Revisiting Amazonian phylogeography: insights into diversification hypotheses and novel perspectives

The Amazon Basin harbors one of the richest biotas on Earth, such that a number of diversification hypotheses have been formulated to explain patterns of Amazonian biodiversity and biogeography. For nearly two decades, phylogeographic approaches have been applied to better understand the underlying causes of genetic differentiation and geographic structure among Amazonian organisms. Although this research program has made progress in elucidating several aspects of species diversification in the region, recent methodological and theoretical developments in the discipline of phylogeography will provide new perspectives through more robust hypothesis testing. Herein, we outline central aspects of Amazonian geology and landscape evolution as well as climate and vegetation dynamics through the Neogene and Quaternary to contextualize the historical settings considered by major hypotheses of diversification. We address each of these hypotheses by reviewing key phylogeographic papers and by expanding their respective predictions. We also propose future directions for devising and testing hypotheses. Specifically, combining the exploratory power of phylogeography with the statistical rigor of coalescent methods will greatly expand analytical inferences on the evolutionary history of Amazonian biota. Incorporation of non-genetic data from Earth science disciplines into the phylogeographic approach is key to a better understanding of the influence of climatic and geophysical events on patterns of Amazonian biodiversity and biogeography. In addition, achieving such an integrative enterprise must involve overcoming issues such as limited geographic and taxonomic sampling. These future challenges likely will be accomplished by a combination of extensive collaborative research and incentives for conducting basic inventories.     

Distance-dependence in two Amazonian palms: effects of spatial and temporal variation in seed predator communities

Animals aid population growth and fitness in tropical forest communities through dispersal and negatively impact populations through seed predation. The interaction between dispersal and seed predation can produce distance- or density-dependence; powerful mechanisms for maintaining species diversity incorporated in the Janzen–Connell model. Large mammals, the highest biomass seed predators of intact Amazonian communities and at risk due to human disturbance, are potentially central to these interactions. This study tests the Janzen–Connell model and investigates the impact of mammalian seed predators on seedling recruitment and maintenance of tree diversity. Patterns of both vertebrate and invertebrate seed predation and seedling recruitment were studied in the two most abundant canopy tree species in western Amazonia (Arecaceae: Astrocaryum murumuru and Iriartea deltoidea). We specifically examined effects of both spatial and temporal variation of the highest biomass seed predator in southwest Amazonian forests, the white-lipped peccary (Tayassu pecari), on recruitment through disturbed and undisturbed sites and through a fortuitous 12 year natural extinction and recolonization event of T. pecari. Distance-dependent seedling recruitment was found in Astrocaryum and Iriartea at both sites. However, the median distance of seedlings was ~1.5× farther from reproductive adults in both palms at the undisturbed site. The number of Iriartea seeds escaping predation increased 6,000% in both space and time due to the decline of T. pecari abundance. The results demonstrate that Janzen–Connell effects are stronger in intact ecosystems and tie these mechanistically to changes in seed predator abundance. This study shows that anthropogenic changes in mammal communities decrease the magnitude of Janzen–Connell effects in Amazonian forests and may result in decreases in tree diversity.     

Prey: predator ratio dependence in the functional response of a freshwater amphipod

1. First known for their shredding activity, freshwater amphipods also behave as active predators with consequences for prey population regulation and amphipod coexistence in the context of biological invasions. 2. A way to quantify predation is to determine the average consumption rate per predator, also known as its functional response (FR). 3. Although amphipods are gregarious and can display social interactions that can alter per capita consumption rates, previous studies using the FR approach to investigate amphipod predation ignored such potential mutual interference because they did not consider variations in predator density. 4. We investigated the FR of Echinogammarus berilloni feeding on dipteran larvae with joint variations in prey and predator densities. This bivariate experimental design allowed us to estimate interference and to compare the fits of the three main classes of theoretical FR models, in which the predation rate is a function of prey density alone (prey‐dependent models), of both prey and predator densities (predator‐dependent models) or of the prey‐to‐predator ratio (ratio‐dependent models). 5. The Arditi–Ginzburg ratio‐dependent FR model provided the best representation of the FR of E. berilloni, whose predation rate showed a decelerating rise to a horizontal asymptote as prey abundance increased. 6. Ratio dependence means that mutual interference between amphipods leads to prey sharing. Mutual interference is likely to vary between amphipod species, depending on their level of aggressiveness.     

