The use of machine learning to detect foraging behaviour in whale sharks: a new tool in conservation

In this study we present the first attempt at modelling the feeding behaviour of whale sharks using a machine learning analytical method. A total of eight sharks were monitored with tri-axial accelerometers and their foraging behaviours were visually observed. Our results highlight that the random forest model is a valid and robust approach to predict the feeding behaviour of the whale shark. In conclusion this novel approach exposes the practicality of this method to serve as a conservation tool and the capability it offers in monitoring potential disturbances of the species.     

Evaluating cetacean body condition; a review of traditional approaches and new developments

The ability to accurately gauge the body condition of free‐swimming cetaceans is invaluable in population and conservation biology, due to the direct implications that this measure has on individual fitness, survival, and reproductive success. Furthermore, monitoring temporal change in body condition offers insight into foraging success over time, and therefore the health of the supporting ecosystem, as well as a species’ resilience. These parameters are particularly relevant in the context of widespread and accelerated, climate‐induced habitat change. There are, however, significant logistical challenges involved with research and monitoring of large cetaceans, which often preclude direct measure of body condition of live individuals. Consequently, a wide variety of indirect approaches, or proxies, for estimating energetic stores have been proposed over past decades. To date, no single, standardized, approach has been shown to serve as a robust estimation of body condition across species, age categories, and in both live and dead individuals. Nonetheless, it is clear that streamlining and advancing body condition measures would carry significant benefits for diverse areas of cetacean research and management. Here, we review traditional approaches and new applications for the evaluation of cetacean energetic reserves. Specific attention is given to the criteria of measure performance (sensitivity and accuracy), level of invasiveness, cost and effort required for implementation, as well as versatility e.g. applicability across different species, age groups, as well as living versus deceased animals. Measures have been benchmarked against these criteria in an effort to identify key candidates for further development, and key research priorities in the field.     

Individual-based analysis opens new insights into understanding population structure and animal behaviour

Studying the movement of individuals in the wild has always been a challenge in ecology. However, estimating such movement is essential in life sciences as it is the base-line for evaluating connectivity, a major component in developing management and conservation plans. Furthermore, movement, or migration, is an essential parameter in population genetics, as it directly affects genetic differentiation. The development of highly variable markers has allowed genetic discrimination between individuals within populations and at larger scales, and the availability of high-throughput technologies means that many samples and hence many individuals can be screened. These advances mean that we can now use genetic identification for tracking individuals, and hence follow both survival and reproductive output through the life cycle. The paper by Morrissey & Ferguson (2011, this issue) is a demonstration of this new capability, as authors were able to infer the movement of salmonid fish initially captured as juveniles, and later as reproductively mature adults.     

Machine analysis of facial behaviour: naturalistic and dynamic behaviour

This article introduces recent advances in the machine analysis of facial expressions. It describes the problem space, surveys the problem domain and examines the state of the art. Two recent research topics are discussed with particular attention: analysis of facial dynamics and analysis of naturalistic (spontaneously displayed) facial behaviour. Scientific and engineering challenges in the field in general, and in these specific subproblem areas in particular, are discussed and recommendations for accomplishing a better facial expression measurement technology are outlined.     

SMS seal: A new technique to measure haul-out behaviour in marine vertebrates

Many marine vertebrates, including pinnipeds, turtles and birds, spend periods of time ashore during their life cycles. Quantification of time spent ashore is important for estimating population parameters such as abundance and productivity in some species, but can prove to be a difficult task. Here we describe a novel telemetry system based on Global Systems for Mobile Communications (GSM), to provide detailed information on the haul-out behaviour of tagged animals. We tested the system on harbour seals in southwest Ireland. The GSM telemetry system proved an effective means of obtaining information on the haul-out activity of harbour seals in the study area and of providing crude movement information that was less labour intensive than VHF telemetry and provides an alternative means of data acquisition offering some advantages over satellite telemetry. The GSM tag with its internal antennae is more robust than a satellite tag. The GSM networks allow more information to be relayed, so the “cost per bit of data” is reduced. Moreover, the large global investment in GSM networks have resulted in a telemetry technology with low running costs and therefore with significantly lower costs of data acquisition via GSM relative to Argos systems. With the ever-expanding global GSM network coverage the system has significant potential applications in behavioural studies of amphibious vertebrates, such as estimating clutch frequency in sea turtles.     

