Conservation and behavior of Africa＇s ＂Big Five＂

We examine the conservation status of Africa＇s ＂Big Five＂： lion, leopard, buffalo, black and white rhinoceros and elephant, and the role of behavioral knowledge in their conservation. Efforts to conserve these flagship species consist of in situ conservation, captive breeding and reintroductions. With a few exceptions, we find limited evidence that knowledge of behavior informs conservation programs targeted at these species. For management in the wild, knowledge of infanticide and ranging can provide guidelines for realistic hunting quotas and corridors between protected areas, respectively. For ex situ and reintroduction programs, behavioral knowledge is chiefly focused on improved animal husbandry. Despite a formidable understanding of these species＇ behavior, the practicalities of using such knowledge may be diminished because exploitation of these species is so forceful and the bulk of efforts aimed at conserving these species （and indeed most other African species） are primarily in situ where behaviorally driven interventions are limited. Our comparative findings suggest that behavior has been of rather narrow use in the conservation of these flagship species [Current Zoology 60 （4）： 486--499, 2014].     

Considerations for determining optimal mouse caging density

At the 2006 National Meeting of the American Association of Laboratory Animal Science, a panel discussed the question of what constitutes optimal or acceptable housing density for mice. Though there is a consensus that present guidelines are somewhat arbitrarily defined, scientific research has not yet been able to provide clear recommendations for amending them. Speakers explored the many factors that influence decisions on mouse housing, including regulatory requirements, scientific data and their interpretation, financial considerations and ethical concems. The panel largely agreed that animal well-being should be the measure of interest in evaluating housing density and that well-being includes not only physical health, but also animals＇ behavior, productivity and preference. Lab Animal 2007,36（10）     

Individual differences in boldness positively correlate with heart rate in orb-weaving spiders of genus Larinioides

Recent years have seen a dramatic increase in the number of studies devoted to consistent individual differences in behavior, termed ＂behavioral syndromes＂ or animal ＂personality＂. In particular, ecologists and evolutionary biologists alike seek to explore the functional consequences of individuals＇ personalities and explanations for their general maintenance. Understand ing the mechanistic underpinnings to personality is arguably key to a deeper understanding of their functional consequences and maintenance. In particular, consistent individual differences in metabolic rate have been proposed as a general explanation for the maintenance of consistent individual differences in boldness, aggressiveness, and activity level. In this paper we explore whether consistent individual differences in boldness are associated with heat rate, a proxy for metabolic rate, in two species of orbweaving spider： Larinioides cornutus and L. patagiatus. We first documented consistent individual differences in boldness in L. cornutus but not L. patagiatus, as estimated by individuals＇ latency to resume movement following an aversive stimulus. We also measured individuals＇ heart rate twice in a separate situation. We then tested for an association between individuals＇ boldness and their heart rate during these two events. We found that increased boldness was associated with increased heart. Thus, indi viduals that resumed movement quickly following an aversive stimulus also exhibited faster heart rates. Our studies provide fur ther evidence that consistent individual differences in key physiological attributes, like metabolic rate, might be a general mecha nism underlying consistent individual differences in behavior .     

The role of behavior in tern conservation

Behavioral research has long had an important role in the conservation of terns （Ayes： Stemidae）. Habitat management and restoration of breeding colony sites depends on knowledge of the cues used to select colony and nest sites. For example, conspecific attraction with playback and decoys is commonly used to bring terns to suitable colony sites and habitat modification is often used to increase the availability of suitable nest sites. Tern colonies are interconnected by dispersal, and a metapopulation approach is needed for effective management. Population dynamics are therefore affected by behaviors that influence the frequency of movement among colony sites： site fidelity, natal and breeding dispersal, and group adherence. The monogamous breeding system of terns should keep effective population size similar to census population size, but variation in sex ratios （likely resulting from sex differences in behavior） and in parental quality can result in a smaller than expected effective population size. In addition to the behavior of terns, knowledge of the behavior of predators on terns contributes to management plans, because predator behavior can sometimes be manipulated and predation is often performed by only a few specialized individuals. Other examples of links between tern behavior and conservation are also briefly reviewed, such as behavioral toxicology research and studies of behavioral responses to human disturbance and manmade structures. More work is needed on the behavior of migratory terns at staging sites, stopover sites and wintering grounds, and on the behavior of less well-studied species and species in less well-studied geographic regions [Current Zoology 60 （4）： 500-514, 2014].     