Testing for predator dependence in predator-prey dynamics: a non-parametric approach

The functional response is a key element in all predator-prey interactions. Although functional responses are traditionally modelled as being a function of prey density only, evidence is accumulating that predator density also has an important effect. However, much of the evidence comes from artificial experimental arenas under conditions not necessarily representative of the natural system, and neglecting the temporal dynamics of the organism (in particular the effects of prey depletion on the estimated functional response). Here we present a method that removes these limitations by reconstructing the functional response non-parametrically from predator-prey time-series data. This method is applied to data on a protozoan predator-prey interaction, and we obtain significant evidence of predator dependence in the functional response. A crucial element in this analysis is to include time-lags in the prey and predator reproduction rates, and we show that these delays improve the fit of the model significantly. Finally, we compare the non-parametrically reconstructed functional response to parametric forms, and suggest that a modified version of the Hassell-Varley predator interference model provides a simple and flexible function for theoretical investigation and applied modelling.     

Advantages of granivory in seasonal environments: feeding ecology of an arboreal seed predator in Amazonian forests

Specialized seed predators are uncommon in arboreal vertebrate assemblages, and the hypothesis that consuming seeds of immature fruits – which may be available for relatively long periods compared to mature fruit – could reduce seasonal food scarcity experienced by generalist frugivores remains largely untested. To test this hypothesis, we examined the diet and feeding ecology of bald‐faced saki monkeys Pithecia irrorata in a largely intact forest mosaic of southeastern Peru based on systematic monitoring of five habituated groups over a three‐year period and compared the relative availability of ripe and unripe fruits in their diet. Plant phenology data from individual tree crowns showed that, compared to ripe fruits, immature fruits were available in more tree species, in greater quantities, and for longer periods. Despite pronounced community‐wide seasonal changes in fruit production at our study area, feeding patterns of bald‐faced saki remained largely invariant: fruits comprised approximately 95% of the species’ monthly diet, with seeds alone accounting for 75%, with no major monthly dietary shifts. The flexible exploitation by this species of a consistently available food supply for which it faces little competition likely reduces foraging effort and consumption of less desirable foods, even during prolonged periods of overall fruit scarcity. The relative rarity of immature fruit specialists in tropical forests may reflect the fact that processing the hard pericarps and neutralizing the toxicities of immature seeds present substantial evolutionary hurdles that few arboreal vertebrate species have overcome.     

Ashéninka amity: a study of social relations in an Amazonian society

Starting with Ashéninka people's avowed preference for living apart, in nuclear family households, this article analyses Ashéninka social practices within the context of ongoing academic debates over reciprocity, kinship, and the relative importance of similarity and difference in Amazonian thought. I argue that instead of attempting to pull others into fixed and narrowly prescribed relationships, particularly those based on kinship, the Ashéninka prefer for all ties to be based on relations of friendship that remain voluntary, limited, and flexible. I show how these relationships are underpinned by a cultural imperative on unilateral giving that is manifested in masateadas , social gatherings centred on the consumption of manioc beer.  

Résumé

À partir de la préférence déclarée des Ashéninkas pour une vie isolée en maisonnées composées de familles nucléaires, l'article analyse les pratiques sociales dans le contexte des débats académiques actuels sur la réciprocité, la parenté et l'importance relative de la similitude et de la différence dans la pensée amazonienne. L'auteur avance qu'au lieu de tenter de contraindre les autres à des relations fixes et strictement prescrites, notamment sur la base de la parenté, les Ashéninkas préfèrent qu'elles soient tissées à partir de liens d'amitié volontaires, limités et souples. L'auteur montre comment ces relations sont sous-tendues par un impératif culturel de don unilatéral, manifesté dans les masateadas , des rassemblements sociaux centrés sur la consommation de bière de manioc.     