Population and behaviour genetics of Drosophila ananassae

Drosophila ananassae is a cosmopolitan and domestic species. It occupies a nuique status among the Drosophila species due to certain peculiarities in its genetic behaviour. The most unusual feature of this species is spontaneous male recombination in appreciable frequency. The present review summarises the work done on population and behaviour genetics of D. ananassae from India. Population dynamics of three cosmopolitan inversions has been studied in Indian population of D. ananassae and it is evident from the results that there is a considerable degree of genetic divergence at the level of inversion polymorphism. In general, the populations from south India show more differentiation than those from the north. These three cosmopolitan inversions, which are coextensive with the species, exhibit heterosis. Interracial hybridization does not lead to beaakdown of heterosis, which suggests that evidence for coadaptation is lacking in geographic populations of D. ananassae. Heterosis appears to be simple luxuriance rather than populational heterosis (coadaptation). Unlinked inversions occur in random associations, indicating no interchromosomal interactions. However, two inversions of the third chromosome often show strong linkage disequilibrium in laboratory populations, which is due to epistatic gene interaction and suppression of crossing-over. Genetic variations for certain allozyme polymorphism and sternoleural bristle phenotypes in Indian populations of D. ananassae have also been observed.A number of investigations have also been carried out on certain aspects of behaviour genetics of Indian D. ananassae. There is evidence for sexual isolation within D. ananassae. Significant variations in mating propensity of several isofemale strains, inversion karyotypes, the diminishing effects of certain mutations on sexual activity of males and positive response to selection for high and low mating propensity provide evidence for genetic control of sexual behaviour in D. ananassae. Males contribute more to variation and thus are more subject to intra-sexual selection than females. Evidence for rare male mating advantage has also been presented. Geographic strains of D. ananassae show variation with respect to oviposition site preference. The results of studies on pupation site preference, which is an important component of larval behaviour, suggest that larval pupation behaviour in D. ananassae is under polygenic control with a substantial amount of additive genetic variation.     

Microalgae wastewater treatment: Biological and technological approaches

Current global environmental issues raise unavoidable challenges for our use of natural resources. Supplying the human population with clean water is becoming a global problem. Numerous organic and inorganic impurities in municipal, industrial, and agricultural waters, ranging from microplastics to high nutrient loads and heavy metals, endanger our nutrition and health. The development of efficient wastewater treatment technologies and circular economic approaches is thus becoming increasingly important. The biomass production of microalgae using industrial wastewater offers the possibility of recycling industrial residues to create new sources of raw materials for energy and material use. This review discusses algae‐based wastewater treatment technologies with a special focus on industrial wastewater sources, the potential of non‐conventional extremophilic (thermophilic, acidophilic, and psychrophilic) microalgae, and industrial algae‐wastewater treatment concepts that have already been put into practice.     

Allomothering behaviour of new and old world monkeys

The holding or transferring of newborn infants at less than 1 month old by individuals other than the mothers was studied in 24 species of New and Old World monkeys under captive conditions. The observed monkey species could be divided into two types. Group A included eight species of three families where the mothers were tolerant to ‘infant transfer’ and readily retrieved their infants from other individuals, the frequency of infant transfer being high. The infant transfer of this group was termed allomothering behaviour. Group B included 16 species of two families where infant transfer did not occur at all or its frequency was very low and the mothers were possessive of their infants. Once transfer did occur, the infant could not be reclaimed with ease. The relationships between the two groups and taxonomic status, life forms and social types were evaluated in a total of 45 species from the present study and the literature. Correspondences were found with social type and taxonomic status. That is, species of Group A were seen only in the family or one-male type, except for one species, although none of this group appeared in the Cercopithecinae regardless of social types. The significance of infant transfer is discussed in relation to the participants' responses to it and the correlations between the two groups and social types.     

