps with more complex 'broken' facial patterns are better fighters and are avoided by rivals. Recent work suggests there is dramatic geographic variation in these visual signals of quality, though this variation has not been explicitly described or quantified. Here, we analyze variation in P. dominulus signals across six populations and explore how environmental conditions may account for this variation. Overall, we found substantial variation in facial pattern brokenness across populations and castes. Workers have less broken facial patterns than gynes and queens, which have similar facial patterns. Strepsipteran parasitism, body size and temperature are all correlated with the facial pattern variation, suggesting that developmental plasticity likely plays a key role in this variation. First, the extent of parasitism varies across populations and parasitized individuals have lower facial pattern brokenness than unparasitized individuals. Second, there is substantial variation in body size across populations and a weak but significant relationship between facial pattern brokenness and body size. Wasps from populations with smaller body size (e.g. Italy) tend to have less broken facial patterns than wasps from populations with larger body size (e.g. New York, USA). Third, there is an apparent association between facial patterns and climate, with wasp from cooler locations tending to have higher facial pattern brokenness than wasps from warmer locations. Additional experimental work testing the causes and consequences of facial pattern variation will be important, as geographic variation in signals has important consequences for the evolution of communication systems and social behavior.

Although certain acquired nongenetic (i.e., epigenetic) traits are known to be heritable in plants, little is known currently about whether environmental parameters can induce adaptive epigenetic responses in plants and whether such effects can persist through generations. We used an experimental design based on classical genetics principles to assess whether plants respond to the environmental conditions of their ancestors in an adaptive epigenetic manner. An extensive examination of genetically identical Arabidopsis thaliana (L.) Heynh lines exposed to mild heat (30 °C) or cold (16 °C) treatments in the parental and F1generations revealed that the prior elevated temperature regime lead to a greater than fivefold improvement in fitness (seed production per individual) for plants exposed to heat in a later generation (F3). The heat-specific fitness improvements among F3plants were observed even though the heat-treated parental and F1generations were followed by a generation grown at a normal temperature (F2) and point towards a temperature-induced adaptive epigenetic phenomenon. No such adaptive responses were detected for cold-treated plants, indicating that there are distinctive biological processes inherent to these two temperature regimes. Overall, the data are consistent with the existence of an environmentally induced epigenetic and heritable adaptive response in plants.

We demonstrate that the evolution of facial recognition in wasps is associated with specialized face-learning abilities. Polistes fuscatus can differentiate among normal wasp face images more rapidly and accurately than nonface images or manipulated faces. A close relative lacking facial recognition, Polistes metricus, however, lacks specialized face learning. Similar specializations for face learning are found in primates and other mammals, although P. fuscatus represents an independent evolution of specialization. Convergence toward face specialization in distant taxa as well as divergence among closely related taxa with different recognition behavior suggests that specialized cognition is surprisingly labile and may be adaptively shaped by species-specific selective pressures such as face recognition.

Although climate policies have been so far mostly focused on mitigation, adaptation to climate change is a growing concern in developed and developing countries. This paper discusses how adaptation fits into the global climate strategy, at the global and national levels. To do so, a partial equilibrium optimization model of climate policies-which includes mitigation, proactive adaptation (ex ante), and reactive adaptation (ex post)-is solved without and with uncertainty. Mitigation, proactive adaptation, and reactive adaptation are found to be generally jointly determined. Uncertainty on the location of damages reduces the benefits of"targeted"proactive adaptation with regard to mitigation and reactive adaptation. However, no single country controls global mitigation policies, and budget constraints might make it difficult for developing countries to finance reactive adaptation, especially if climate shocks affect the fiscal base. Rainy-day funds are identified as a supplemental instrument that can alleviate future budget constraints while avoiding the risk of misallocating resources when the location of damages is uncertain.

Although a significant number of behavioral studies of desert tenebrionids have been done, almost nothing is recorded of Trichoton sordidum (LeConte) (Coleoptera: Tenebrionidae), an inhabitant of the sunny, sparsely vegetated US/Mexican borderlands. For this small, flightless beetle successful predator evasion and adaptation to a desert environment has required development of complicated, quickly utilizable behavioral mechanisms for regulating exposure to extremes of heat, light, humidity, and habitat structure. In this study, T. sordidum was exposed to sudden changes in temperature, illumination, and habitat complexity, and some patterns representing its normal aggregation were recorded. Minimum Risk Distribution models ([Floater 2001][1]) predict changes in spatial distribution patterns of groups of individuals as they are exposed to environmental change. A successful species must have a large percentage of individuals adhering to changes with a set pattern of behaviors. All groups of T. sordidum tested demonstrated both rapid and cohesive dispersal patterns. They normally showed little tendency toward clustering, except clear adhesive aggregation patterns in cases of limited resources in a fragmented environment. Under conditions of extreme heat or light, aggregations in the form of clumping did occur. The formation of clumps from simple two-stacks to groups of up to ten is documented here. The sophistication, consistency of use, and rapid initiation of clumps suggest clumping might well be a highly evolved and successful mechanism for group threat evasion. The morphology of T. sordidum shows how clumping is achieved. An examination of the conditions leading to clumping gives clues to why clumps are formed. * Abbreviations : MRD : Minimum Risk Distribution: A model of spatial distribution of individuals that results in the minimum number of premature deaths in a population, and leads to maximized population growth ([Floater 2001][1]). C-value : A statistical measurement used in this study to quantify relative clump sizes for Trichoton sordidum rather than total number of individuals in a clump. Homogeneous environment : Environment composed only of uniform, similar features with no irregular detail. In this experiment, open areas of sand, cloth, or fine debris were used. Habitat complexity : Structural interference in a habitat which leads to spatial variability. The result is predicted to be a change in the spatial distribution of individuals within the habitat. In this study pebbles were added to the homogeneous environment to break up a uniform surface area. [1]: #ref-6

