trajr: An R package for characterisation of animal trajectories

Quantitative characterisation of the trajectories of moving animals is an important component of many behavioural and ecological studies, however methods are complicated and varied, and sometimes require well‐developed programming skills to implement. Here, we introduce trajr, an R package that serves to analyse animal paths, from unicellular organisms, through insects to whales. It makes a variety of statistical characterisations of trajectories, such as tortuosity, speed and changes in direction, available to biologists who may not have a background in programming. We discuss a range of indices that have been used by researchers, describe the package in detail, then use movement observations of whales and clearwing moths to demonstrate some of the capabilities of trajr. As an open‐source R package, trajr encourages open and reproducible research. It supports the implementation of additional methods by providing access to trajectory analysis “building blocks,” allows the full suite of R statistical analysis tools to be applied to trajectory analysis, and the source code can be independently validated.     

The assembly and disassembly of ecological networks

Global change has created a severe biodiversity crisis. Species are driven extinct at an increasing rate, and this has the potential to cause further coextinction cascades. The rate and shape of these coextinction cascades depend very much on the structure of the networks of interactions across species. Understanding network structure and how it relates to network disassembly, therefore, is a priority for system-level conservation biology. This process of network collapse may indeed be related to the process of network build-up, although very little is known about both processes and even less about their relationship. Here we review recent work that provides some preliminary answers to these questions. First, we focus on network assembly by emphasizing temporal processes at the species level, as well as the structural building blocks of complex ecological networks. Second, we focus on network disassembly as a consequence of species extinctions or habitat loss. We conclude by emphasizing some general rules of thumb that can help in building a comprehensive framework to understand the responses of ecological networks to global change.     

A 3D building blocks approach to analyzing and predicting structure of proteins

A new approach is introduced for analyzing and ultimately predicting protein structures, defined at the level of C alpha coordinates. We analyze hexamers (oligopeptides of six amino acid residues) and show that their structure tends to concentrate in specific clusters rather than vary continuously. Thus, we can use a limited set of standard structural building blocks taken from these clusters as representatives of the repertoire of observed hexamers. We demonstrate that protein structures can be approximated by concatenating such building blocks. We have identified about 100 building blocks by applying clustering algorithms, and have shown that they can "replace" about 76% of all hexamers in well-refined known proteins with an error of less than 1 A, and can be joined together to cover 99% of the residues. After replacing each hexamer by a standard building block with similar conformation, we can approximately reconstruct the actual structure by smoothly joining the overlapping building blocks into a full protein. The reconstructed structures show, in most cases, high resemblance to the original structure, although using a limited number of building blocks and local criteria of concatenating them is not likely to produce a very precise global match. Since these building blocks reflect, in many cases, some sequence dependency, it may be possible to use the results of this study as a basis for a protein structure prediction procedure.     

The ecology,behaviour and physiology of fishes on coral reef flats,and the potential impacts of climate change

Reef flats, typically a low‐relief carbonate and sand habitat in shallow water leeward of the reef crest, are one of the most extensive zones on Pacific coral reefs. This shallow zone often supports an abundant and diverse fish assemblage that is exposed to more significant variations in physical factors, such as water depth and movement, temperature and ultraviolet (UV) radiation levels, than most other reef fishes. This review examines the characteristics of reef flat fish assemblages, and then investigates what is known about how they respond to their biophysical environment. Because of the challenges of living in shallow, wave‐exposed water, reef flats typically support a distinct fish assemblage compared to other reef habitats. This assemblage clearly changes across tidal cycles as some larger species migrate to deeper water at low tide and other species modify their behaviour, but quantitative data are generally lacking. At least some reef flat fish species are well‐adapted to high temperatures, low oxygen concentrations and high levels of UV radiation. These behavioural and physiological adaptations suggest that there may be differences in the demographic processes between reef flat assemblages and those in deeper water. Indeed, there is some evidence that reef flats may act as nurseries for some species, but more research is required. Further studies are also required to predict the effects of climate change, which is likely to have multifaceted impacts on reef flats by increasing temperature, water motion and sediment load. Sea‐level rise may also affect reef flat fish assemblages and food webs by increasing the amount of time that larger species are able to forage in this zone. The lack of data on reef flats is surprising given their size and relative ease of access, and a better understanding of their functional role within tropical marine seascapes is urgently required.     

A behavioural study of hybridization between Barbus barbus and Barbus meridionalis

The reproductive behaviour of two species of barbel ( Barbus barbus and Barbus meridionalis ) was investigated by means of aquarium experiments in several matings of six combinations. The reproductive behaviour of the two species appears to be similar and hybridizations were observed, showing that no complete behavioural barrier blocks the mating of the two species.     

