Consistent patterns of common species across tropical tree communities

Trees structure the Earth's most biodiverse ecosystem, tropical forests. The vast number of tree species presents a formidable challenge to understanding these forests, including their response to environmental change, as very little is known about most tropical tree species. A focus on the common species may circumvent this challenge. Here we investigate abundance patterns of common tree species using inventory data on 1,003,805 trees with trunk diameters of at least 10 cm across 1,568 locations1-6 in closed-canopy, structurally intact old-growth tropical forests in Africa, Amazonia and Southeast Asia. We estimate that 2.2%, 2.2% and 2.3% of species comprise 50% of the tropical trees in these regions, respectively. Extrapolating across all closed-canopy tropical forests, we estimate that just 1,053 species comprise half of Earth's 800 billion tropical trees with trunk diameters of at least 10 cm. Despite differing biogeographic, climatic and anthropogenic histories7, we find notably consistent patterns of common species and species abundance distributions across the continents. This suggests that fundamental mechanisms of tree community assembly may apply to all tropical forests. Resampling analyses show that the most common species are likely to belong to a manageable list of known species, enabling targeted efforts to understand their ecology. Although they do not detract from the importance of rare species, our results open new opportunities to understand the world's most diverse forests, including modelling their response to environmental change, by focusing on the common species that constitute the majority of their trees.

MASTREE+: Time-series of plant reproductive effort from six continents

Significant gaps remain in understanding the response of plant reproduction to environmental change. This is partly because measuring reproduction in long-lived plants requires direct observation over many years and such datasets have rarely been made publicly available. Here we introduce MASTREE+, a data set that collates reproductive time-series data from across the globe and makes these data freely available to the community. MASTREE+ includes 73,828 georeferenced observations of annual reproduction (e.g. seed and fruit counts) in perennial plant populations worldwide. These observations consist of 5971 population-level time-series from 974 species in 66 countries. The mean and median time-series length is 12.4 and 10 years respectively, and the data set includes 1122 series that extend over at least two decades (≥20 years of observations). For a subset of well-studied species, MASTREE+ includes extensive replication of time-series across geographical and climatic gradients. Here we describe the open-access data set, available as a.csv file, and we introduce an associated web-based app for data exploration. MASTREE+ will provide the basis for improved understanding of the response of long-lived plant reproduction to environmental change. Additionally, MASTREE+ will enable investigation of the ecology and evolution of reproductive strategies in perennial plants, and the role of plant reproduction as a driver of ecosystem dynamics.

Fine root dynamics across pantropical rainforest ecosystems

Fine roots constitute a significant component of the net primary productivity (NPP) of forest ecosystems but are much less studied than aboveground NPP. Comparisons across sites and regions are also hampered by inconsistent methodologies, especially in tropical areas. Here, we present a novel dataset of fine root biomass, productivity, residence time, and allocation in tropical old-growth rainforest sites worldwide, measured using consistent methods, and examine how these variables are related to consistently determined soil and climatic characteristics. Our pantropical dataset spans intensive monitoring plots in lowland (wet, semi-deciduous, and deciduous) and montane tropical forests in South America, Africa, and Southeast Asia (n = 47). Large spatial variation in fine root dynamics was observed across montane and lowland forest types. In lowland forests, we found a strong positive linear relationship between fine root productivity and sand content, this relationship was even stronger when we considered the fractional allocation of total NPP to fine roots, demonstrating that understanding allocation adds explanatory power to understanding fine root productivity and total NPP. Fine root residence time was a function of multiple factors: soil sand content, soil pH, and maximum water deficit, with longest residence times in acidic, sandy, and water-stressed soils. In tropical montane forests, on the other hand, a different set of relationships prevailed, highlighting the very different nature of montane and lowland forest biomes. Root productivity was a strong positive linear function of mean annual temperature, root residence time was a strong positive function of soil nitrogen content in montane forests, and lastly decreasing soil P content increased allocation of productivity to fine roots. In contrast to the lowlands, environmental conditions were a better predictor for fine root productivity than for fractional allocation of total NPP to fine roots, suggesting that root productivity is a particularly strong driver of NPP allocation in tropical mountain regions.