Monogonont rotifers live in habitats that display extensively variation in both biotic and abiotic components. Much of this variation is seasonal and therefore predictable for a given pond or lake. In 1972, King proposed one physiological and two genetic models presenting alternative modes of adaptation to this temporal variation. Our purpose in the present paper is to review and evaluate how our knowledge of the seasonal structure of rotifer populations has changed in the past 25 years. Seasonal changes in clone frequencies have been reported from three studies of natural populations using electrophoretic analysis of isozymes. In one of these studies there was evidence for substantial temporal overlap of multilocus genotypes suggesting that these clones were broad-niched generalists. By contrast, both the genetic and ecological analyses in the other two studies support a non-overlap model in which clonal groups are composed of narrow-niched specialists that undergo seasonal succession. In both of these studies the clonal groups appear to have achieved the status of sibling species, a phenomenon that we conclude is probably common in monogonont rotifers. Strong competition promotes reproductive isolation between successive groups of seasonal specialists. The existence of this competition has been inferred from natural populations and demonstrated by studies in the laboratory. Also required, and also supported by field observations, is a temporal separation of periods of mictic (sexual) reproduction. A final requirement of the nonoverlap model is seasonal variation in the timing of resting egg hatching. That is, clones established from hatching of resting eggs must enter a physiologically appropriate habitat if they are to increase in number and achieve a competitive advantage. Unfortunately, we still have little information on this topic. Finally, we present the results of a study analyzing the effects of variation in the mictic ratio (i.e., the relative frequency of mictic females) on the adaptive structure of rotifer populations. Mixis may shift the balance between costs and benefits of specialization thereby producing seasonally specialized populations that overlap in space but not time. Life history patterns may therefore provide fundamental insights on the adaptation of rotifers to the extensive temporal variation in their environments.

The contributors explore such issues as the nature of species, how species are counted, limits on diversity, mechanisms of speciation and adaptation, and speciation rates.

Summary Plants that successfully acclimate to stress can resume growth under stressful conditions. The grass Brachypodium distachyon can grow a cold‐adaptive morphology during cold acclimation. Studies on transcriptional memory (TM) have revealed that plants can be primed for stress by adjusting their transcriptional responses, but the function of TM in stress acclimation is not well understood. We investigated the function of TM during cold acclimation in B. distachyon.Quantitative polymerase chain reaction (qPCR), RNA‐seq and chromatin immunoprecipitation qPCR analyses were performed on plants exposed to repeated episodes of cold to characterize the presence and stability of TM during the stress and growth responses of cold acclimation.Transcriptional memory mainly dampened stress responses as growth resumed and as B. distachyon became habituated to cold stress. Although permanent on vernalization gene VRN1, TMs were short‐term and reversible on cold‐stress genes. Growing under cold conditions also coincided with the acquisition of new and targeted cold‐induced transcriptional responses.Overall, TM provided plasticity to cold stress responses during cold acclimation in B. distachyon, leading to stress habituation, acquired stress responses, and resumed growth. Our study shows that chromatin‐associated TMs are involved in tuning plant responses to environmental change and, as such, regulate both stress and developmental components that characterize cold‐climate adaptation in B. distachyon.

Nonhuman primates have a highly diverse locomotor repertoire defined by an equally diverse hand use. Based on how primates use their hands during locomotion, we can distinguish between terrestrial and arboreal taxa. The 'arboreal' hand is likely adapted towards high wrist mobility and grasping, whereas the 'terrestrial' hand will show adaptations to loading. While the morphology of the forearm and hand bones have been studied extensively, functional adaptations in the forearm and hand musculature to locomotor behaviour have been documented only scarcely. In this paper, we investigate the forelimb musculature of the highly arboreal gibbons (including Hylobates lar,Hylobates pileatus,Nomascus leucogenys,Nomascus concolor and Symphalangus syndactylus) and compare this with the musculature of the semi-terrestrial rhesus macaques (Macaca mulatta). Anatomical data from previous dissections on knuckle-walking bonobos (Pan paniscus) and bipedal humans (Homo sapiens) are also included to further integrate the analyses in the scope of catarrhine hand adaptation. This study indicates that the overall configuration of the arm and hand musculature of these primates is very similar but there are some apparent differences in relative size which can be linked to differences in forelimb function and which might be related to their specific locomotor behaviour. In macaques, there is a large development of wrist deviators, wrist and digital flexors, and m. triceps brachii, as these muscles are important during the different phases of palmi- and digitigrade quadrupedal walking to stabilize the wrist and elbow. In addition, their m. flexor carpi ulnaris is the most important contributor to the total force-generating capacity of the wrist flexors and deviators, and is needed to counteract the adducting torque at the elbow joint during quadrupedal walking. Gibbons show a relatively high force-generating capacity in their forearm rotators, wrist and digital flexors, which are important muscles in brachiation to actively regulate forward movement of the body. The results also stress the importance of the digital flexors in bonobos, during climbing and clambering, and in humans, which is likely linked to our advanced manipulation skills. ispartof: JOURNAL OF ANATOMY vol:238 issue:2 pages:321-337 ispartof: location:England status: published

