This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five nuclear loci from the East Asian brown frogs is used to illustrate four different analyses, including estimation of species divergence times and population size parameters under the multispecies coalescent model on a fixed species phylogeny （A00）, species tree estimation when the assignment and species delimitation are fixed （A01）, species delimitation using a fixed guide tree （A10）, and joint species delimitation and species-tree estimation or unguided species delimitation （A11）. For the joint analysis （A11）, two new priors are introduced, which assign uniform probabilities for the different numbers of delimited species, which may be useful when assignment, species delimitation, and species phylogeny are all inferred in one joint analysis. The paper ends with a discussion of the assumptions, the strengths and weaknesses of the BPP analysis [Current Zoology 61 （5）： 854-865, 2015].
Comparative studies of trait evolution require accounting for the shared evolutionary history. This is done by includ- ing phylogenetic hypotheses into statistical analyses of species＇ traits, for which birds often serve as excellent models. The online publication of the most complete molecular phylogeny of extant bird species （www.birdtree.org, BirdTree hereafter） now allows evolutionary biologists to rapidly obtain sets of equally plausible phylogenetic trees for any set of species to be incorporated as a phylogenetic hypothesis in comparative analyses. We discuss methods to use BirdTree tree sets for comparative studies, either by building a consensus tree that can be incorporated into standard comparative analyses, or by using tree sets to account for the ef- fect of phylogenetie uncertainty. Methods accounting for phylogenetic uncertainty should be preferred whenever possible because they should provide more reliable parameter estimates and realistic confidence intervals around them. Based on a real compara- tive dataset, we ran simulations to investigate the effect of variation in the size of the random tree sets downloaded from BirdTree on the variability of parameter estimates from a bivariate relationship between mass-specific productivity and body mass. Irre- spective of the method of analysis, using at least 1,000 trees allows obtaining parameter estimates with very small （〈 0.15%） co- efficients of variation. We argue that BirdTree, due to the ease of use and the major advantages over previous ＇traditional＇ meth- ods to obtain phylogenetic hypotheses of bird species （e.g. supertrees or manual coding of published phylogenies）, will become the standard reference in avian comparative studies for years to come.
DNA-based approaches to systematics have changed dramatically during the last two decades with the rise of DNA barcoding methods and newer multi-locus methods for species delimitation. During the last half-decade, partly driven by the new sequencing technologies, the focus has shifted to multi-locus sequence data and the identification of species within the frame-work of the multi-species coalescent （MSC）. In this paper, I discuss model-based Bayesian methods for species delimitation that have been developed in recent years using the MSC. Several approximate methods for species delimitation （and their limitations） are also discussed. Explicit species delimitation models have the advantage of clarifying more precisely what is being delimited and what assumptions we are making in doing so. Moreover, the methods can be very powerful when applied to large multi-locus datasets and thus take full advantage of data generated using today＇s technologies [Current Zoology 61 （5）： 846-853,2015].
The study of animal personality has attracted considerable attention, as it has revealed a number of similarities in personality between humans and several nonhuman species. At the same time the adaptive value and evolutionary maintenance of different personalities are the subject of debate. Since Pavlov’s work on dogs, students of comparative cognition have been aware that animals display vast individual differences on cognitive tasks, and that these differences may not be entirely accounted for differences in cognitive abilities. Here, we argue that personality is an important source of variation that may affect cognitive performance and we hypothesise mutual influences between personality and cognition across an individual’s lifespan. In particular, we suggest that: 1) personality profiles may be markers of different cognitive styles; 2) success or failure in cognitive tasks could affect different personalities differently; 3) ontogenetic changes of personality profiles could be reflected in changes in cognitive performance. The study of such interplay has implications in animal welfare as well as in neuroscience and in translational medicine.