The emergence of leaders and followers in foraging pairs when the qualities of individuals differ

Background  

Foraging in groups offers animals a number of advantages, such as increasing their likelihood of finding food or detecting and avoiding predators. In order for a group to remain together, there has to be some degree of coordination of behaviour and movement between its members (which may in some cases be initiated by a decision-making leader, and in other cases may emerge as an underlying property of the group). For example, behavioural synchronisation is a phenomenon where animals within a group initiate and then continue to conduct identical behaviours, and has been characterised for a wide range of species. We examine how a pair of animals should behave using a state-dependent approach, and ask what conditions are likely to lead to behavioural synchronisation occurring, and whether one of the individuals is more likely to act as a leader.     

Understanding the dynamic behavior of genetic regulatory networks by functional decomposition

A number of mechanistic and predictive genetic regulatory networks (GRNs) comprising dozens of genes have already been characterized at the level of cis-regulatory interactions. Reconstructions of networks of 100's to 1000's of genes and their interactions are currently underway. Understanding the organizational and functional principles underlying these networks is probably the single greatest challenge facing genomics today. We review the current approaches to deciphering large-scale GRNs and discuss some of their limitations. We then propose a bottom-up approach in which large-scale GRNs are first organized in terms of functionally distinct GRN building blocks of one or a few genes. Biological processes may then be viewed as the outcome of functional interactions among these simple, well-characterized functional building blocks. We describe several putative GRN functional building blocks and show that they can be located within GRNs on the basis of their interaction topology and additional, simple and experimentally testable constraints.     

HPMA as a scaffold for the modular assembly of functional peptide polymers by native chemical ligation

Synthetic peptides are valuable tools in fundamental and applied biomedical research. On one hand, these molecules provide highly efficient access to competitive inhibitors of molecular interactions and enzyme substrates by rational design. On the other hand, peptides may serve as powerful vectors to mediate cellular uptake of molecules that otherwise enter cells only poorly. The coupling of both such functionalities provides access to molecules interfering with molecular processes inside the cell. However, the combination of several functionalities on one synthetic peptide may be compromised by problems associated with the synthesis of long peptides. Native chemical ligation enables the chemoselective coupling of fully deprotected functional building blocks. However, peptide thioesters are still not accessible by standard solid-phase peptide synthesis. Here, we demonstrate the cofunctionalization of a thioester-activated N-hydroxypropyl methacrylamide (HPMA) copolymer (28,500 Da) with the cell-penetrating peptide (CPP) nonaarginine and a bioactive peptide as independent building blocks by native chemical ligation. Nonaarginine was employed as a cell-penetrating peptide (CPP), a fluorescein-labeled analogue of a pro-apoptotic peptide as a biofunctional cargo. Incorporation of the fluorescein label enabled the highly sensitive quantification of the coupling stoichiometry by fluorescence correlation spectroscopy (FCS) using 0.4 pmol/12 ng of labeled construct. A construct only bearing the functional cargo peptide required cellular import by electroporation in order to show activity. In contrast, a construct combining all functionalities was active upon incubation of cells, validating the modular nature of the approach.     

Aberrant nest building and prolactin secretion in vitamin D receptor mutant mice

1,25(OH)₂D₃, the hormonal form of vitamin D, is a neuroactive seco-steroid hormone with multiple functions in the brain. Most of these effects are mediated through the nuclear vitamin D receptor (VDR), widely distributed in the central nervous system. Our earlier studies showed that mutant mice lacking functional VDR have specific behavioural abnormalities, including anxiety and aberrant maternal behaviour, which may be hormonally regulated. Here we describe impaired nest building behaviour in VDR mutant mice. Since prolactin plays a key role in the regulation of nest building in both sexes, we also examine whether VDR mutant mice have altered prolactin levels. Overall, serum prolactin levels were increased in VDR mutant mice, accompanied by marked impairments in their nest building activity. In contrast, there were no differences in prolactin mRNA expression levels between wildtype control mice and VDR mutant mice. Collectively, these data suggest that partial genetic ablation of VDR affects prolactin system in mice, and that altered serum prolactin levels in VDR mutants may underlie some of their behavioural abnormalities, such as impaired nest building.     