Electrochemical monitoring of cell behaviour in vitro: a new technology

This article describes a novel electrochemical technique for the real-time monitoring of changes in the behaviour of adherent human cells in vitro: i.e., a biosensor that combines a biological recognition mechanism with a physical transduction technique, described collectively as Oncoprobe. Confluent viable cells adherent to gold electrodes (sensors) modify the extracellular microenvironment at the cell:sensor interface to produce a change in the electrochemical potential compared to that measured in the absence of cells. The potential was measured as an open circuit potential (OCP) with respect to a saturated calomel reference in the bulk culture medium. Typical OCP values for confluent cultures of human breast carcinoma cells, 8701-BC, approximated -100 mV compared with cell-free values of approximately -15 mV. The OCP for 8701-BC cells was modified in response to temperature changes over the range 32 to 40 degrees C and also to treatments with phytohemagglutinin (PHA, 25 microg/mL), cycloheximide (30 microM) and interleukin-1 beta (IL-1, 0.5 ng/mL) over 24 h. Cultures of synovial fibroblasts also responded to the same treatments with similar responses, producing negative shifts in the OCP signal with PHA and IL-I, but a positive shift in OCP signal with cycloheximide, all relative to the untreated control cultures. From experimental data and theoretical considerations it is proposed that the cell-derived signals are mixed electrode potentials reflecting a "conditioned," more reducing environment at the cell:sensor interface. Only viable cells caused a negative shift in the OCP signal, this being lost when cells were rendered nonviable by formalin exposure. This technology appears unique in its ability to passively "listen in" on cell surface activities, suggesting numerous applications in the fields of drug discovery, chemotherapy, and cell behaviour.     

Whole‐genome sequencing approaches for conservation biology: Advantages,limitations and practical recommendations

Whole‐genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled‐individual DNA (Pool‐seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.     

Yangtze finless porpoises along the main channel of Poyang Lake,China: Implications for conservation

Poyang Lake is the largest freshwater lake in China and flows into the Yangtze River. It is a traditional habitat for the endangered Yangtze finless porpoise, which has not been well investigated. To reveal the distribution of the porpoise in Poyang Lake, 12 passive acoustic surveys were conducted along 123 km of the main channel of the lake during different seasons (spring transition season, wet season, autumn transition season, and dry season) from 2008 to 2012. We counted the number of phonating porpoises encountered and calculated the detection rate (encountered individuals detected per kilometer). The median porpoise detection rates ranged from 0 to 0.65 individuals per kilometer during the different surveys. The highest median detection rate of 0.50 was detected in the autumn transition season. The seasonal shrinking of the lake during the dry season may cause a concentration of porpoises in the narrow channels and a high incidence of collisions with cargo ships and fishing boats. Conservation actions should be focused on the main channel of the lake during the dry and transition seasons. In addition, the expansion of the existing reserve to include areas with high porpoise detection rates is necessary.     

Geographic structure in the searching behaviour of a specialist parasitoid: combining molecular and behavioural approaches

An increasing number of studies have shown that the traits important to species interactions may differ geographically among populations or groups of populations within a single interacting species. We examined geographic structure in the searching behaviour of a recently discovered parasitoid in the genus Agathis (Hymenoptera: Braconidae) by examining the pattern of population structure obtained from sequence data of mitochondrial DNA cytochrome oxidase I and the pattern of population differentiation in female searching behaviour. Analyses of population structure showed no isolation by distance and suggested long distance dispersal among populations. This pattern is consistent with recent post‐glacial expansion of Agathis n. sp. Observations of searching behaviour demonstrated that populations of Agathis n. sp. differed in a subset of the behavioural traits examined and also one morphological trait. These population differences appear to be driven in part by local host plant characteristics, and based on the population structure of Agathis n. sp., have arisen relatively quickly in evolutionary time. This study suggests that the interaction between parasitoids and their host insects may exhibit substantial geographic variation, and studies that focus at the level of single populations or the species‐level may be missing much of the evolutionary dynamics of parasitoid–host interactions.     