Changes in frequency and severity of heat waves due to climate change pose a considerable challenge to livestock production systems. Although it is well known that heat stress reduces feed intake in cattle, effects of heat stress vary between animal genotypes and climatic conditions and are context specific. To derive a generic global prediction that accounts for the effects of heat stress across genotypes, management and environments, we conducted a systematic literature review and a meta-analysis to assess the relationship between dry matter intake (DMI) and the temperature-humidity index (THI), two reliable variables for the measurement of feed intake and heat stress in cattle, respectively. We analysed this relationship accounting for covariation in countries, breeds, lactation stage and parity, as well as the efficacy of various physical cooling interventions. Our findings show a significant negative correlation (r = − 0.82) between THI and DMI, with DMI reduced by 0.45 kg/day for every unit increase in THI. Although differences in the DMI-THI relationship between lactating and non-lactating cows were not significant, effects of THI on DMI varied between lactation stages. Physical cooling interventions (e.g. provision of animal shade or shelter) significantly alleviated heat stress and became increasingly important after THI 68, suggesting that this THI value could be viewed as a threshold for which cooling should be provided. Passive cooling (shading) was more effective at alleviating heat stress compared with active cooling interventions (sprinklers). Our results provide a high-level global equation for THI-DMI across studies, allowing next-users to predict effects of heat stress across environments and animal genotypes.

Along with intrinsic evolution, adaptation to selective pressure in new environments might have resulted in the circulatory SARS-CoV-2 strains in response to the geoenvironmental conditions of a country and the demographic profile of its population. With this target, the current study traced the evolutionary route and mutational frequency of 198 Bangladesh-originated SARS-CoV-2 genomic sequences available in the GISAID platform over a period of 13 weeks as of 14 July 2020. The analyses were performed using MEGA X, Swiss Model Repository, Virus Pathogen Resource and Jalview visualization. Our analysis identified that majority of the circulating strains strikingly differ from both the reference genome and the first sequenced genome from Bangladesh. Mutations in nonspecific proteins (NSP2-3, NSP-12(RdRp), NSP-13(Helicase)), S-Spike, ORF3a, and N-Nucleocapsid protein were common in the circulating strains with varying degrees and the most unique mutations (UM) were found in NSP3 (UM-18). But no or limited changes were observed in NSP9, NSP11, Envelope protein (E) and accessory factors (NSP7a, ORF 6, ORF7b) suggesting the possible conserved functions of those proteins in SARS-CoV-2 propagation. However, along with D614G mutation, more than 20 different mutations in the Spike protein were detected basically in the S2 domain. Besides, mutations in SR-rich region of N protein and P323L in RDRP were also present. However, the mutation accumulation showed a significant association (p = 0.003) with sex and age of the COVID-19-positive cases. So, identification of these mutational accumulation patterns may greatly facilitate vaccine development deciphering the age and the sex-dependent differential susceptibility to COVID-19. Supplementary Information The online version contains supplementary material available at 10.1007/s11262-021-01860-x.

All land plants encode large multigene families of xyloglucan endotransglucosylase/hydrolases (XTHs), plant-specific enzymes that cleave and reconnect plant cell-wall polysaccharides. Despite the ubiquity of these enzymes, considerable uncertainty remains regarding the evolutionary history of the XTH family. Phylogenomic and comparative analyses in this study traced the non-plant origins of the XTH family to Alphaproteobacteria ExoKs, bacterial enzymes involved in loosening biofilms, rather than Firmicutes licheninases, plant biomass digesting enzymes, as previously supposed. The relevant horizontal gene transfer (HGT) event was mapped to the divergence of non-swimming charophycean algae in the Cryogenian geological period. This HGT event was the likely origin of charophycean EG16-2s, which are putative intermediates between ExoKs and XTHs. Another HGT event in the Cryogenian may have led from EG16-2s or ExoKs to fungal Congo Red Hypersensitive proteins (CRHs) to fungal CRHs, enzymes that cleave and reconnect chitin and glucans in fungal cell walls. This successive transfer of enzyme-encoding genes may have supported the adaptation of plants and fungi to the ancient icy environment by facilitating their sessile lifestyles. Furthermore, several protein evolutionary steps, including coevolution of substrate-interacting residues and putative intra-family gene fusion, occurred in the land plant lineage and drove diversification of the XTH family. At least some of those events correlated with the evolutionary gain of broader substrate specificities, which may have underpinned the expansion of the XTH family by enhancing duplicated gene survival. Together, this study highlights the Precambrian evolution of life and the mode of multigene family expansion in the evolutionary history of the XTH family.