Resistance of African tropical forests to an extreme climate anomaly

The responses of tropical forests to environmental change are critical uncertainties in predicting the future impacts of climate change. The positive phase of the 2015-2016 El Niño Southern Oscillation resulted in unprecedented heat and low precipitation in the tropics with substantial impacts on the global carbon cycle. The role of African tropical forests is uncertain as their responses to short-term drought and temperature anomalies have yet to be determined using on-the-ground measurements. African tropical forests may be particularly sensitive because they exist in relatively dry conditions compared with Amazonian or Asian forests, or they may be more resistant because of an abundance of drought-adapted species. Here, we report responses of structurally intact old-growth lowland tropical forests inventoried within the African Tropical Rainforest Observatory Network (AfriTRON). We use 100 long-term inventory plots from six countries each measured at least twice prior to and once following the 2015-2016 El Niño event. These plots experienced the highest temperatures and driest conditions on record. The record temperature did not significantly reduce carbon gains from tree growth or significantly increase carbon losses from tree mortality, but the record drought did significantly decrease net carbon uptake. Overall, the long-term biomass increase of these forests was reduced due to the El Niño event, but these plots remained a live biomass carbon sink (0.51 ± 0.40 Mg C ha-1 y-1) despite extreme environmental conditions. Our analyses, while limited to African tropical forests, suggest they may be more resistant to climatic extremes than Amazonian and Asian forests.

Recent genetic connectivity and clinal variation in chimpanzees

Much like humans, chimpanzees occupy diverse habitats and exhibit extensive behavioural variability. However, chimpanzees are recognized as a discontinuous species, with four subspecies separated by historical geographic barriers. Nevertheless, their range-wide degree of genetic connectivity remains poorly resolved, mainly due to sampling limitations. By analyzing a geographically comprehensive sample set amplified at microsatellite markers that inform recent population history, we found that isolation by distance explains most of the range-wide genetic structure of chimpanzees. Furthermore, we did not identify spatial discontinuities corresponding with the recognized subspecies, suggesting that some of the subspecies-delineating geographic barriers were recently permeable to gene flow. Substantial range-wide genetic connectivity is consistent with the hypothesis that behavioural flexibility is a salient driver of chimpanzee responses to changing environmental conditions. Finally, our observation of strong local differentiation associated with recent anthropogenic pressures portends future loss of critical genetic diversity if habitat fragmentation and population isolation continue unabated.

Long-term collapse in fruit availability threatens Central African forest megafauna

Afrotropical forests host much of the world's remaining megafauna, although these animals are confined to areas where direct human influences are low. We used a rare long-term dataset of tree reproduction and a photographic database of forest elephants to assess food availability and body condition of an emblematic megafauna species at Lopé National Park, Gabon. Our analysis reveals an 81% decline in fruiting over a 32-year period (1986-2018) and an 11% decline in body condition of fruit-dependent forest elephants from 2008 to 2018. Fruit famine in one of the last strongholds for African forest elephants should raise concern about the ability of this species and other fruit-dependent megafauna to persist in the long term, with potential consequences for broader ecosystem and biosphere functioning.

Human impact erodes chimpanzee behavioral diversity

Chimpanzees possess a large number of behavioral and cultural traits among nonhuman species. The "disturbance hypothesis" predicts that human impact depletes resources and disrupts social learning processes necessary for behavioral and cultural transmission. We used a dataset of 144 chimpanzee communities, with information on 31 behaviors, to show that chimpanzees inhabiting areas with high human impact have a mean probability of occurrence reduced by 88%, across all behaviors, compared to low-impact areas. This behavioral diversity loss was evident irrespective of the grouping or categorization of behaviors. Therefore, human impact may not only be associated with the loss of populations and genetic diversity, but also affects how animals behave. Our results support the view that "culturally significant units" should be integrated into wildlife conservation.

Improving cost-efficiency of faecal genotyping: New tools for elephant species

Despite the critical need for non-invasive tools to improve monitoring of wildlife populations, especially for endangered and elusive species, faecal genetic sampling has not been adopted as regular practice, largely because of the associated technical challenges and cost. Substantial work needs to be undertaken to refine sample collection and preparation methods in order to improve sample set quality and provide cost-efficient tools that can effectively support wildlife management. In this study, we collected an extensive set of forest elephant (Loxodonta cyclotis) faecal samples throughout Gabon, Central Africa, and prepared them for genotyping using 107 single-nucleotide polymorphism assays. We developed a new quantitative polymerase chain reaction (PCR) assay targeting a 130-bp nuclear DNA fragment and demonstrated its suitability for degraded samples in all three elephant species. Using this assay to compare the efficacy of two sampling methods for faecal DNA recovery, we found that sampling the whole surface of a dung pile with a swab stored in a small tube of lysis buffer was a convenient method producing high extraction success and DNA yield. We modelled the influence of faecal quality and storage time on DNA concentration in order to provide recommendations for optimized collection and storage. The maximum storage time to ensure 75% success was two months for samples collected within 24 hours after defecation and extended to four months for samples collected within one hour. Lastly, the real-time quantitative PCR assay allowed us to predict genotyping success and pre-screen DNA samples, thus further increasing the cost-efficiency of our approach. We recommend combining the validation of an efficient sampling method, the build of in-country DNA extraction capacity for reduced storage time and the development of species-specific quantitative PCR assays in order to increase the cost-efficiency of routine non-invasive DNA analyses and expand the use of next-generation markers to non-invasive samples.