Role of prey and intraspecific density dependence on the population growth of an avian top predator

Exploring predator–prey systems in diverse ecosystems increases our knowledge about ecological processes. Predator population growth may be positive when conspecific density is low but predators also need areas with prey availability, associated with competition, which increases the risk of suffering losses but stabilises populations. We studied relationships between European rabbits Oryctolagus cuniculus (prey) and adult eagle owls Bubo bubo (predators) in south-western Europe. We assessed models explaining the predator population growth and stability. We estimated the abundance of rabbits and adult eagle owls during three years in eight localities of central-southern Spain. We explored models including rabbit and adult eagle owl abundance, accounting for yearly variations and including the locality as a random variable. We found that population growth of adult eagle owls was positive in situations with low conspecific abundance and tended to be negative but approaching equilibrium in situations of higher conspecific abundance. Population growth was also positively related to previous summer rabbit density when taking into account eagle owl conspecific abundance, possibly indicating that rabbits may support recruitment. Furthermore, abundance stability of adult eagle owls was positively related to previous winter–spring rabbit density, which could suggest predator population stabilisation through quick territory occupation in high-quality areas. These results exemplify the trade-off between prey availability and abundance of adult predators related to population growth and abundance stability in the eagle owl–rabbit system in south-western Europe. Despite rabbits have greatly declined during the last decades and eagle owls locally specialise on them, eagle owls currently have a favourable conservation status. As eagle owls are the only nocturnal raptor with such dependence on rabbits, this could point out that predators may overcome prey decreases in areas with favourable climate and prey in the absence of superior competitors with similar foraging mode.     

Effect of genotype on the development of aggressive and submissive behavior in the mouse

Aggressive and submissive behaviour was studied in CBA/Lac and C57BL/6J strains of mice during long-term intermale interaction with syngenic partners. It was shown that the aggressiveness of aggressive C57BL/6J animals was more expressive than that of CBA/Lac' ones. The structure of submissive behaviour of this strains' encounters was also significantly different. Prolonged-defeat experience changed the character of submissive behaviour of C57BL/6J, but not of CBA/Lac' ones. Aggression of dominant animals considerably decreased in both strains. It is suggested that CBA/Lac and C57BL/6J mice had different mechanisms of suppression of intermale aggression.     

The grimace and gecker: A submissive display among patas monkeys

Observations of captive patas monkeys, plus a review of the literature, suggest that this species possesses at least three submissive/appeasement signals: (1) grimacing accompanied by a geckering vocalization; (2) cowering; and (3) a crouch face display. These findings are in contrast to earlier reports that patas monkeys have no such signals.     

Learning of submissive behavior in mice: A new model

The experience of winning or loosing fights plays an important role in subsequent aggressive or submissive behaviors. In this study agonistic behavior of male mice was chosen to investigate learning mechanisms in the context of a biologically meaningful situation.An ICR mouse introduced into a group of five C57BL/6 mice was attacked by mice of high social status (Fighter, F), but not by lower ranking animals (Non-Fighter, NF). On this basis the following model was developed to study learning of submissive behavior. Day 1 (baseline trial): An ICR mouse was introduced to a single NF-C57 mouse. Few submissive behaviors (crouch) were observed in naive ICR mice upon contact with NF-C57 mice. Day 2 (learning trial): The same ICR mouse was defeated by an F-C57 mouse until it showed defensive upright posture upon approach. This criterion was reached after a mean latency of 3.5 min and after being exposed to a mean number of 14 bites. Day 3 (retest trial): The same pairs as on day 1 confronted each other. Without being attacked, the ICR mouse showed a significant increase of submissive behavior (crouch, defensive sideways and upright) upon mere contact with the NF-C57 mouse when compared to day 1 and to control mice on day 3. Controls, confronted on all three days with NF-C57 mice, showed no increase in submissive behaviors.The results are discussed in terms of acquisition, memory, retrieval and extinction of learned submissive behavior. It is suggested that the mechanisms underlying learning of submissive behavior include generalization of conditioning and specific extinction processes. The further use of the learning scheme to assess drug effects is illustrated.     