A miniaturized assay to quantify effects of chemicals or physical stimuli upon locust activity

Solitary and gregarious locusts differ in many traits, such as body color, morphometrics and behavior. With respect to behavior, solitary animals shun each other, while gregarious animals seek each other＇s company, hence their crowding behavior. General activity, depending on the temperature, occurs throughout the day but is much lower in solitary locusts. Solitary locusts occasionally fly by night while gregarious locusts fly regularly during daytime （swarming）. In search of new assays to identify substances that control or modify aspects of （phase） behavior, we designed a simple activity assay, meant to complement existing behavioral measurement tools. The general activity is reflected in the number of wall hits, that is, the number of contacts between the locust and the vertical walls of a small arena. Using this single parameter we were able to quantify differences in total activity of both nymphs and adults of isolation-reared （solitary）, regrouped- and crowdreared （gregarious） locusts under different conditions. Furthermore, we demonstrate that there are inter- and intra-phase dependent differences in activities of 5th instar nymphs afar injections of the three different adipokinetic hormones.     

Insights from the study of complex systems for the ecology and evolution of animal populations

Populations of animals comprise many individuals,interacting in multiple contexts,and displaying heterogeneous behaviors.The interactions among individuals can often create population dynamics that are fundamentally deterministic yet display unpredictable dynamics.Animal populations can,therefore,be thought of as complex systems.Complex systems display properties such as nonlinearity and uncertainty and show emergent properties that cannot be explained by a simple sum of the interacting components.Any system where entities compete,cooperate,or interfere with one another may possess such qualities,making animal populations similar on many levels to complex systems.Some fields are already embracing elements of complexity to help understand the dynamics of animal populations,but a wider application of complexity science in ecology and evolution has not occurred.We review here how approaches from complexity science could be applied to the study of the interactions and behavior of individuals within animal populations and highlight how this way of thinking can enhance our understanding of population dynamics in animals.We focus on 8 key characteristics of complex systems:hierarchy,heterogeneity,selforganization,openness,adaptation,memory,nonlinearity,and uncertainty.For each topic we discuss how concepts from complexity theory are applicable in animal populations and emphasize the unique insights they provide.We finish by outlining outstanding questions or predictions to be evaluated using behavioral and ecological data.Our goal throughout this article is to familiarize animal ecologists with the basics of each of these concepts and highlight the new perspectives that they could bring to variety of subfields.     

An Experimental Analysis of Overcoming Obstacle in Human Walking

In this paper, an experimental analysis of overcoming obstacle in human walking is carried out by means of a motion capture system. In the experiment, the lower body of an adult human is divided into seven segments, and three markers are pasted to each segment with the aim to obtain moving trajectory and to calculate joint variation during walking. Moreover, kinematic data in terms of displacement, velocity and acceleration are acquired as well. In addition, ground reaction forces are measured using force sensors. Based on the experimental results, features of overcoming obstacle in human walking are ana- lyzed. Experimental results show that the reason which leads to smooth walking can be identified as that the human has slight movement in the vertical direction during walking; the reason that human locomotion uses gravity effectively can be identified as that feet rotate around the toe joints during toe-off phase aiming at using gravitational potential energy to provide propulsion for swing phase. Furthermore, both normal walking gait and obstacle overcoming gait are characterized in a form that can provide necessary knowledge and useful databases for the implementation of motion planning and gait planning towards overcoming obstacle for humanoid robots.     

Animal venom studies: Current benefits and future developments

Poisonous organisms are represented in many taxa, including kingdom Animalia. During evolution, animals have developed special organs for production and injection of venoms. Animal venoms are complex mixtures, compositions of which depend on species producing venom. The most known and studied poisonous terrestrial animals are snakes, scorpions and spiders. Among marine animals, these are jellyfishes, anemones and cone snails. The toxic substances in the venom ofthese animals are mainly of protein and peptide origin. Recent studies have indicated that the single venom may contain up to several hundred different components producing diverse physiological effects. Bites or stings by certain poisonous species result in severe envenomations leading in some cases to death. This raises the problem of bite treatment. The most effective treatment so far is the application of antivenoms. To enhance the effectiveness of such treatments, the knowledge of venom composition is needed. On the other hand, venoms contain substances with unique biological properties, which can be used both in basic science and in clinical applications. The best example of toxin application in basic science is α-bungarotoxin the discovery of which made a big impact on the studies of nicotinic acetylcholine receptor. Today compositions of venom from many species have already been examined. Based on these data, one can conclude that venoms contain a large number of individual components belonging to a limited number of structural types. Often minor changes in the amino acid sequence give rise to new biological properties. Change in the living conditions of poisonous animals lead to alterations in the composition of venoms resulting in appearance of new toxins. At the same time introduction of new methods of proteomics and genomics lead to discoveries of new compounds, which may serve as research tools or as templates for the development of novel drugs. The application of these sensitive and comprehensive methods allows studying either of venoms available in tiny amounts or of low abundant components in already known venoms.     