ENSO Drives interannual variation of forest woody growth across the tropics

Meteorological extreme events such as El Niño events are expected to affect tropical forest net primary production (NPP) and woody growth, but there has been no large-scale empirical validation of this expectation. We collected a large high-temporal resolution dataset (for 1-13 years depending upon location) of more than 172 000 stem growth measurements using dendrometer bands from across 14 regions spanning Amazonia, Africa and Borneo in order to test how much month-to-month variation in stand-level woody growth of adult tree stems (NPP_stem) can be explained by seasonal variation and interannual meteorological anomalies. A key finding is that woody growth responds differently to meteorological variation between tropical forests with a dry season (where monthly rainfall is less than 100 mm), and aseasonal wet forests lacking a consistent dry season. In seasonal tropical forests, a high degree of variation in woody growth can be predicted from seasonal variation in temperature, vapour pressure deficit, in addition to anomalies of soil water deficit and shortwave radiation. The variation of aseasonal wet forest woody growth is best predicted by the anomalies of vapour pressure deficit, water deficit and shortwave radiation. In total, we predict the total live woody production of the global tropical forest biome to be 2.16 Pg C yr^-1, with an interannual range 1.96-2.26 Pg C yr^-1 between 1996-2016, and with the sharpest declines during the strong El Niño events of 1997/8 and 2015/6. There is high geographical variation in hotspots of El Niño-associated impacts, with weak impacts in Africa, and strongly negative impacts in parts of Southeast Asia and extensive regions across central and eastern Amazonia. Overall, there is high correlation (r = -0.75) between the annual anomaly of tropical forest woody growth and the annual mean of the El Niño 3.4 index, driven mainly by strong correlations with anomalies of soil water deficit, vapour pressure deficit and shortwave radiation.This article is part of the discussion meeting issue 'The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications'.

Guns, germs, and trees determine density and distribution of gorillas and chimpanzees in Western Equatorial Africa

We present a range-wide assessment of sympatric western lowland gorillas Gorilla gorilla gorilla and central chimpanzees Pan troglodytes troglodytes using the largest survey data set ever assembled for these taxa: 59 sites in five countries surveyed between 2003 and 2013, totaling 61,000 person-days of fieldwork. We used spatial modeling to investigate major drivers of great ape distribution and population trends. We predicted density across each taxon's geographic range, allowing us to estimate overall abundance: 361,900 gorillas and 128,700 chimpanzees in Western Equatorial Africa-substantially higher than previous estimates. These two subspecies represent close to 99% of all gorillas and one-third of all chimpanzees. Annual population decline of gorillas was estimated at 2.7%, maintaining them as Critically Endangered on the International Union for Conservation of Nature and Natural Resources (IUCN) Red List. We quantified the threats to each taxon, of which the three greatest were poaching, disease, and habitat degradation. Gorillas and chimpanzees are found at higher densities where forest is intact, wildlife laws are enforced, human influence is low, and disease impacts have been low. Strategic use of the results of these analyses could conserve the majority of gorillas and chimpanzees. With around 80% of both subspecies occurring outside protected areas, their conservation requires reinforcement of anti-poaching efforts both inside and outside protected areas (particularly where habitat quality is high and human impact is low), diligent disease control measures (including training, advocacy, and research into Ebola virus disease), and the preservation of high-quality habitat through integrated land-use planning and implementation of best practices by the extractive and agricultural industries.

Single-nucleotide polymorphism discovery and panel characterization in the African forest elephant

The continuing decline in forest elephant (Loxodonta cyclotis) numbers due to poaching and habitat reduction is driving the search for new tools to inform management and conservation. For dense rainforest species, basic ecological data on populations and threats can be challenging and expensive to collect, impeding conservation action in the field. As such, genetic monitoring is being increasingly implemented to complement or replace more burdensome field techniques. Single-nucleotide polymorphisms (SNPs) are particularly cost-effective and informative markers that can be used for a range of practical applications, including population census, assessment of human impact on social and genetic structure, and investigation of the illegal wildlife trade. SNP resources for elephants are scarce, but next-generation sequencing provides the opportunity for rapid, inexpensive generation of SNP markers in nonmodel species. Here, we sourced forest elephant DNA from 23 samples collected from 10 locations within Gabon, Central Africa, and applied double-digest restriction-site-associated DNA (ddRAD) sequencing to discover 31,851 tags containing SNPs that were reduced to a set of 1,365 high-quality candidate SNP markers. A subset of 115 candidate SNPs was then selected for assay design and validation using 56 additional samples. Genotyping resulted in a high conversion rate (93%) and a low per allele error rate (0.07%). This study provides the first panel of 107 validated SNP markers for forest elephants. This resource presents great potential for new genetic tools to produce reliable data and underpin a step-change in conservation policies for this elusive species.