Moderate water stress affects tomato leaf water relations in dependence on the nitrogen supply

The responses of water relations, stomatal conductance (g_s) and growth parameters of tomato (Lycopersicon esculentum Mill. cv. Royesta) plants to nitrogen fertilisation and drought were studied. The plants were subjected to a long-term, moderate and progressive water stress by adding 80 % of the water evapotranspirated by the plant the preceding day. Well-watered plants received 100 % of the water evapotranspirated. Two weeks before starting the drought period, the plants were fertilised with Hoagland’s solution with 14, 60 and 110 mM NO₃ ⁻ (N14, N60 and N110, respectively). Plants of the N110 treatment had the highest leaf area. However, g_s was higher for N60 plants and lower for N110 plants. At the end of the drought period, N60 plants showed the lowest values of water potential (Ψ_w) and osmotic potential (Ψ_s), and the highest values of pressure potential (Ψ_p). N60 plants showed the highest Ψ_s at maximum Ψ_p and the highest bulk modulus of elasticity.     

Reconstructing history: the Amazonian Mura Indians

We studied demographic characteristics of two Mura Indian villages. Two-hundred six inhabitants of these villages and another population were tested in relation to 30 blood and 4 saliva genetic systems. These groups exhibit high mobility and exogamy rates and high fertility but relatively low mortality and variance in number of children per woman. Hb J Oxford and albumin Maku were observed, and they show high prevalences of GPT*1 and RH*R1 but low of HP*1 compared to other South American Indians. Four electrophoretic saliva systems are reported here for the first time in a predominantly Amerindian group. The amount of polymorphism was more limited than that found in Caucasian, black, and Oriental populations. The Mura are still predominantly Indian (82%) but have African (11%) and Caucasoid (7%) admixture. Using these values, the putative ancestral Mura gene frequencies were assessed. Problems related to quantitative estimations of admixture and the factors that influence the process are discussed.     

Testing the threat-sensitive predator avoidance hypothesis: physiological responses and predator pressure in wild rabbits

Predation is a strong selective force with both direct and indirect effects on an animal’s fitness. In order to increase the chances of survival, animals have developed different antipredator strategies. However, these strategies have associated costs, so animals should assess their actual risk of predation and shape their antipredator effort accordingly. Under a stressful situation, such as the presence of predators, animals display a physiological stress response that might be proportional to the risk perceived. We tested this hypothesis in wild European rabbits (Oryctolagus cuniculus), subjected to different predator pressures, in Doñana National Park (Spain). We measured the concentrations of fecal corticosterone metabolites (FCM) in 20 rabbit populations. By means of track censuses we obtained indexes of mammalian predator presence for each rabbit population. Other factors that could modify the physiological stress response, such as breeding status, food availability and rabbit density, were also considered. Model selection based on information theory showed that predator pressure was the main factor triggering the glucocorticoid release and that the physiological stress response was positively correlated with the indexes of the presence of mammalian carnivore predators. Other factors, such as food availability and density of rabbits, were considerably less important. We conclude that rabbits are able to assess their actual risk of predation and show a threat-sensitive physiological response.     

Population dynamics of a South American rodent: seasonal structure interacting with climate,density dependence and predator effects

Understanding the role of interactions between intrinsic feedback loops and external climatic forces is one of the central challenges within the field of population ecology. For rodent dynamics, the seasonal structure of the environment necessitates changes between two stages: reproductive and non-reproductive. Nevertheless, the interactions between seasonality, climate, density dependence and predators have been generally ignored. We demonstrate that direct climate effects, the nonlinear effect of predators and the nonlinear first-order feedback embedded in a seasonal structure are key elements underlying the large and irregular fluctuations in population numbers exhibited by a small rodent in a semi-arid region of central Chile. We found that factors influencing population growth rates clearly differ between breeding and non-breeding seasons. In addition, we detected nonlinear density dependencies as well as nonlinear and differential effects of generalist and specialist predators. Recent climatic changes may account for dramatic perturbations of the rodent's population dynamics. Changes in the predator guild induced by climate are likely to result, through the food web, in a large impact on small rodent demography and population dynamics. Assuming such interactions to be typical of ecological systems, we conclude that appropriate predictions of the ecological consequences of climate change will depend on having an in-depth understanding of the community-weather system.     