Rapid technical advances in the field of computer animation ( CA) and virtual reality ( VR) have opened new avenues in animal behavior research. Animated stimuli are powerful tools as they offer standardization, repeatability, and complete control over the stimulus presented, thereby "reducing" and "replacing" the animals used, and "refining" the experimental design in line with the 3Rs. However, appropriate use of these technologies raises conceptual and technical questions. In this review, we offer guidelines for common technical and conceptual considerations related to the use of animated stimuli in animal behavior research. Following the steps required to create an animated stimulus, we discuss ( I) the creation, ( II) the presentation, and ( III) the validation of CAs and VRs. Although our review is geared toward computer-graphically designed stimuli, considerations on presentation and validation also apply to video playbacks. CA and VR allow both new behavioral questions to be addressed and existing questions to be addressed in new ways, thus we expect a rich future for these methods in both ultimate and proximate studies of animal behavior.
In the past decade there has been a profusion of studies highlighting covariation between individual differences in stress physiology and behavioural profiles, here called personalities. Such individual differences in ways of coping with stress are relevant both in biomedicine, since different personalities may experience a different stress and disease vulnerability, and in behavioural ecology, since their adaptive value and evolutionary maintenance are the subject of debate. However, the precise way in which individual stress differences and personalities are linked is unclear. Here we provide an updated overview of this covariation across different species and taxa, consider its functional significance and present working hypotheses for how behavioural and physiological responses to stress might be causally linked, affecting life-history traits such as dispersal and life-span [Current Zoology 56 (6): 728-740, 2010].
Global climate change is impacting organisms, biological communities and ecosystems around the world. While most research has focused on characterizing how the climate is changing, including modeling future climatic conditions and predicting the impacts of these conditions on biodiversity, it is also the case that climate change is altering the environmental impacts of chemical pollution. Future climate conditions are expected to influence both the worldwide distribution of chemicals and the toxicological consequences of chemical exposures to organisms. Many of the environmental changes associated with a warming global climate (e.g., increased average - and possibly extreme - temperatures; intense periods of drier and wetter conditions; reduced ocean pH; altered salinity dynamics in estuaries) have the potential to enhance organism susceptibility to chemical toxicity. Additionally, chemical exposures themselves may impair the ability of organisms to cope with the changing environmental conditions of the shifting climate. Such reciprocity in the interactions between climate change and chemicals illustrates the complexity inherent in predicting the toxicological consequences of chemical exposures under future climate scenarios. Here, we summarize what is currently known about the potential reciprocal effects of climate change and chemical toxicity on wildlife, and depict current approaches and ongoing challenges for incorporating climate effects into chemical testing and assessment. Given the rapid pace of new man-made chemistries, the development of accurate and rapid methods to evaluate multiple chemical and non-chemical stressors in an ecologically relevant context will be critical to understanding toxic and endocrine-disrupting effects of chemical pollutants under future climate scenarios
Population genomic approaches are making rapid inroads in the study of non-model organisms, including marine taxa. To date, these marine studies have predominantly focused on rudimentary metrics describing the spatial and environmental context of their study region （e.g., geographical distance, average sea surface temperature, average salinity）. We contend that a more nuanced and considered approach to quantifying seascape dynamics and patterns can strengthen population genomic investigations and help identify spatial, temporal, and environmental factors associated with differing selective regimes or demographic histories. Nevertheless, approaches for quantifying marine landscapes are complicated. Characteristic features of the marine environment, including pelagic living in flowing water （experienced by most marine taxa at some point in their life cycle）, require a well-designed spatial-temporal sampling strategy and analysis. Many genetic summary statistics used to describe populations may be inappropriate for marine species with large population sizes, large species ranges, stochastic recruitment, and asymmetrical gene flow. Finally, statistical approaches for testing associations between seascapes and population genomic patterns are still maturing with no single approach able to capture all relevant considerations. None of these issues are completely unique to marine systems and therefore similar issues and solutions will be shared for many organisms regardless of habitat. Here, we outline goals and spatial approaches for land- scape genomics with an emphasis on marine systems and review the growing empirical literature on seascape genomics. We review established tools and approaches and highlight promising new strategies to overcome select issues including a strategy to spatially optimize sampling. Despite the many challenges, we argue that marine systems may be especially well suited for identifying candidate genomic regions under environmentally mediated selection and that seascape genomic approaches are especially useful for identifying robust locus-by-environment associations.