African Savanna-Forest Boundary Dynamics: A 20-Year Study

Recent studies show widespread encroachment of forest into savannas with important consequences for the global carbon cycle and land-atmosphere interactions. However, little research has focused on in situ measurements of the successional sequence of savanna to forest in Africa. Using long-term inventory plots we quantify changes in vegetation structure, above-ground biomass (AGB) and biodiversity of trees ≥10 cm diameter over 20 years for five vegetation types: savanna; colonising forest (F1), monodominant Okoume forest (F2); young Marantaceae forest (F3); and mixed Marantaceae forest (F4) in Lopé National Park, central Gabon, plus novel 3D terrestrial laser scanning (TLS) measurements to assess forest structure differences. Over 20 years no plot changed to a new stage in the putative succession, but F1 forests strongly moved towards the structure, AGB and diversity of F2 forests. Overall, savanna plots showed no detectable change in structure, AGB or diversity using this method, with zero trees ≥10 cm diameter in 1993 and 2013. F1 and F2 forests increased in AGB, mainly as a result of adding recruited stems (F1) and increased Basal Area (F2), whereas F3 and F4 forests did not change substantially in structure, AGB or diversity. Critically, the stability of the F3 stage implies that this stage may be maintained for long periods. Soil carbon was low, and did not show a successional gradient as for AGB and diversity. TLS vertical plant profiles showed distinctive differences amongst the vegetation types, indicating that this technique can improve ecological understanding. We highlight two points: (i) as forest colonises, changes in biodiversity are much slower than changes in forest structure or AGB; and (ii) all forest types store substantial quantities of carbon. Multi-decadal monitoring is likely to be required to assess the speed of transition between vegetation types.

Chimpanzee accumulative stone throwing

The study of the archaeological remains of fossil hominins must rely on reconstructions to elucidate the behaviour that may have resulted in particular stone tools and their accumulation. Comparatively, stone tool use among living primates has illuminated behaviours that are also amenable to archaeological examination, permitting direct observations of the behaviour leading to artefacts and their assemblages to be incorporated. Here, we describe newly discovered stone tool-use behaviour and stone accumulation sites in wild chimpanzees reminiscent of human cairns. In addition to data from 17 mid- to long-term chimpanzee research sites, we sampled a further 34 Pan troglodytes communities. We found four populations in West Africa where chimpanzees habitually bang and throw rocks against trees, or toss them into tree cavities, resulting in conspicuous stone accumulations at these sites. This represents the first record of repeated observations of individual chimpanzees exhibiting stone tool use for a purpose other than extractive foraging at what appear to be targeted trees. The ritualized behavioural display and collection of artefacts at particular locations observed in chimpanzee accumulative stone throwing may have implications for the inferences that can be drawn from archaeological stone assemblages and the origins of ritual sites.

Fine-scale genetic structure and cryptic associations reveal evidence of kin-based sociality in the African forest elephant

Spatial patterns of relatedness within animal populations are important in the evolution of mating and social systems, and have the potential to reveal information on species that are difficult to observe in the wild. This study examines the fine-scale genetic structure and connectivity of groups within African forest elephants, Loxodonta cyclotis, which are often difficult to observe due to forest habitat. We tested the hypothesis that genetic similarity will decline with increasing geographic distance, as we expect kin to be in closer proximity, using spatial autocorrelation analyses and Tau K_r tests. Associations between individuals were investigated through a non-invasive genetic capture-recapture approach using network models, and were predicted to be more extensive than the small groups found in observational studies, similar to fission-fusion sociality found in African savanna (Loxodonta africana) and Asian (Elephas maximus) species. Dung samples were collected in Lopé National Park, Gabon in 2008 and 2010 and genotyped at 10 microsatellite loci, genetically sexed, and sequenced at the mitochondrial DNA control region. We conducted analyses on samples collected at three different temporal scales: a day, within six-day sampling sessions, and within each year. Spatial autocorrelation and Tau K_r tests revealed genetic structure, but results were weak and inconsistent between sampling sessions. Positive spatial autocorrelation was found in distance classes of 0–5 km, and was strongest for the single day session. Despite weak genetic structure, individuals within groups were significantly more related to each other than to individuals between groups. Social networks revealed some components to have large, extensive groups of up to 22 individuals, and most groups were composed of individuals of the same matriline. Although fine-scale population genetic structure was weak, forest elephants are typically found in groups consisting of kin and based on matrilines, with some individuals having more associates than observed from group sizes alone.