Examen des effets de la lumiere et de la temperature sur la germination des graines de B.p. d'origines geographiques differentes

Astyanax brucutu is a peculiar species of Neotropical tetra endemic from the Chapada Diamantina, a large plateau in northeastern Brazil. Individuals of this species undergo a dramatic ontogenetic shift in their diet that is accompanied by equally remarkable changes in their feeding apparatus. Whereas juveniles of A. brucutu feed mostly on algae, adults feed almost exclusively on an endemic species of hydrobiid snail and other associated living organisms that inhabit their dead shells (including infaunal invertebrates and algae). Skeletal adaptations associated with this change in diet were previously reported, but until now, the changes in the musculature remained mostly unknown. The present paper describes the facial and gular muscles, as well as the buccal ligaments of A. brucutu in different life stages, and identifies the major ontogenetic changes in these systems associated with the diet shift in the species. Such changes primarily involve expansions of specific portions of the adductor mandibulae and associated tendons and ligaments that likely represent adaptations to increase the biting power necessary to crush copious amounts of shells ingested by larger individuals of A. brucutu. Those adaptations are absent in specimens of any size of Astyanax cf. fasciatus, a sympatric congener lacking durophagous feeding habits. Anatomical comparisons and landmark-based principal components analysis (PCA) suggest that most specializations to durophagy in A. brucutu arose by peramorphosis. We also found that several of the muscular specializations of adults of A. brucutu are paralleled in species of Creagrutus and Piabina, two other characid genera distantly related to Astyanax, but that also feed on hard food items.

This paper critically supports the modern evolutionary explanation of religion popularised by David Sloan Wilson, by comparing it with those of his predecessors, namely Emile Durkheim and Thomas Hobbes, and to some biological examples which seem analogous to religions as kinds of superorganisms in their own right. The aim of the paper is to draw out a theoretical pedigree in philosophy and sociology that is reflected down the lines of various other evolutionarily minded contributors on the subject of religion. The general theme is of evolved large-scale cooperative structures. A scholarly concern is as follows: Wilson (Darwin’s Cathedral: Evolution, Religion, And The Nature Of Society, University of Chicago Press, Chicago, 2002) draws on Durkheim, (The elementary forms of religious life. Free Press, New york, 1912) using Calvinism as an example without mentioning Hobbes (Leviathan, Edited by E. Curley, Cambridge, Hackett, 1651), but it was Thomas Hobbes (1588–1679) who used Calvinism as an example of a leviathanesque religious structure—which is not acknowledged by either Wilson or Durkheim. If there are even any similarities between these authors, there appears to be an omission somewhere which should rightly be accounted for by giving credit to Hobbes where it is due. I issue on conclusion, what it is that makes Wilson’s approach radically different to that it skates on. I also issue it with a cautionary word.

Ligand binding and temperature play important roles in riboswitch RNAs’ structures and functions. However, most studies focused on studying structural dynamics or gene-regulation function of riboswitches from the aspect of ligand, instead of temperature. Here we combined NMR, ITC, stopped-flow and in vivo assays to investigate the ligand-triggered switch of adenine riboswitch from 10 to 45°C. Our results demonstrated that at single-nucleotide resolution, structural regions sensed ligand and temperature diversely. Temperature had opposite effects on ligand-binding and gene-regulation of adenine riboswitch. Compared with higher temperature, the RNA bound with its cognate ligand obviously stronger, while its regulatory capacity was weakened at lower temperature. In addition, application of specific-labelled RNAs to the stopped-flow experiments identified the real-time folding of the specific positions upon ligand addition at different temperatures. The kissing loop and internal loop at the riboswitch responded to ligand and temperature differently. The distinct thermo-dynamics of adenine riboswitch exposed here may contribute to the fields of RNA sensors and drug design.

DNA methylation plays a crucial role in the regulation of gene expression, activity of transposable elements, defense against foreign DNA, and inheritance of specific gene expression patterns. The link between stress exposure and sequence-specific changes in DNA methylation was hypothetical until it was shown that stresses can induce changes in the gene expression through hypomethylation or hypermethylation of DNA. To detect changes in DNA methylation under herbicide stress in two local Zea mays inbred lines exhibiting differential susceptibility to Roundup®, the methylation-sensitive amplified polymorphism (MSAP) technique was used. The overall DNA methylation levels were determined at approximately 60% for both tested lines. The most significant changes were observed for the more sensitive Z. mays line, where 6 h after the herbicide application, a large increase in the level of DNA methylation (attributed to the increase in fully methylated bands (18.65%)) was noted. DNA sequencing revealed that changes in DNA methylation profiles occurred in genes encoding heat shock proteins, membrane proteins, transporters, kinases, lipases, methyltransferases, zinc-finger proteins, cytochromes, and transposons. Herbicide stress-induced changes depended on the Z. mays variety, and the large increase in DNA methylation level in the sensitive line resulted in a lower ability to cope with stress conditions.