New length–weight relationships and Lmax values for fishes from the Southeastern Mediterranean Sea

Length–weight relationships (LWR) of fish serve as building blocks in ichthyology and fishery science. In this study LWR knowledge is extended to some species, regions and sizes of fish either incomplete or missing from the literature or from the online databank (FishBase). For several species data are presented for the first time, while other entries are improved and expanded. Organisms were captured by trawl from the continental shelf of the Israeli coast, where fishes were hypothesized as being small due to low productivity and high water temperatures – a phenomenon called ‘Levantine Nanism’. Despite this, for nine of the 43 species presented here the maximum length values exceeded their L_max in FishBase. The dominance of fishes of Indo‐Pacific origin among the species with exceptionally large specimens (7 of 9) is in agreement with Bergmann's rule; it is thus hypothesized here that these large specimens result from the low temperatures in the Mediterranean compared to their warm Indo‐Pacific sources. This is an example of the superb adaptation of tropical species to the Mediterranean and suggests that Levantine Nanism may be limited to indigenous species.     

Behavioural responses of wildlife to urban environments

Increased urbanization represents a formidable challenge for wildlife. Nevertheless, a few species appear to thrive in the evolutionarily novel environment created by cities, demonstrating the remarkable adaptability of some animals. We argue that individuals that can adjust their behaviours to the new selection pressures presented by cities should have greater success in urban habitats. Accordingly, urban wildlife often exhibit behaviours that differ from those of their rural counterparts, from changes to food and den preferences to adjustments in the structure of their signals. Research suggests that behavioural flexibility (or phenotypic plasticity) may be an important characteristic for succeeding in urban environments. Moreover, some individuals or species might possess behavioural traits (a particular temperament) that are inherently well suited to occupying urban habitats, such as a high level of disturbance tolerance. This suggests that members of species that are less ‘plastic’ or naturally timid in temperament are likely to be disadvantaged in high‐disturbance environments and consequently may be precluded from colonizing cities and towns.     

Genetics of behavioural adaptation of livestock to farming conditions

Behavioural adaptation of farm animals to environmental changes contributes to high levels of production under a wide range of farming conditions, from highly controlled indoor systems to harsh outdoor systems. The genetic variation in livestock behaviour is considerable. Animals and genotypes with a larger behavioural capacity for adaptation may cope more readily with varying farming conditions than those with a lower capacity for adaptation. This capacity should be exploited when the aim is to use a limited number of species extensively across the world. The genetics of behavioural traits is understood to some extent, but it is seldom accounted for in breeding programmes. This review summarizes the estimates of genetic parameters for behavioural traits in cattle, pigs, poultry and fish. On the basis of the major studies performed in the last two decades, we focus the review on traits of common interest in the four species. These concern the behavioural responses to both acute and chronic stressors in the physical environment (feed, temperature, etc.) and those in the social environment (other group members, progeny, humans). The genetic strategies used to improve the behavioural capacity for adaptation of animals differ between species. There is a greater emphasis on responses to acute environmental stress in fish and birds, and on responses to chronic social stress in mammals.     

Wanting,liking and welfare: The role of affective states in proximate control of behaviour in vertebrates

Animals choose a course of action countless times each day. To do so, they need to prioritise their behaviour within a set of alternative actions and decide which of these actions to perform at any one time and for how long, that is, determine when the behaviour has reached its desired effect. This process has classically been called the proximate behavioural control mechanism. Several aspects contribute to this process: internal and external stimuli, the emotions that they elicit, motivation (wants), behavioural goals, valuation, decision‐making and its modulation by mood, and the assessment of behavioural outcomes (liking). I will address all these aspects in the form of an integrated conceptual model. In the process of behavioural control, options need to be valued, and I will refer to evidence showing that an affective hedonic process in respect to (future) reward and punishment heavily affects this value. Moreover, I view motivation, the force that finally drives a specific behavioural output, as being primarily influenced by affective states or even corresponding fully to them. Given the feedback in behavioural control by (dis‐)liking outcomes of behaviour, I reason that in respect to welfare it is more important for animals to reach proximate goals than to avoid negative stimuli. All behavioural choices are modulated, and I show how mood, a long‐term affective state, can cause such modulation. Proximate control of behaviour takes place in the brain, and I will briefly discuss how current and future brain research may elucidate how the brain computes these processes. Furthermore, the inclusion of affective states in the conceptual model raises the question of the subjective experience of animals, and I will address some of the important open questions in this area of research. I will conclude that neural studies cannot currently provide a detailed and general theory on the algorithms of proximate behavioural control. In parallel to further developing these approaches, I propose to strengthen a refined ethological approach with a focus on the states of “wanting” and “liking” in ecologically meaningful circumstances and with a strong ontogenetic (within species) and comparative (between species) component. I consider this ethological approach to be a highly promising step in understanding proximate behavioural control.     