When incompletely isolated taxa coexist in a patchy environment （e.g. mosaic hybrid zones, host-race complexes）, patterns of variation may differ between selected traits/genes and neutral markers. While the genetic structure of selected traits/loci tends to coincide with habitat variables （producing Genetic-Environment Association or GEA）, genetic differentiation at neutral loci unlinked to any selected locus rather depends on geographic connectivity at a large scale （e.g. Isolation- By-Distance or IBD）, although these loci often display GEA at a small scale. This discrepancy has been repeatedly taken as evi- dence for parallel primary divergence driven by local adaptation. We argue that this interpretation needs to be addressed more thoroughly by considering the alternative hypothesis that speciation was initiated in allopatry and secondary introgression has subsequently erased the signal of past differentiation at neutral loci. We present a model of neutral introgression after secondary contact in a mosaic hybrid zone, which describes how GEAs dissipate with time and how neutral variation self-organizes accord- ing to the environmental and geographic structures. We show that although neutral loci can be affected by environmental selection they are often more affected by history and connectivity： the neutral structure retains the initial geographic separation more than it correlates with the environment during the colonization and introgression phases, and then converges to a migration-drift balance, the most frequent outcome of which is GEA at a local scale but IBD at a large scale. This is the exact pattern usually attributed to parallel ecological speciation. Introgression is heterogeneous in space and depends on the landscape structure （e.g. it is faster in small patches, which are more impacted by immigration）. Furthermore, there is no directionality in the association and it is possi- ble to observe reversed GEAs between distant regions. We argue that the history of differentiation should ideally be reconstructed with selected loci or neutral loci linked to them, not neutral ones, and review some case studies for which the hypothesis of a long co-existence of co-adapted genetic backgrounds might have been refuted too hastily [Current Zoology 59 （1）： 72-86, 2013].
In contrast to the cries of human infants, sounds made by non-human infants in different stressful behavioral contexts （hunger or physical discomfort, isolation, capture by humans or predators） are usually treated as distinct types of vocalizations. However, if distress vocalizations produced by different species and in different contexts share a common motivational state and associated neurochemical pathways, we can expect them to share a common acoustic structure and adaptive function, showing only limited variation that corresponds to the infant＇s level of arousal. Based on this premise, we review the acoustic structure and adaptive function of two types of distress calls, those given when infants were isolated from their mothers （isolation caUs） or captured by humans （capture calls）. We conducted a within-context comparison examining the two call types across a diverse se- lection of mammalian species and other vertebrate groups, followed by a comparison of how acoustic structure and function dif- fers between these contexts. In addition, we assessed acoustic traits that are critical to the response of caregivers. Across verte- brate species, distress vocalizations produced in these two behavioral contexts tend to be tonal with a simple chevron, flat or de- scending pattern of frequency modulation. Reports that both isolation and capture calls of vertebrate infants serve to attract care- givers are universal, and the fundamental frequency of infant vocalizations is often critical to this response. The results of our re- view are consistent with the hypothesis that differences in the acoustic structure of isolation and capture distress vocalizations re- flect differences in arousal, and not discrete functions. The similarity in acoustic structure and caregiver response observed across vertebrates adds support to the hypothesis that the production and processing of distress vocalizations are part of a highly-conserved system of social vocal behaviour in vertebrates. Bioacoustic research may move forward by recognizing the commonality among different forms of infant solicitations that attract caregivers, and the commonality of these solicitations with vocalizations that attract conspecifics in still other behavioral contexts [Current Zoology 58 （5）： 698-726, 2012].
Chaotic genetic patchiness （CGP） refers to surprising patterns of spatial and temporal genetic structure observed in some marine species at a scale where genetic variation should be efficiently homogenized by gene flow via larval dispersal. Here we review and discuss 4 mechanisms that could generate such unexpected patterns： selection, sweepstakes reproductive success, collective dispersal, and temporal shifts in local population dynamics. First, we review examples where genetic differentiation at specific loci was driven by diversifying selection, which was historically the first process invoked to explain CGP. Second, we turn to neutral demographic processes that may drive genome-wide effects, and whose effects on CGP may be enhanced when they act together. We discuss how sweepstakes reproductive success accelerates genetic drift and can thus generate genetic structure, provided that gene flow is not too strong. Collective dispersal is another mechanism whereby genetic structure can be maintained regardless of dispersal intensity, because it may prevent larval cohorts from becoming entirely mixed. Theoretical analyses of both the sweepstakes and the collective dispersal ideas are presented. Finally, we discuss an idea that has received less attention than the other ones just mentioned, namely temporal shifts in local population dynamics.