The adaptation of tumour cells to hypoxic microenvironment is one of the most significant characteristics of many malignant tumour diseases including hepatocarcinoma. Recently, long non-coding RNAs (lncRNAs) have been reported to play important roles in the various levels of gene regulation thus functioning in growth and survival of tumour cells. Here, new hypoxia-related lncRNAs in hepatocarcinoma cells were screened and validated by lncRNA chip-array as well as real-time RT-PCR. Among them, a hypoxia-activated lncRNA that we identified and termed Hypoxia-Activated BNIP3 Overlapping Non-coding RNA (HABON), was not only regulated by hypoxic-induced factor-1α (HIF-1α) but its expression increased significantly under hypoxia in tumour cells. We deciphered the biological characteristics of HABON including its cell localization, genomic location, as well as its full-length sequence, and proved HABON could promote growth, proliferation and clone-formation of hepatocarcinoma cells under hypoxia. Then, we revealed that HABON was transcriptionally activated by HIF-1α in hypoxic cells, furthermore, it could interact with HIF-1α and promote its protein degradation, thus affecting transcription of HIF-1α’s target genes to exert its effects on cells. Besides, the elevated expression of HABON under hypoxia could promote the transcriptional activation of BNIP3 through HIF-1α, and increasing the expression level of BNIP3. This research provides a novel clue for the adaptive survival and growth mechanism of tumour under hypoxia, and gives a way to reveal the nature of tumour cells’ resistance characteristics to harsh microenvironment.

Sporadic spreads of swine-origin influenza H3N2 variant (H3N2v) viruses were reported in humans, resulting in 437 human infections between 2011 and 2021 in the USA. Thus, an effective vaccine is needed to better control a potential pandemic for these antigenically distinct viruses from seasonal influenza. In this study, a candidate vaccine strain with efficient growth capacity in chicken embryos was established through serial blind passaging of A/Indiana/08/2011 (H3N2)v in mice and chicken embryos. Seven amino acid substitutions (M21I in PA; A138T, N165K, and V226A in HA; S312L in NP; T167I in M1; G62A in NS1 proteins) were found in the passaged viruses without a major change in the antigenicity. This mouse- and egg-adapted virus was used as a vaccine and challenge strain in mice to evaluate the efficacy of the H3N2v vaccine in different doses. Antibodies with high neutralizing titers were induced in mice immunized with 100 mu g of inactivated whole-virus particles, and those mice were significantly protected from the challenge of homologous strain. The findings indicated that the established strain in the study was useful for vaccine study in mouse models.

This paper examines how cognitive processes in living beings become conscious. Consciousness is often assumed to be a human quality only. While the basis of this paper is that consciousness is as much present in animals as it is in humans, the human form is shown to be fundamentally different. Animal consciousness expresses itself in sensory images, while human consciousness is largely verbal. Because spoken language is not an individual quality – thoughts are shared with others via communication – consciousness in humans is complex and difficult to understand. The theory proposed postulates that consciousness is an inseparable part of the body’s adaptation mechanism. In adaptation to a new environmental disturbance, the outcome of the neural cognitive process – a possible solution to the problem posed by the disturbance – is transformed into a sensory image. Sensory images are essentially conscious as they are the way living creatures experience new environmental information. Through the conversion of neural cognitive activity – thoughts – about the state of the outside world into the way that world is experienced through the senses, the thoughts gain the reality that sensory images have. The translation of thoughts into sensory images makes them real and understandable which is experienced as consciousness. The theory proposed in this paper is corroborated by functional block diagrams of the processes involved in the complex regulated mechanism of adaptation and consciousness during an environmental disturbance. All functions in this mechanism and their interrelations are discussed in detail.

Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize the key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 22 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related 13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of its D homeolog and the association of its A homeologous alleles with the spring/winter growth habit. Furthermore, the Norin 61 genome carries typical East Asian functional variants different from CS, ranging from a single nucleotide to multi-Mb scale. Examples of such variation are the Fhb1 locus, which confers Fusarium head-blight resistance, Ppd-D1a, which confers early flowering, Glu-D1f for Asian noodle quality and Rht-D1b, which introduced semi-dwarfism during the green revolution. The adoption of Norin 61 as a reference assembly for functional and evolutionary studies will enable comprehensive characterization of the underexploited Asian bread wheat diversity.