Bioinspired 4D Trajectory Generation for a UAS Rapid Point-to-Point Movement

A bioinspired trajectory generation approach for Unmanned Aerial System （UAS） rapid Point-to-Point （PTP） movement was presented. The approach was based on general tau theory developed by biologists from observing and studying the behavior of birds and some other animals. We applied the bioinspired approach to the rapid PTP movement problem of a rotary UAS and derived two different trajectory planning strategies, namely, the tau coupling strategy and the intrinsic tau gravity guidance strategy. Based on general tau theory, according to the dynamic model of UAS, we presented a new strategy named intrinsic tau jerk guidance which can fit the movement that the initial acceleration of the UAS is zero. With new strategies, flight trajectory generation examples with a UAS were presented. The kinematics and dynamics analyses of the UAS for rapid PTP movement were presented with simulation results which show that the generated trajectories were feasible.     

How territoriality affects the density of an egg predator： Habitat renovation and reintroduction as a method of conserving two endangered desert spring fish

Conservation of endangered sympatric species must be carefully executed to ensure that the protection of one species does not negatively impact the survival of another. Critically endangered Pecos gambusia Gambusia nobilis and Leon Springs pupfish Cyprinodon bovinus, which are endemic to a threatened desert spring habitat, exemplify one such scenario. Recently, this habitat has been expanded, and captively bred C. bovinus were released to repopulate an area historically known to contain this species. A previous study suggested that G. nobilis are detrimental to C. bovinus populations, due to their tendency to congregate near spawning pairs and feed on their eggs. Whether G. nobilis are attracted to territorial C. bovinus, regardless of spawning behavior, remains unclear. To determine this, the number of G. nobilis in occupied and unoccupied breeding territories of both wild and captively bred C. bovinus was measured. Gambusia nobilis densities were similar between unoccupied and occupied territorial sites, suggesting that they do not show a preference for C. bovinus territories. Regardless of habitat location or prior captivity, territorial C. bovinus significantly excluded G. nobilis within their direct vicinity （5 cm）, but not from their entire territory. Decreased G. nobilis density within the habitat may allow C. bovinus to defend their breeding territories more readily during the summer spawning season. This study provides empirical evidence of captively raised individuals behaving similarly to wild indi- viduals upon reintroduction to their natural habitat and support for conservation methods that focus on common limiting factors between endangered species [Current Zoology 60 （4）： 527-533, 2014].     

Validation of the binary designation Symbiodinium thermophilum (Dinophyceae)

The binary designation Symbiodinium thermophilum was invalid due to the absence of an illustration as required by Article 44.2 of the ICN. Herein, it is validated. This species is the most common symbiont in reef corals in the southern Persian/Arabian Gulf, the world's hottest body of water sustaining reef coral growth.     

Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry

Background

The 1000 Genome project paved the way for sequencing diverse human populations. New genome projects are being established to sequence underrepresented populations helping in understanding human genetic diversity. The Kuwait Genome Project an initiative to sequence individual genomes from the three subgroups of Kuwaiti population namely, Saudi Arabian tribe; “tent-dwelling” Bedouin; and Persian, attributing their ancestry to different regions in Arabian Peninsula and to modern-day Iran (West Asia). These subgroups were in line with settlement history and are confirmed by genetic studies. In this work, we report whole genome sequence of a Kuwaiti native from Persian subgroup at >37X coverage.