A theoretical account of cue averaging in the rodent head direction system

Head direction (HD) cell responses are thought to be derived from a combination of internal (or idiothetic) and external (or allothetic) sources of information. Recent work from the Jeffery laboratory shows that the relative influence of visual versus vestibular inputs upon the HD cell response depends on the disparity between these sources. In this paper, we present simulation results from a model designed to explain these observations. The model accurately replicates the Knight et al. data. We suggest that cue conflict resolution is critically dependent on plastic remapping of visual information onto the HD cell layer. This remap results in a shift in preferred directions of a subset of HD cells, which is then inherited by the rest of the cells during path integration. Thus, we demonstrate how, over a period of several minutes, a visual landmark may gain cue control. Furthermore, simulation results show that weaker visual landmarks fail to gain cue control as readily. We therefore suggest a second longer term plasticity in visual projections onto HD cell areas, through which landmarks with an inconsistent relationship to idiothetic information are made less salient, significantly hindering their ability to gain cue control. Our results provide a mechanism for reliability-weighted cue averaging that may pertain to other neural systems in addition to the HD system.

Weighted cue integration in the rodent head direction system

How the brain combines information from different sensory modalities and of differing reliability is an important and still-unanswered question. Using the head direction (HD) system as a model, we explored the resolution of conflicts between landmarks and background cues. Sensory cue integration models predict averaging of the two cues, whereas attractor models predict capture of the signal by the dominant cue. We found that a visual landmark mostly captured the HD signal at low conflicts: however, there was an increasing propensity for the cells to integrate the cues thereafter. A large conflict presented to naive rats resulted in greater visual cue capture (less integration) than in experienced rats, revealing an effect of experience. We propose that weighted cue integration in HD cells arises from dynamic plasticity of the feed-forward inputs to the network, causing within-trial spatial redistribution of the visual inputs onto the ring. This suggests that an attractor network can implement decision processes about cue reliability using simple architecture and learning rules, thus providing a potential neural substrate for weighted cue integration.

Integration of visual motion and locomotion in mouse visual cortex

Successful navigation through the world requires accurate estimation of one's own speed. To derive this estimate, animals integrate visual speed gauged from optic flow and run speed gauged from proprioceptive and locomotor systems. The primary visual cortex (V1) carries signals related to visual speed, and its responses are also affected by run speed. To study how V1 combines these signals during navigation, we recorded from mice that traversed a virtual environment. Nearly half of the V1 neurons were reliably driven by combinations of visual speed and run speed. These neurons performed a weighted sum of the two speeds. The weights were diverse across neurons, and typically positive. As a population, V1 neurons predicted a linear combination of visual and run speeds better than either visual or run speeds alone. These data indicate that V1 in the mouse participates in a multimodal processing system that integrates visual motion and locomotion during navigation.

Place field repetition and purely local remapping in a multicompartment environment

Hippocampal place cells support spatial memory using sensory information from the environment and self-motion information to localize their firing fields. Currently, there is disagreement about whether CA1 place cells can use pure self-motion information to disambiguate different compartments in environments containing multiple visually identical compartments. Some studies report that place cells can disambiguate different compartments, while others report that they do not. Furthermore, while numerous studies have examined remapping, there has been little examination of remapping in different subregions of a single environment. Is remapping purely local or do place fields in neighboring, unaffected, regions detect the change? We recorded place cells as rats foraged across a 4-compartment environment and report 3 new findings. First, we find that, unlike studies in which rats foraged in 2 compartments, place fields showed a high degree of spatial repetition with a slight degree of rate-based discrimination. Second, this repetition does not diminish with extended experience. Third, remapping was found to be purely local for both geometric change and contextual change. Our results reveal the limited capacity of the path integrator to drive pattern separation in hippocampal representations, and suggest that doorways may play a privileged role in segmenting the neural representation of space.

Above-ground biomass and structure of 260 African tropical forests

We report above-ground biomass (AGB), basal area, stem density and wood mass density estimates from 260 sample plots (mean size: 1.2 ha) in intact closed-canopy tropical forests across 12 African countries. Mean AGB is 395.7 Mg dry mass ha⁻¹ (95% CI: 14.3), substantially higher than Amazonian values, with the Congo Basin and contiguous forest region attaining AGB values (429 Mg ha⁻¹) similar to those of Bornean forests, and significantly greater than East or West African forests. AGB therefore appears generally higher in palaeo- compared with neotropical forests. However, mean stem density is low (426 ± 11 stems ha⁻¹ greater than or equal to 100 mm diameter) compared with both Amazonian and Bornean forests (cf. approx. 600) and is the signature structural feature of African tropical forests. While spatial autocorrelation complicates analyses, AGB shows a positive relationship with rainfall in the driest nine months of the year, and an opposite association with the wettest three months of the year; a negative relationship with temperature; positive relationship with clay-rich soils; and negative relationships with C : N ratio (suggesting a positive soil phosphorus-AGB relationship), and soil fertility computed as the sum of base cations. The results indicate that AGB is mediated by both climate and soils, and suggest that the AGB of African closed-canopy tropical forests may be particularly sensitive to future precipitation and temperature changes.