Exploiting root system variations related to drought stress adaptation using quantitative genetics and genomics approaches has potential in developing resilient varieties of cereal crops., Cereals are important crops worldwide that help meet food demands and nutritional needs. In recent years, cereal production has been challenged globally by frequent droughts and hot spells. A plant’s root is the most relevant organ for the plant adaptation to stress conditions, playing pivotal roles in anchorage and the acquisition of soil-based resources. Thus, dissecting root system variations and trait selection for enhancing yield and sustainability under drought stress conditions should aid in future global food security. This review highlights the variations in root system attributes and their interplay with shoot architecture features to face water scarcity and maintain thus yield of major cereal crops. Further, we compile the root-related drought responsive quantitative trait loci/genes in cereal crops including their interspecies relationships using microsynteny to facilitate comparative genomic analyses. We then discuss the potential of an integrated strategy combining genomics and phenomics at genetic and epigenetic levels to explore natural genetic diversity as a basis for knowledge-based genome editing. Finally, we present an outline to establish innovative breeding leads for the rapid and optimized selection of root traits necessary to develop resilient crop varieties.

Selection experiments can elucidate the varying course of adaptive changes across generations. We examined the appendicular skeleton of house mice from four replicate High Runner (HR) lines bred for physical activity on wheels and four non-selected Control (C) lines. HR mice reached apparent selection limits between generations 17 and 27, running ~3-fold more than C. Studies at generations 11, 16, and 21 found that HR mice had evolved thicker hindlimb bones, heavier feet, and larger articular surface areas of the knee and hip joint. Based on biomechanical theory, any or all of these evolved differences may be beneficial for endurance running. Here, we studied mice from generation 68, plus a limited sample from generation 58, to test whether the skeleton continued to evolve after selection limits were reached. Contrary to our expectations, we found few differences between HR and C mice for these later generations, and some of the differences in bone dimensions identified in earlier generations were no longer statistically significant. We hypothesize that the loss of apparently coadapted lower-level traits reflects (1) deterioration related to a gradual increase in inbreeding and/or (2) additional adaptive changes that replace the functional benefits of some skeletal changes.

Temperature response of stem elongation in wheat grown under field conditions indicated that temperature response is highly heritable and linked to the flowering pathway., In wheat, temperature affects the timing and intensity of stem elongation. Genetic variation for this process is therefore important for adaptation. This study investigates the genetic response to temperature fluctuations during stem elongation and its relationship to phenology and height. Canopy height of 315 wheat genotypes (GABI wheat panel) was scanned twice weekly in the field phenotyping platform (FIP) of ETH Zurich using a LIDAR. Temperature response was modelled using linear regressions between stem elongation and mean temperature in each measurement interval. This led to a temperature-responsive (slope) and a temperature-irresponsive (intercept) component. The temperature response was highly heritable (H2=0.81) and positively related to a later start and end of stem elongation as well as final height. Genome-wide association mapping revealed three temperature-responsive and four temperature-irresponsive quantitative trait loci (QTLs). Furthermore, putative candidate genes for temperature-responsive QTLs were frequently related to the flowering pathway in Arabidopsis thaliana, whereas temperature-irresponsive QTLs corresponded to growth and reduced height genes. In combination with Rht and Ppd alleles, these loci, together with the loci for the timing of stem elongation, accounted for 71% of the variability in height. This demonstrates how high-throughput field phenotyping combined with environmental covariates can contribute to a smarter selection of climate-resilient crops.

Anthropogenic acidification in SW‐Scotland, from the early 19th Century onwards, led to the extinction of several loch (lake) brown trout (Salmo trutta) populations and substantial reductions in numbers in many others. Higher altitude populations with no stocking influence, which are isolated above natural and artificial barriers and subjected to the greatest effect of acidification, exhibited the least intrapopulation genetic diversity (34% of the allelic richness of the populations accessible to anadromous S. trutta). These, however, were characterised by the greatest interpopulation divergence (highest pairwise D EST 0.61 and F ST 0.53 in contemporary samples) based on 16 microsatellite loci and are among the most differentiated S. trutta populations in NW‐Europe. Five lochs above impassable waterfalls, where S. trutta were thought to be extinct, are documented as having been stocked in the late 1980s or 1990s. All five lochs now support self‐sustaining S. trutta populations; three as a direct result of restoration stocking and two adjoining lochs largely arising from a small remnant wild population in one, but with some stocking input. The genetically unique Loch Grannoch S. trutta, which has been shown to have a heritable increased tolerance to acid conditions, was successfully used as a donor stock to restore populations in two acidic lochs. Loch Fleet S. trutta, which were re‐established from four separate donor sources in the late 1980s, showed differential contribution from these ancestors and a higher genetic diversity than all 17 natural loch populations examined in the area. Genetically distinct inlet and outlet spawning S. trutta populations were found in this loch. Three genetically distinct sympatric populations of S. trutta were identified in Loch Grannoch, most likely representing recruitment from the three main spawning rivers. A distinct genetic signature of Loch Leven S. trutta, the progenitor of many Scottish farm strains, facilitated detection of stocking with these strains. One artificially created loch was shown to have a population genetically very similar to Loch Leven S. trutta. In spite of recorded historical supplemental stocking with Loch Leven derived farm strains, much of the indigenous S. trutta genetic diversity in the area remains intact, aside from the effects of acidification induced bottlenecks. Overall genetic diversity and extant populations have been increased by allochthonous stocking.