The mosaic of ancestral karyotype blocks in the Sinapis alba L. genome

The organisation of the Sinapis alba genome, comprising 12 linkage groups (n = 12), was compared with the Brassicaceae ancestral karyotype (AK) genomic blocks previously described in other crucifer species. Most of the S. alba genome falls into conserved triplicated genomic blocks that closely match the AK-defined genomic blocks found in other crucifer species including the A, B, and C genomes of closely related Brassica species. In one instance, an S. alba linkage group (S05) was completely collinear with one AK chromosome (AK1), the first time this has been observed in a member of the Brassiceae tribe. However, as observed for other members of the Brassiceae tribe, ancestral genomic blocks were fragmented in the S. alba genome, supporting previously reported comparative chromosome painting describing rearrangements of the AK karyotype prior to the divergence of the Brassiceae from other crucifers. The presented data also refute previous phylogenetic reports that suggest S. alba was more closely related to Brassica nigra (B genome) than to B. rapa (A genome) and B. oleracea (C genome). A comparison of the S. alba and Arabidopsis thaliana genomes revealed many regions of conserved gene order, which will facilitate access to the rich genomic resources available in the model species A. thaliana for genetic research in the less well-resourced crop species S. alba.     

Social learning in non-grouping animals

Social learning is widespread in the animal kingdom and is involved in behaviours from navigation and predator avoidance to mate choice and foraging. While social learning has been extensively studied in group-living species, this article presents a literature review demonstrating that social learning is also seen in a range of non-grouping animals, including arthropods, fishes and tetrapod groups, and in a variety of behavioural contexts. We should not be surprised by this pattern, since non-grouping animals are not necessarily non-social, and stand to benefit from attending to and responding to social information in the same ways that group-living species do. The article goes on to ask what non-grouping species can tell us about the evolution and development of social learning. First, while social learning may be based on the same cognitive processes as other kinds of learning, albeit with social stimuli, sensory organs and brain regions associated with detection and motivation to respond to social information may be under selection. Non-grouping species may provide useful comparison taxa in phylogenetic analyses investigating if and how the social environment drives selection on these input channels. Second, non-grouping species may be ideal candidates for exploring how ontogenetic experience of social cues shapes the development of social learning, allowing researchers to avoid some of the negative welfare implications associated with raising group-living animals under restricted social conditions. Finally, while non-grouping species may be capable of learning socially under experimental conditions, there is a need to consider how non-grouping restricts access to learning opportunities under natural conditions and whether this places a functional constraint on what non-grouping animals actually learn socially in the wild.     

Potential folding-function interrelationship in proteins

The possibility is addressed that protein folding and function may be related via regions that are critical for both folding and function. This approach is based on the building blocks folding model that describes protein folding as binding events of conformationally fluctuating building blocks. Within these, we identify building block fragments that are critical for achieving the native fold. A library of such critical building blocks (CBBs) is constructed. Then, it is asked whether the functionally important residues fall in these CBB fragments. We find that for over two-thirds of the proteins in our library with available functional information, the catalytic or binding site residues lie within the CBB regions. From the evolutionary standpoint, a folding-function relationship is advantageous, since the need to guard against mutations is limited to one region. Furthermore, conformationally similar CBBs are found in globally unrelated proteins with different functions. Hence, substituting CBBs may lead to designed proteins with altered functions. We further find that the CBBs in our library are conformationally unstable.     

Chronotype and beyond: 17 building blocks to reconcile and explore internal time architecture

Chronotype, defined as the temporal phenotype of an organism, has been addressed in Chronobiology International in some 200 publications between 1997 and 2018. Readers may thus be interested in what roles chronotype may play in studies concerning chronobiology and health. In line with Karl Popper, our objective is to synthesize terms and concepts for falsifiable experimental, field, and ultimately epidemiological research. To this end, we offer 17 building blocks where each should follow from one or more others. Such “causal” tabulation may be requisite for understanding chronotype and multi-faceted internal time architecture beyond intuition and common sense. Overall, our “causal” box tabulation allows to challenge, explore, falsify, modify, or corroborate complex facets regarding internal time, step-by-step. Clearly, if our espousal of building blocks were to lead to refined replacement blocks, thereby forcing researchers to produce more and more convincing evidence and chronobiological insights, individuals and populations would benefit.     

Reagent-based and product-based computational approaches in library design

The design of combinatorial libraries involves the consideration of all synthesizable compounds (the virtual library), followed by the selection of a suitably sized subset for actual synthesis and experimentation. Several approaches to this task can be envisaged, involving either reagent-based or product-based considerations. Reagent-based design considers the properties of the building blocks rather than those of the final products. Although popular with chemists, this approach overlooks the extent of chemical transformations involved in generating products. In effect, several important properties cannot be derived from building blocks alone and require access to product structures. Several studies have demonstrated the superiority of product-based designs in yielding diverse and representative subsets. Although more computationally intensive, the latter approach provides a basis for more sophisticated designs where reagent-based and product based considerations can be combined for a best-of-breed approach.