We aimed to review the history of the introduction and colonization of the raccoon dog Nyctereutes procyonoides in Europe, the features behind its successful expansion and its impact on native fauna. The raccoon dog quickly colonized new areas after being introduced to the European part of the former Soviet Union. Today it is widespread in Northern and Eastern Europe and is still spreading in Central Europe. Features behind its success include its adaptability, high reproductive potential, omnivory, hibernation in northern areas, multiple introductions with > 9000 individuals from different localities, and tendency to wander enabling gene flow between populations. Firm evidence of the raccoon dog's negative impact on native fauna, such as a reduction in bird populations, is still scarce. Raccoon dogs may destroy waterfowl nests, although a nest predation study in Latvia did not confirm this. Predator removal studies in Finland suggested that the raccoon dog's impact on game birds is smaller than expected. However, raccoon dogs may have caused local extinction of frog populations, especially on islands. Raccoon dogs may compete with other carnivores for food, for example for carrion in winter, or for the best habitat patches. In northern Europe potential competitors include the red fox Vulpes vulpes and the badger Meles meles, but studies of their diets or habitat preferences do not indicate severe competition. The raccoon dog is an important vector of diseases and parasites, such as rabies, Echinococcus multilocularis and Trichinella spp. and this is no doubt the most severe consequence arising from the spread of this alien species in Europe [Current Zoology 57 (5): 584-598, 2011].
Satellite-tracking technology has allowed scientists to make a quantum leap in the field of migration ecology. Nowadays, the basic description of migratory routes of many species of birds has been reported. However, the investigation of bird migration at individual level (i.e. repeatability in migratory routes and timing) still remains seldom explored. Here, we investigated repeated migratory trips of a trans-Saharan endangered migratory raptor, the Egyptian Vulture Neophron percnopterus, tracked by GPS satellite telemetry. We compared between-and within-individual variation in migratory routes and timing in order to assess the degree of repeatability (or conversely, the flexibility) in migration. To this end, we analysed a dataset of 48 trips (23 springs and 25 autumns) recorded for six adult birds during 2007-2013. Our results showed consistent migration timing at the individual level, both in spring and autumn. Interestingly, there was a high degree of flexibility in the routes followed by the same individual in different years, probably due to variations in meteorological conditions. Contrary to expectations of a faster migration in spring than in autumn owing to a time-minimization strategy for breeding, birds spent less time in autumn migration (13 +/- 2 days, range = 9-18 d) than in spring migration (19 +/- 3 days, range = 13-26 d), which can be explained by differences in environmental conditions en route. Egyptian vultures showed a consistent clockwise loop migration through western Africa, following more easterly routes in autumn than in spring. Finally, our results provide supporting evidence of low phenotypic plasticity in timing of migration (i.e. strong endogenous control of migration) and high flexibility in routes
A growing body of evidence from across taxa suggests that exposure to elevated levels of glucocorticoids during early development can have long-term effects upon physiological and behavioral phenotypes. Additionally, there is some, though limited, evidence that similar early exposure can also negatively impact cognitive ability. Following pioneering mammalian studies, several avian studies have revealed that the responsiveness of the hypothalamo-pituitary-adrenal (HPA) axis as an adult can be explained by levels of corticosterone, the avian glucocorticoid, the individual experienced as a nestling or even as an embryo via yolk exposure. Studies also suggest that perinatal exposure to corticosterone can have effects upon avian ‘personalities’ or coping styles, and findings from mammalian studies suggest that these long-term effects are mediated epigenetically via altered expression of relevant DNA sequences. Although a consistent pattern across-species has yet to emerge, recent work in Florida scrub-jays Aphelocoma coerulescens found that baseline corticosterone levels in 11-day-old nestlings explained 84% of the variation in ‘personality’ (bold vs. timid) when those individuals were tested approximately seven months later. Nestlings with elevated corticosterone levels were more timid than those individuals that as nestlings experienced relatively low corticosterone levels. Some researchers have suggested that parents might use such mechanisms to ‘program’ their offsprings’ phenotype to best fit prevailing environmental conditions. This review will visit what is known about the links between stressful developmental conditions that result in exposure to elevated corticosterone and the short- and long-term effects of this steroid hormone upon central nervous system function and whether alterations thereof are beneficial, deleterious, or neutral. It will concentrate on examples from birds, although critical supporting studies from the mammalian literature will be included as appropriate.