Who killed Porthos? Genetic tracking of a gorilla death

We describe a novel application of "forensic" genetics to study a key demographic event in a population of wild gorillas. We used microsatellite genotyping and non-invasively collected DNA samples to identify one individual western lowland gorilla as being most likely to have caused the death of another in Lopé National Park, Gabon. Data from relatively few genotypes permitted the identification of female transfer events and the interpretation of individual behavior that was previously impossible using observational methods, thus providing rare behavioral data on an elusive forest-dwelling species. Importantly, this study highlights the need for future studies of dispersal and local population structuring in forest populations, and more accurate population census methods. Genetic studies focusing on individual identification may play a valuable role in future gorilla conservation efforts.

Theoretical accounts of spatial learning: a neurobiological view (commentary on Pearce, 2009)

Theories of learning have historically taken, as their starting point, the assumption that learning processes have universal applicability. This position has been argued on grounds of parsimony, but has received two significant challenges: first, from the observation that some kinds of learning, such as spatial learning, seem to obey different rules from others, and second, that some kinds of learning take place in processing modules that are separate from each other. These challenges arose in the behavioural literature but have since received considerable support from neurobiological studies, particularly single neuron studies of spatial learning, confirming that there are indeed separable (albeit highly intercommunicating) processing modules in the brain, which may not always interact (within or between themselves) according to classic associative principles. On the basis of these neurobiological data, reviewed here, it is argued that rather than assuming universality of associative rules, it is more parsimonious to assume sets of locally operating rules, each specialized for a particular domain. By this view, although almost all learning is associative in one way or another, the behavioural-level characterization of the rules governing learning may vary depending on which neural modules are involved in a given behaviour. Neurobiological studies, in tandem with behavioural studies, can help reveal the nature of these modules and the local rules by which they interact.

How heterogeneous place cell responding arises from homogeneous grids--a contextual gating hypothesis

How entorhinal grids generate hippocampal place fields remains unknown. The simplest hypothesis-that grids of different scales are added together-cannot explain a number of place field phenomena, such as (1) Summed grids form a repeating, dispersed activation pattern whereas place fields are focal and nonrepeating; (2) Grid cells are active in all environments but place cells only in some, and (3) Partial environmental changes cause either heterogeneous ("partial") remapping in place cells whereas they result in all-or-nothing "realignment" remapping in grid cells. We propose that this dissociation between grid cell and place cell behavior arises in the entorhinal-dentate projection. By our view, the grid-cell/place-cell projection is modulated by context, both organizationally and activationally. Organizationally, we propose that when the animal first enters a new environment, the relatively homogeneous input from the grid cells becomes spatially clustered by Hebbian processes in the dendritic tree so that inputs active in the same context and having overlapping fields come to terminate on the same sub-branches of the tree. Activationally, when the animal re-enters the now-familiar environment, active contextual inputs select (by virtue of their clustered terminations) which parts of the dendritic tree, and therefore which grid cells, drive the granule cell. Assuming this pattern of projections, our model successfully produces focal hippocampal place fields that remap appropriately to contextual changes.

Integration of the sensory inputs to place cells: what, where, why, and how?

The hippocampal place cells are a highly multimodal class of neurons, receiving information from many different sensory sources to correctly localize their firing to restricted regions of an environment. Evidence suggests that the sensory information is processed upstream of the hippocampus, to extract both angular and linear metric information, and also contextual information. These various kinds of information need to be integrated for coherent firing fields to be generated, and the present article reviews recent evidence concerning how this occurs. It is concluded that there is a functional dissociation of the cortical inputs, with one class of incoming information comprising purely metric information concerning distance and orientation, probably routed via the grid cells and head direction cells. The other class of information is much more heterogeneous and serves, at least in part, to contextualize the spatial inputs so as to provide a unique representation of the place the animal is in. Evidence from remapping studies suggests that the metric and contextual inputs interact upstream of the place cells, perhaps in entorhinal cortex. A full understanding of the generation of the hippocampal place representation will require elucidation of the representational functions of the afferent cortical areas.

Do discrimination tasks discourage multi-dimensional stimulus processing?Evidence from a cross-modal object discrimination in rats

Neurobiologists are becoming increasingly interested in how complex cognitive representations are formed by the integration of sensory stimuli. To this end, discrimination tasks are frequently used to assess perceptual and cognitive processes in animals, because they are easy to administer and score, and the ability of an animal to make a particular discrimination establishes beyond doubt that the necessary perceptual/cognitive processes are present. It does not, however, follow that absence of discrimination means the animal cannot make a particular perceptual judgement; it may simply mean that the animal did not manage to discover the relevant discriminative stimulus when trying to learn the task. Here, it is shown that rats did not learn a cross-modal object discrimination (requiring association of each object's visual appearance with its odour) when trained on the complete task from the beginning. However, they could eventually make the discrimination when trained on the component parts step by step, showing that they were able to do the necessary cross-modal integration in the right circumstances. This finding adds to growing evidence that discrimination tasks tend to encourage feature-based discrimination, perhaps by engaging automatic, habit-based brain systems. Thus, they may not be the best way to assess the formation of multi-dimensional stimulus representations of the kind needed in more complex cognitive processes such as declarative memory. Instead, more natural tasks such as spontaneous exploration may be preferable.