转录组研究新技术:RNA-Seq及其应用

转录组是特定组织或细胞在某一发育阶段或功能状态下转录出来的所有RNA的集合。转录组研究能够从整体水平研究基因功能以及基因结构,揭示特定生物学过程以及疾病发生过程中的分子机理。RNA-Seq作为一种新的高效、快捷的转录组研究手段正在改变着人们对转录组的认识。RNA-Seq利用高通量测序技术对组织或细胞中所有RNA反转录而成的cDNA文库进行测序,通过统计相关读段(reads)数计算出不同RNA的表达量,发现新的转录本;如果有基因组参考序列,可以把转录本映射回基因组,确定转录本位置、剪切情况等更为全面的遗传信息,已广泛应用于生物学研究、医学研究、临床研究和药物研发等。文章主要介绍了RNA-Seq原理、技术特点及其应用,并就RNA-Seq技术面临的挑战和未来发展前景进行了讨论,为今后该技术的研究与应用提供参考。     

Gel-forming algal polysaccharides: structural characterisation and technological applications

Abstract

Some aspects of both the chemical and physico-chemical properties of gelling algal polysaccharides are reviewed in connection with their technological and biotechnological uses. In fact, besides the traditional applications, which are mainly in the field of food industry, recent sophisticated biotechnological manipulations opened the way for the exploitation of these molecules for very advanced applications like the formulation of micro spheres for cell incubation. Some aspects of the structure of alginate gel beads used for cell immobilisation are illustrated.     

长瓣杓兰（Cypripedium lentiginosum）种群数量动态与生殖行为的相关性

尽管种群数量动态分析已广泛应用于濒危物种,但很少应用于中国兰科植物.根据中国云南特有的兰科物种长瓣杓兰(Cypnpedium lentiginosum)的生物学特征调查和生殖行为观察,计算出其各龄级的存活数、出现频率和子代数,描述其生殖行为和机制.利用基株出现频率计算其空间分布格局;利用其各龄级的存活数和平均生产子代数编制种群静态生命表和生殖力表、绘制存活曲线和年龄锥体,构建Leslie矩阵模型和连续增长模型N1=658e0.211t对种群数量动态过程进行预测;利用物候特征和传粉生物学观察结果分析其生殖行为和繁殖策略.在此基础上分析其生殖行为与其空间格局、年龄锥体和种群数量动态的关系.结果表明:长瓣杓兰的空间结构为成群分布,种群的年龄锥体属于金字塔-钟型锥体,种群存活表现为Deevey Ⅰ型;其种群的净增长率、内禀增长率和周限增长率较高,为增长型种群;种群增长受自身密度影响,连续增长模型不适用该种群的动态预测;引入密度制约因子构建的预测模型Nt=6000/(1 e2.094-0.211t)适用于其种群数量动态预测.长瓣杓兰的生殖行为表现在兼具无性繁殖和有性繁殖,无性繁殖不增加种群的个体数量,仅延续基株的寿命以维持现行种群数量和为有性生殖积累营养.有性繁殖通过花模拟繁殖地欺骗食蚜蝇进入唇瓣而传粉,致使54.37%±6.08%的花产生果实,果实产生充足幼龄植株并多数能进入有性繁殖阶段.有性繁殖在很长的一段时期多次生殖后代而成为种群发展的基础,显示出繁殖方式是影响种群数量动态变化的主要因素.其成功的生殖对策和这种对策在空间格局、年龄锥体上对种群数量动态的影响具有密切的相关性,表明长瓣杓兰的种群发展与其生物学特性相吻合,适生地的生长空间不连续性和狭窄成为其种群发展的制约因素,但该物种现在不需要也不适宜进行迁地保护.