Growing concern about the influence of climate change on flowering plants, pollinators, and the mutualistic interac- tions between them has led to a recent surge in research. Much of this research has addressed the consequences of warming for phenological and distributional shifts. In contrast, relatively little is known about the physiological responses of plants and insect pollinators to climate warming and, in particular, how these responses might affect plant-pollinator interactions. Here, we summa- rize the direct physiological effects of temperature on flowering plants and pollinating insects to highlight ways in which plant and pollinator responses could affect floral resources for pollinators, and pollination success for plants, respectively. We also con- sider the overall effects of these responses on plant-pollinator interaction networks. Plant responses to wanning, which include altered flower, nectar, and pollen production, could modify floral resource availability and reproductive output of pollinating in- sects. Similarly, pollinator responses, such as altered foraging activity, body size, and life span, could affect patterns of pollen flow and pollination success of flowering plants. As a result, network structure could be altered as interactions are gained and lost, weakened and strengthened, even without the gain or loss of species or temporal overlap. Future research that addresses not only how plant and pollinator physiology are affected by warming but also how responses scale up to affect interactions and networks should allow us to better understand and predict the effects of climate change on this important ecosystem service .
Telomeres are protective structures at the ends of eukaryotic chromosomes. The loss of telomeres through cell division and oxidative stress is related to cellular aging, organismal growth and disease. In this way, telomeres link molecular and cellular mechanisms with organismal processes, and may explain variation in a number of important life-history traits. Here, we discuss how telomere biology relates to the study of physiological ecology and life history evolution. We emphasize current knowledge on how telomeres may relate to growth, survival and lifespan in natural populations. We finish by examining interesting new connections between telomeres and the glucocorticoid stress response. Glucocorticoids are often employed as indices of physiological condition, and there is evidence that the glucocorticoid stress response is adaptive. We suggest that one way that glucocorticoids impact organismal survival is through elevated oxidative stress and telomere loss. Future work needs to establish and explore the link between the glucocorticoid stress response and telomere shortening in natural populations. If a link is found, it provides an explanatory mechanism by which environmental perturbation impacts life history trajectories [Current Zoology 56 (6): 714-727, 2010].
It has been 25 years since the formalization of the Sensory Drive hypothesis was published in the American Naturalist (1992). Since then, there has been an explosion of research identifying its utility in contributing to our understanding of inter-and intra-specific variation in sensory systems and signaling properties. The main tenet of Sensory Drive is that environmental characteristics will influence the evolutionary trajectory of both sensory (detecting capabilities) and signaling (detectable features and behaviors) traits in predictable directions. We review the accumulating evidence in 154 studies addressing these questions and categorized their approach in terms of testing for environmental influence on sensory tuning, signal characteristics, or both. For the subset of studies that examined sensory tuning, there was greater support for Sensory Drive processes shaping visual than auditory tuning, and it was more prevalent in aquatic than terrestrial habitats. Terrestrial habitats and visual traits were the prevalent habitat and sensory modality in the 104 studies showing support for environmental influence on signaling properties. An additional 19 studies that found no supporting evidence for environmental influence on signaling traits were all based in terrestrial ecosystems and almost exclusively involved auditory signals. Only 29 studies examined the complete coevolutionary process between sensory and signaling traits and were dominated by fish visual communication. We discuss biophysical factors that may contribute to the visual and aquatic bias for Sensory Drive evidence, as well as biotic factors that may contribute to the lack of Sensory Drive processes in terrestrial acoustic signaling systems.