Experience-dependent rescaling of entorhinal grids

The firing pattern of entorhinal 'grid cells' is thought to provide an intrinsic metric for space. We report a strong experience-dependent environmental influence: the spatial scales of the grids (which are aligned and have fixed relative sizes within each animal) vary parametrically with changes to a familiar environment's size and shape. Thus grid scale reflects an interaction between intrinsic, path-integrative calculation of location and learned associations to the external environment.

Do rats use shape to solve "shape discriminations"?

Visual discrimination tasks are increasingly used to explore the neurobiology of vision in rodents, but it remains unclear how the animals solve these tasks: Do they process shapes holistically, or by using low-level features such as luminance and angle acuity? In the present study we found that when discriminating triangles from squares, rats did not use shape but instead relied on local luminance differences in the lower hemifield. A second experiment prevented this strategy by using stimuli-squares and rectangles-that varied in size and location, and for which the only constant predictor of reward was aspect ratio (ratio of height to width: a simple descriptor of "shape"). Rats eventually learned to use aspect ratio but only when no other discriminand was available, and performance remained very poor even at asymptote. These results suggest that although rats can process both dimensions simultaneously, they do not naturally solve shape discrimination tasks this way. This may reflect either a failure to visually process global shape information or a failure to discover shape as the discriminative stimulus in a simultaneous discrimination. Either way, our results suggest that simultaneous shape discrimination is not a good task for studies of visual perception in rodents.

Behavioral correlates of the distributed coding of spatial context

Hippocampal place cells respond heterogeneously to elemental changes of a compound spatial context, suggesting that they form a distributed code of context, whereby context information is shared across a population of neurons. The question arises as to what this distributed code might be useful for. The present study explored two possibilities: one, that it allows contexts with common elements to be disambiguated, and the other, that it allows a given context to be associated with more than one outcome. We used two naturalistic measures of context processing in rats, rearing and thigmotaxis (boundary-hugging), to explore how rats responded to contextual novelty and to relate this to the behavior of place cells. In experiment 1, rats showed dishabituation of rearing to a novel reconfiguration of familiar context elements, suggesting that they perceived the reconfiguration as novel, a behavior that parallels that of place cells in a similar situation. In experiment 2, rats were trained in a place preference task on an open-field arena. A change in the arena context triggered renewed thigmotaxis, and yet navigation continued unimpaired, indicating simultaneous representation of both the altered contextual and constant spatial cues. Place cells similarly exhibited a dual population of responses, consistent with the hypothesis that their activity underlies spatial behavior. Together, these experiments suggest that heterogeneous context encoding (or "partial remapping") by place cells may function to allow the flexible assignment of associations to contexts, a faculty that could be useful in episodic memory encoding.

A metric for the cognitive map: found at last?

A network of brain areas collectively represent location, but the underlying nature of this "cognitive map" has remained elusive. A recent study reports that the activity patterns of some entorhinal cortical neurons form a remarkably regular array of evenly spaced peaks across the surface of the environment. These "grid cells" might be the basis of a metric used for calculating position, and their discovery could greatly advance our understanding of how navigational computations are performed.

A role for terrain slope in orienting hippocampal place fields

The three-dimensional topography of the environment is a potentially important source of orienting information for animals, but little is known about how such features affect either navigational behaviour or the neural representation of place. One component of the neural place representation comprises the hippocampal place cells, which show location-specific firing that can be oriented by directional cues in the environment. The present study investigated whether a simple topographical feature, terrain slope, could provide such orienting information to place cells. Place cells were recorded as rats explored a tilted (30 degrees) square box located in the centre of a dark, curtained and visually symmetrical circular enclosure. The orientation of the tilted surface was varied, first in conjunction with that of a visible cue card (to stabilise the system) and then in the absence of the cue card, when the slope of the box was the only remaining stable polarising cue in the environment. In the latter condition, place fields continued to be reliably oriented by the slope. Thus, terrain slope provides sufficient orienting information to set and probably maintain the orientation of the hippocampal place system. This may explain previous behavioural observations that spatial orientation is improved when slope information is available.