Darfur farming and pastoralist livelihoods are both adaptations to the environmental variability that characterises the region. This article describes this adaptation and the longer‐term transformation of these specialised livelihoods from the perspective of local communities. Over several decades farmers and herders have experienced a continuous stream of climate, conflict and other shocks, which, combined with wider processes of change, have transformed livelihoods and undermined livelihood institutions. Their well‐rehearsed specialist strategies are now combined with new strategies to cope. These responses help people get by in the short term but risk antagonising not only their specialist strategies but also those of others. A combination of factors has undermined the former integration between farming and pastoralism and their livelihood institutions. Efforts to build resilience in similar contexts must take a long‐term view of livelihood adaptation as a specialisation, and consider the implications of new strategies for the continuity and integration of livelihood specialisations.

Hynobiidae are a clade of salamanders that diverged early within the crown radiation and that retain a considerable number of features plesiomorphic for the group. Their evolutionary history is informed by a fossil record that extends to the Middle Jurassic Bathonian time. Our understanding of the evolution within the total group of Hynobiidae has benefited considerably from recent discoveries of stem hynobiids but is constrained by inadequate anatomical knowledge of some extant forms. Pseudohynobius is a derived hynobiid clade consisting of five to seven extant species living endemic to southwestern China. Although this clade has been recognized for over 37 years, osteological details of these extant hynobiids remain elusive, which undoubtedly has contributed to taxonomic controversies over the hynobiid complex Liua‐Protohynobius‐Pseudohynobius. Here we provide a bone‐by‐bone study of the cranium in the five extant species of Pseudohynobius (Ps. flavomaculatus, Ps. guizhouensis, Ps. jinfo, Ps. kuankuoshuiensis and Ps. shuichengensis) based on x‐ray computer tomography data for 18 specimens. Our results indicate that the cranium in each of these species has a combination of differences in morphology, proportions and articulation patterns in both dermal and endochondral bones. Our study establishes a range of intraspecific differences that will serve as organizing hypotheses for future studies as more extensive collections of these species become available. Morphological features in the cranium for terrestrial ecological adaptation in Hynobiidae are summarized. Based on the results, we also discuss the evolution and development of several potential synapomorphies of Hynobiidae, including features of the orbitosphenoid and articular.

Intrinsic protein disorder is an interesting structural feature where fully functional proteins lack a three-dimensional structure in solution. In this work, we estimated the relative content of intrinsic protein disorder in 96 plant proteomes including monocots and eudicots. In this analysis, we found variation in the relative abundance of intrinsic protein disorder among these major clades; the relative level of disorder is higher in monocots than eudicots. In turn, there is an inverse relationship between the degree of intrinsic protein disorder and protein length, with smaller proteins being more disordered. The relative abundance of amino acids depends on intrinsic disorder and also varies among clades. Within the nucleus, intrinsically disordered proteins are more abundant than ordered proteins. Intrinsically disordered proteins are specialized in regulatory functions, nucleic acid binding, RNA processing, and in response to environmental stimuli. The implications of this on plants' responses to their environment are discussed.

Reconstructing locomotor behaviour for fossil animals is typically done with postcranial elements. However, for species only known from cranial material, locomotor behaviour is difficult to reconstruct. The semicircular canals (SCCs) in the inner ear provide insight into an animal's locomotor agility. A relationship exists between the size of the SCCs relative to body mass and the jerkiness of an animal's locomotion. Additionally, studies have also demonstrated a relationship between SCC orthogonality and angular head velocity. Here, we employ two metrics for reconstructing locomotor agility, radius of curvature dimensions and SCC orthogonality, in a sample of twelve fossil rodents from the families Ischyromyidae, Sciuridae and Aplodontidae. The method utilizing radius of curvature dimensions provided a reconstruction of fossil rodent locomotor behaviour that is more consistent with previous studies assessing fossil rodent locomotor behaviour compared to the method based on SCC orthogonality. Previous work on ischyromyids suggests that this group displayed a variety of locomotor modes. Members of Paramyinae and Ischyromyinae have relatively smaller SCCs and are reconstructed to be relatively slower compared to members of Reithroparamyinae. Early members of the Sciuroidea clade including the sciurid Cedromus wilsoni and the aplodontid Prosciurus relictus are reconstructed to be more agile than ischyromyids, in the range of extant arboreal squirrels. This reconstruction supports previous inferences that arboreality was likely an ancestral trait for this group. Derived members of Sciuridae and Aplodontidae vary in agility scores. The fossil squirrel Protosciurus cf. rachelae is inferred from postcranial material as arboreal, which is in agreement with its high agility, in the range of extant arboreal squirrels. In contrast, the fossil aplodontid Mesogaulus paniensis has a relatively low agility score, similar to the fossorial Aplodontia rufa, the only living aplodontid rodent. This result is in agreement with its postcranial reconstruction as fossorial and with previous indications that early aplodontids were more arboreal than their burrowing descendants.