Influence of predator density on nonindependent effects of multiple predator species

Interactions between multiple predator species are frequent in natural communities and can have important implications for shared prey survival. Predator density may be an important component of these interactions between predator species, as the frequency of interactions between species is largely determined by species density. Here we experimentally examine the importance of predator density for interactions between predator species and subsequent impacts on prey. We show that aggressive interactions between the predatory shore crabs Carcinus maenas and Hemigrapsus sanguineus increased with predator density, yet did not increase as fast as negative interactions between conspecifics. At low density, interactions between conspecific and heterospecific predators had similar inhibitory impacts on predator function, whereas conspecific interference was greater than interference from heterospecifics at high predator density. Thus the impact of conspecific interference at high predator density was sufficient in itself that interactions with a second predator species had no additional impact on per capita predation. Spatial and temporal variability in predator density is a ubiquitous characteristic of natural systems that should be considered in studies of multiple predator species.     

Dynamics of predator and modular prey: effects of module consumption on stability of prey–predator system

In traditional models of predator–prey population dynamics, it is usually assumed that consumed prey are immediately removed from the population. However, in plant–herbivore interactions, damaged plants are generally alive after attacks by herbivores. This can result in successive or simultaneous attacks by multiple predators on a single prey item (here, the term prey is expanded to include plants). We constructed a mathematical model with two time scales, taking into account predation processes within a generation, considering post‐predation survival and the modularity of prey. We assumed that a prey item can be divided into modules and that it can be fed on by multiple predators or parasitized by multiple parasites at the same time. The model includes two essential factors: the modularity of prey for predators (n) and the detaching/attaching ratio of predators to prey (ε). Based on the formulae, we revealed a general property of realistic dynamics in plant–herbivore and host–parasite interactions. The analysis showed that the model could be approximated by models with the type I, type II or Beddington–DeAngelis functional responses by taking appropriate limits to the situations. When modularity is low or the detaching/attaching ratio is high, population dynamics tend to be stabilized. These stabilizing effects may be related to interference competition among predator individuals or increases in free prey modules and free predator individuals. In the limit of high modularity, the ratio of the attached prey modules to the total prey modules becomes negligible and the dynamics tend to be destabilized. However, if quantity and quality of prey modules are negatively correlated, the equilibrium is likely to be stabilized at high modularity as long as it remains feasible. These results suggest that considering post‐predation survival and modularity of prey is crucial to understand predator–prey interactions.     

Studies of the impact ofEuseius species (Acari: Phytoseiidae) on citrus mites using predator exclusion and predator release experiments

To create plots with differential levels ofEuseius, malathion sprays, highly toxic to phytoseiids but of low toxicity to citrus red mite,Panonychus citri (CRM), and citrus thrips,Scirtothrips citri, were applied to blocks of Valencia oranges for three seasons (1984, 1985 and 1986) and Eureka lemons for one season (1985). Releases ofEuseius spp. were made in plots within the treated blocks. In 1984, CRM populations were highest in the treated/no release plot, lowest in the untreated and intermediate in the treated/Euseius stipulatus-release plot. In 1985, CRM populations were high in all plots in the oranges (including theE. tularensis release) except theE. stipulatus-release plot, and in all plots in the lemons except the untreated.Euseius releases in the lemons had no effect, apparently because they were followed by very hot weather. In 1986, CRM was very low in all plots.Euseius stipulatus became the dominant phytoseiid species even in theE. tularensis-release plots after a few weeks, indicating that this species colonized more readily and spread to other trees more rapidly than didE. tularensis. The results support the hypothesis thatE. stipulatus is an important mortality factor contributing to CRM control at low levels.Euseius stipulatus also may have a negative impact on the citrus rust mite,Phyllocoptruta oleivora. Citrus thrips populations were low during the entire study period and did not differ significantly between plots.     

Hydropower and the future of Amazonian biodiversity

In an effort to ensure energy independence and exploit mineral resources, the governments of Amazonian countries are embarking on a major dam building drive on the basin’s rivers, with 191 dams finished and a further 246 planned or under construction. This rush to harvest the basin’s vast renewable energy capacity has come without proper consideration of the likely negative environmental externalities on the world’s most speciose freshwater and terrestrial biotas. Here we highlight the economic drivers for hydropower development and review the literature to summarise the impacts of dam building on Amazonian biodiversity. We identify both direct and indirect impacts through the anticipated loss, fragmentation and degradation of riparian habitats. We then propose a series of measures to assess, curb and mitigate the impacts of destructive dams on Amazonian biodiversity.