The expanding scale and increasing rate of marine biological invasions have been documented since the early 20th century. Besides their global ecological and economic impacts, non-indigenous species （NIS） also have attracted much attention as opportunities to explore important eco-evolutionary processes such as rapid adaptation, long-distance dispersal and range expansion, and secondary contacts between divergent evolutionary lineages. In this context, genetic tools have been extensively used in the past 20 years. Three important issues appear to have emerged from such studies. First, the study of NIS has revealed unexpected cryptic diversity in what had previously been assumed homogeneous entities. Second, there has been surprisingly little evidence of strong founder events accompanying marine introductions, a pattern possibly driven by large propagule loads. Third, the evolutionary processes leading to successful invasion have been difficult to ascertain due to faint genetic signals. Here we explore the potential of novel tools associated with high-throughput sequencing （HTS） to address these still pressing issues. Dramatic increase in the number of loci accessible via HTS has the potential to radically increase the power of analyses aimed at species delineation, exploring the population genomic consequences of range expansions, and examining evolutionary processes such as admixture, introgression, and adaptation. Nevertheless, the value of this new wealth of genomic data will ultimately depend on the ability to couple it with expanded ＂traditional＂ efforts, including exhaustive sampling of marine populations over large geographic scales, integrated taxonomic analyses, and population level exploration of quantitative trait differentiation through common-garden and other laboratory experiments.
In animal societies, behavioral idiosyncrasies of the individuals often guide which tasks theyshould perform. Such personality-specific task participation can increase individual task efficiency,thereby improving group performance. While several recent studies have documented group-levelbenefits of within-group behavioral （i.e., personality） diversity, how these benefits are realized atthe individual level is unclear. Here we probe the individual-level benefits of personality-driven taskparticipation in the social spider Stegodyphus dumicola. In S. dumicola, the presence of at leastone highly bold individual catalyzes foraging behavior in shy colony members, and all group con-stituents heavily compete for prey. We assessed boldness by examining how quickly spidersresumed normal movement after a simulated predator attack. We test here whether （1） participantsin collective foraging gain more mass from prey items and （2） whether bold individuals are less re-sistant to starvation than shy spiders, which would motivate the bold individuals to forage more.Next, we assembled colonies of shy spiders with and without a bold individual, added one preyitem, and then tracked the mass gain of each individual spider after this single feeding event. Wefound that spiders that participated in prey capture （whether bold or shy） gained more mass thannonparticipators, and colonies containing a single bold spider gained more total mass than purelyshy colonies. We also found that bold spiders participated in more collective foraging events andwere more susceptible to starvation than shy spiders, suggesting that the aggressive foraging ofbold individuals may represent a strategy to offset starvation risk. These findings add to the bodyof evidence that animal personality can shape social organization, individual performance, andgroup success.
Highly fecund marine species with dispersive life-history stages often display large population sizes and wide geographic distribution ranges. Consequently, they are expected to experience reduced genetic drift, efficient selection fueled by frequent adaptive mutations, and high migration loads. This has important consequences for understanding how local adaptation proceeds in the sea. A key issue in this regard, relates to the genetic architecture underlying fitness traits. Theory predicts that adaptation may involve many genes but with a high variance in effect size. Therefore, the effect of selection on allele frequencies may be substantial for the largest effect size loci, but insignificant for small effect genes. In such a context, the performance of population genomic methods to unravel the genetic basis of adaptation depends on the fraction of adaptive genetic variance explained by the cumulative effect of outlier loci. Here, we address some methodological challenges associated with the detection of local adaptation using molecular approaches. We provide an overview of genome scan methods to detect selection, including those assuming complex demographic models that better describe spatial population structure. We then focus on quantitative genetics approaches that search for genotype-phenotype associations at different genomic scales, including genome-wide methods evaluating the cumulative effect of variants. We argue that the limited power of single locus tests can be alleviated by the use of polygenic scores to estimate the joint contribution of candidate variants to phenotypic variation.