Temperature is a key environmental parameter affecting both the phenotypes and distributions of organisms, particularly ectotherms. Rapid organismal responses to thermal environmental changes have been described for several ectotherms; however, the underlying molecular mechanisms often remain unclear. Here, we studied whole genome cytosine methylation patterns of European grayling (Thymallus thymallus) embryos from five populations with contemporary adaptations of early life history traits at either 'colder' or 'warmer' spawning grounds. We reared fish embryos in a common garden experiment using two temperatures that resembled the 'colder' and 'warmer' conditions of the natal natural environments. Genome-wide methylation patterns were similar in populations originating from colder thermal origin subpopulations, whereas single nucleotide polymorphisms uncovered from the same data identified strong population structure among isolated populations, but limited structure among interconnected populations. This was surprising because the previously studied gene expression response among populations was mostly plastic, and mainly influenced by the developmental temperature. These findings support the hypothesis of the magnified role of epigenetic mechanisms in modulating plasticity. The abundance of consistently changing methylation loci between two warmer-to-colder thermal origin population pairs suggests that local adaptation has shaped the observed methylation patterns. The dynamic nature of the methylomes was further highlighted by genome-wide and site-specific plastic responses. Our findings support both the presence of a plastic response in a subset of CpG loci, and the evolutionary role of methylation divergence between populations adapting to contrasting thermal environments.

Measurements of agronomic and fruit quality traits in a multi-environment trial using a multi-parental advanced generation intercross population identify QTLs for plasticity and QTL × environment interactions in response to abiotic stresses in tomato., Deciphering the genetic basis of phenotypic plasticity and genotype × environment interactions (G×E) is of primary importance for plant breeding in the context of global climate change. Tomato (Solanum lycopersicum) is a widely cultivated crop that can grow in different geographical habitats and that displays a great capacity for expressing phenotypic plasticity. We used a multi-parental advanced generation intercross (MAGIC) tomato population to explore G×E and plasticity for multiple traits measured in a multi-environment trial (MET) comprising optimal cultural conditions together with water deficit, salinity, and heat stress over 12 environments. Substantial G×E was observed for all the traits measured. Different plasticity parameters were estimated by employing Finlay–Wilkinson and factorial regression models and these were used together with genotypic means for quantitative trait loci (QTL) mapping analyses. In addition, mixed linear models were also used to investigate the presence of QTL × environment interactions. The results highlighted a complex genetic architecture of tomato plasticity and G×E. Candidate genes that might be involved in the occurrence of G×E are proposed, paving the way for functional characterization of stress response genes in tomato and for breeding climate-adapted cultivars.

Natural populations of Populus euphratica in northwest China are divided into four clades exhibiting strong geographical distribution patterns. A total of 38 single nucleotide polymorphisms were associated with salinity tolerance, located in or near 82 genes., Populus euphratica is a dominant tree species in desert riparian forests and possesses extraordinary adaptation to salinity stress. Exploration of its genomic variation and molecular underpinning of salinity tolerance is important for elucidating population evolution and identifying stress-related genes. Here, we identify approximately 3.15 million single nucleotide polymorphisms using whole-genome resequencing. The natural populations of P. euphratica in northwest China are divided into four distinct clades that exhibit strong geographical distribution patterns. Pleistocene climatic fluctuations and tectonic deformation jointly shaped the extant genetic patterns. A seed germination rate-based salinity tolerance index was used to evaluate seed salinity tolerance of P. euphratica and a genome-wide association study was implemented. A total of 38 single nucleotide polymorphisms were associated with seed salinity tolerance and were located within or near 82 genes. Expression profiles showed that most of these genes were regulated under salt stress, revealing the genetic complexity of seed salinity tolerance. Furthermore, DEAD-box ATP-dependent RNA helicase 57 and one undescribed gene (CCG029559) were demonstrated to improve the seed salinity tolerance in transgenic Arabidopsis. These results provide new insights into the demographic history and genetic architecture of seed salinity tolerance in desert poplar.

The remobilization and resorption of plant nutrients is considered as a crucial aspect of the seasonal senescence of plant organs. In leaves, the mechanisms responsible for the relocation of valuable compounds are well understood while the related processes in roots are still being debated. Some research indicates that remobilization in roots occurs, while other studies have not found evidence of this process. Considering that the total biomass of fine roots is equal to or greater than that of leaves, clarifying the conflicting reports and ambiguities may provide critical information on the circulation of chemical elements in forest ecosystems. This study provides new information concerning the basis for remobilization processes in roots by combining physiological data with gene expression and protein levels. We suggest that, as in leaves, molecular mechanisms involved in nitrogen (N) resorption are also activated in senescent roots. An analysis of N concentration indicated that N levels decreased during the senescence of both organs. The decrease was associated with an increase in the expression of a glutamine synthetase (GS) gene and a concomitant elevation in the amount of GS—one of the most important enzymes in N metabolism. In addition, significant accumulation of carbohydrates was observed in fine roots, which may represent an adaptation to unfavorable weather conditions that would allow remobilization to occur rather than a rapid death in response to ground frost or cold. Our results provide new insights into the senescence of plant organs and clarify contentious topics related to the remobilization process in fine roots