Results

We document 3,573,824 SNPs, 404,090 insertions/deletions, and 11,138 structural variations. Out of the reported SNPs and indels, 85,939 are novel. We identify 295 ‘loss-of-function’ and 2,314 ’deleterious’ coding variants, some of which carry homozygous genotypes in the sequenced genome; the associated phenotypes include pharmacogenomic traits such as greater triglyceride lowering ability with fenofibrate treatment, and requirement of high warfarin dosage to elicit anticoagulation response. 6,328 non-coding SNPs associate with 811 phenotype traits: in congruence with medical history of the participant for Type 2 diabetes and β-Thalassemia, and of participant’s family for migraine, 72 (of 159 known) Type 2 diabetes, 3 (of 4) β-Thalassemia, and 76 (of 169) migraine variants are seen in the genome. Intergenome comparisons based on shared disease-causing variants, positions the sequenced genome between Asian and European genomes in congruence with geographical location of the region. On comparison, bead arrays perform better than sequencing platforms in correctly calling genotypes in low-coverage sequenced genome regions however in the event of novel SNP or indel near genotype calling position can lead to false calls using bead arrays.

Conclusions

We report, for the first time, reference genome resource for the population of Persian ancestry. The resource provides a starting point for designing large-scale genetic studies in Peninsula including Kuwait, and Persian population. Such efforts on populations under-represented in global genome variation surveys help augment current knowledge on human genome diversity.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1233-x) contains supplementary material, which is available to authorized users.     

Observations of stranded and swimming whale sharks Rhincodon typus in Khor Al-Zubair,NW Arabian Gulf and Shatt Al-Arab Estuary,Iraq

This study is the first record of a whale shark Rhincodon typus in Iraqi waters and the second record from the Arabian (Persian) Gulf portion of the north-west Indian Ocean. The stranding and sighting events were documented by photos of three individuals: the stranded specimen was 6.5 m total length (L_T) and the free-swimming individuals were c. 1–2 and 2–3 m L_T respectively_. An appeal is made for Iraqi policy makers to participate in regional and international organizations for the conservation of this endangered species.     

Fish communities on the world's warmest reefs: what can they tell us about the effects of climate change in the future?

To examine the role of climatic extremes in structuring reef fish communities in the Arabian region, reef fish communities were visually surveyed at four sites within the southern Persian Gulf (also known as the Arabian Gulf and The Gulf), where sea-surface temperatures are extreme (range: 12-35° C annually), and these were compared with communities at four latitudinally similar sites in the biogeographically connected Gulf of Oman, where conditions are more moderate (range: 22-31° C annually). Although sites were relatively similar in the cover and composition of coral communities, substantial differences in the structure and composition of associated fish assemblages were apparent. Fish assemblages in the southern Persian Gulf held significantly lower estimates of abundance, richness and biomass, with significantly higher abundances of smaller sized individuals than Gulf of Oman assemblages. Functionally, southern Persian Gulf sites held significantly lower abundances of nearly all the common fish trophic guilds found on Gulf of Oman sites, although higher abundances of herbivorous grazers were apparent. These results suggest the potential for substantial changes in the structure of reef-associated fish communities, independent of changes in habitat within an environment of increasing fluctuations in oceanic climate.     

Vegetation Mapping of the Mond Protected Area of Bushehr Province （South-west Iran）

Arid regions of the world occupy up to 35% of the earth＇s surface, the basis of various definitions of climatic conditions, vegetation types or potential for food production. Due to their high ecological value, monitoring of arid regions is necessary and modern vegetation studies can help in the conservation and management of these areas. The use of remote sensing for mapping of desert vegetation is difficult due to mixing of the spectral reflectance of bright desert soils with the weak spectral response of sparse vegetation. We studied the vegetation types in the semiarid to arid region of Mond Protected Area, south-west Iran, based on unsupervised classification of the Spot XS bands and then produced updated maps. Sixteen map units covering 12 vegetation types were recognized in the area based on both field works and satellite mapping. Halocnemum strobilaceum and Suaeda fruticosa vegetation types were the dominant types and Ephedra foliata, Salicornia europaea-Suaeda heterophylla vegetation types were the smallest. Vegetation coverage decreased sharply with the increase in salinity towards the coastal areas of the Persian Gulf. The highest vegetation coverage belonged to the riparian vegetation along the Mond River, which represents the northern boundary of the protected area. The location of vegetation types was studied on the separate soil and habitat diversity maps of the study area, which helped in final refinements of the vegetation map produced.     

The dispersal of Halimeda in northern hemisphere mid-latitudes: Palaeobiogeographical insights

The bryopsidalean alga Halimeda gained an important role as carbonate producer in Cenozoic tropical coral reefs and became a significant constituent of the modern Mediterranean seaweed flora. There are, however, open questions at which time the thermophile alga appeared in the cooler Mediterranean Sea and why it is not detected in coral reefs of the modern Persian Gulf. To unravel the biogeography and ecology of Halimeda at its northern margin of distribution, we use fossil Halimeda records of the Central Paratethys/Medditerranean for comparison of the geological, (palaeo)ecological and evolutionary dispersal constraints of the alga in the Miocene and Holocene Persian Gulf. The revealed spatial and temporal distribution patterns of Halimeda in the regions of the Mediterranean and Arabian seas identify water temperature as the major ecological constraint and the extreme Plio-Pleistocene climate changes as the motor for the dispersal and evolution of Halimeda in higher latitudes. Generally, the distribution of tropical species in higher latitudes was related to warm climate intervals during the Neogene. Accordingly, the available (palaeo)biogeographic data implies that the warm-adapted ancestors of the present-day Mediterranean H. tuna population possibly entered the Mediterranean Sea during the mid-Pliocene global warmth and became isolated during subsequent cooling. It also implies that the warm Persian Gulf water is probably unsuitable for the cool-adapted H. discoidea population in the Gulf of Oman and that its tropical ancestors could have reached the Gulf of Oman only during a Pleistocene glacial phase when monsoon-induced upwelling of cold water in the Arabian Sea was reduced and the Persian Gulf fell dry. This example demonstrates the limitation of the actualistic palaeontological approach when using biota at the edges of their distribution range as palaeoclimate proxy.     

First record of mudskipper Boleophthalmus dussumieri (Gobiidae: Oxudercinae) on the coast of Mozambique and evidence of two putative lineages along its known distribution range

Boleophthalmus dussumieri is one of the most widely distributed mudskippers and is native to the Persian Gulf in Iran down to the northeast of the Arabian Sea and the coast of India. Nonetheless, the present study is the first to confirm the presence of B. dussumieri in the marine areas of the Mozambique coast. In addition, molecular analysis revealed strong evidence for the existence of two lineages with a high level of nucleotide divergence along the sampled area, revealing a still-neglected taxonomic condition for this lineage/species.     

Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Bracbypodium distacbyon

This work evaluates the phenotypic response of the model grass （Brachypodium distacbyon （L.） P. Beauv.） to nitrogen and phosphorus nutrition using a combination of imaging techniques and destructive harvest of shoots and roots. Reference line Bd21-3 was grown in pots using 11 phosphorus and 11 nitrogen concentrations to establish a dose-response curve. Shoot biovolume and biomass, root length and biomass, and tissue phosphorus and nitrogen concentrations increased with nutrient concentration. Shoot biovolume, estimated by imaging, was highly correlated with dry weight （R2 〉 0.92） and both biovolume and growth rate responded strongly to nutrient availability. Higher nutrient supply increased nodal root length more than other root types. Photochemical efficiency was strongly reduced by low phosphorus concentrations as early as 1 week after germination, suggesting that this measurement may be suitable for high throughput screening of phosphorus response. In contrast, nitrogen concentration had little effect on photochemical efficiency. Changes in biovolume over time were used to compare growth rates of four accessions in response tonitrogen and phosphorus supply. We demonstrate that a time series image-based approach coupled with mathematical modeling provides higher resolution of genotypic response to nutrient supply than traditional destructive techniques and shows promise for high throughput screening and determina- tion of genomic regions associated with superior nutrient use efficiency.     

Identification and characterization of genes involved in the jasmonate biosynthetic and signaling pathways in mulberry （Morus notabilis）

Jasmonate （JA） is an important phytohormone regulating growth, development, and environmental response in plants, particularly defense response against herbivorous insects. Recently, completion of the draft genome of the mulberry （Morus notabilis） in conjunction with genome sequencing of silkworm （Bombyx mori） provides an opportuni-ty to study this unique plant-herbivore interaction. Here, we identified genes involved in JA biosynthetic and signaling pathways in the genome of mulberry for the first time, with the majority of samples showing a tissue-biased expression pattern. The analysis of the representative genes 12-oxophy-todienoic acid reductase （OPRs） and jasmonate ZIM-domain （JAZs） was performed and the results indicated that the mulberry genome contains a relatively smal number of JA biosynthetic and signaling pathway genes. A gene encoding an＆amp;nbsp;important repressor, MnNINJA, was identified as an alternative splicing variant lacking an ethylene-responsive element binding factor-associated amphiphilic repression motif. Having this fundamental information wil facilitate future functional study of JA-related genes pertaining to mulberry-silkworm interactions.