Context-independent directional cue learning by hippocampal place cells

In a symmetrical environment possessing no other polarizing visual cues, the spatially localized firing of hippocampal place cells can be primarily orientated by a reliable distal visual stimulus, such as a white cue card. However, if such a directional cue is made unreliable by being frequently moved in full view of the rat, the rat's internal sense of direction comes, over the course of a few days, to control the orientation of place fields instead. We investigated whether this simple form of 'cue-instability' learning would transfer to a new context, in which the firing patterns of the place cells become reorganized and in which a new spatial representation is thus active. We found that after cue-instability learning, the 'remapped' place field representation in the new environment was also orientated by the internal sense of direction of the rat rather than by the cue card, showing that the cue learning generalized from one context (and hence spatial representation) to another. This contrasts with another kind of place cell learning, in which the cells can acquire the ability to discriminate two spatial locations in one context but do not transfer this discrimination to a new context. We discuss the different effects of context changes on learned place cell activity in terms of the possible architecture of the inputs to place cells.

Mitochondrial DNA phylogeography of western lowland gorillas (Gorilla gorilla gorilla)

The geographical distribution of genetic variation within western lowland gorillas (Gorilla gorilla gorilla) was examined to clarify the population genetic structure and recent evolutionary history of this group. DNA was amplified from shed hair collected from sites across the range of the three traditionally recognized gorilla subspecies: western lowland (G. g. gorilla), eastern lowland (G. g. graueri) and mountain (G. g. beringei) gorillas. Nucleotide sequence variation was examined in the first hypervariable domain of the mitochondrial control region and was much higher in western lowland gorillas than in either of the other two subspecies. In addition to recapitulating the major evolutionary split between eastern and western lowland gorillas, phylogenetic analysis indicates a phylogeographical division within western lowland gorillas, one haplogroup comprising gorilla populations from eastern Nigeria through to southeast Cameroon and a second comprising all other western lowland gorillas. Within this second haplogroup, haplotypes appear to be partitioned geographically into three subgroups: (i) Equatorial Guinea, (ii) Central African Republic, and (iii) Gabon and adjacent Congo. There is also evidence of limited haplotype admixture in northeastern Gabon and southeast Cameroon. The phylogeographical patterns are broadly consistent with those predicted by current Pleistocene refuge hypotheses for the region and suggest that historical events have played an important role in shaping the population structure of this subspecies.

Path integration in mammals

It is often assumed that navigation implies the use, by animals, of landmarks indicating the location of the goal. However, many animals (including humans) are able to return to the starting point of a journey, or to other goal sites, by relying on self-motion cues only. This process is known as path integration, and it allows an agent to calculate a route without making use of landmarks. We review the current literature on path integration and its interaction with external, location-based cues. Special importance is given to the correlation between observable behavior and the activity pattern of particular neural cell populations that implement the internal representation of space. In mammals, the latter may well be the first high-level cognitive representation to be understood at the neural level.

A proposed architecture for the neural representation of spatial context

The role of context in guiding animal behavior has attracted increasing attention in recent years, but little is known about what constitutes a context, nor how and where in the brain it is represented. Contextual stimuli can take many forms, but of particular importance are those that collectively define a particular place or situation. The representation of place has been linked to the hippocampus, because its principal neurons ('place cells') are spatially responsive; behavioral experiments also implicate this structure in the processing of contextual stimuli. Together, these findings suggest a hippocampal role in representing 'spatial context'. The present article outlines a proposed architecture for the encoding of spatial context in which spatial inputs to place cells are modulated (or 'gated') by non-spatial stimuli. We discuss recent experimental evidence that spatial context is population-coded, a property which could allow both discrimination between overlapping contexts and generalization across them, and thus provide a foundation for animals' capacity for flexible context-linked place learning.

Context-specific acquisition of location discrimination by hippocampal place cells

The spatially localized firing of rodent hippocampal place cells is strongly determined by the local geometry of the environment. Over time, however, the cells can acquire additional inputs, including inputs from more distal cues. This is manifest as a change in firing pattern ('remapping') when the new inputs are manipulated. Place cells also reorganize their firing in response to non-geometric changes in 'context', such as a change in the colour or odour of the environment. The present study investigated whether the new inputs acquired by place cells in one context were still available to the cells when they expressed their altered firing patterns in a new context. We found that the acquired information did not transfer to the new context, suggesting that the context inputs and the acquired inputs must interact somewhere upstream of the place cells themselves. We present a model of one possible such interaction, and of how such an interaction could be modified by experience in a Hebbian manner, thus explaining the context specificity of the new learning.

Plasticity of the Hippocampal Place Cell Representation

The role of the hippocampus in the representation of 'place' has been attributed to the place cells, whose spatially localised firing suggests their participation in forming a cognitive map of the environment. That this map is necessary for spatial memory formation is indicated by the propensity of almost all navigational tasks to be disrupted by hippocampal damage. The hippocampus has also long been implicated in the formation of episodic memories, and the unusually plastic nature of hippocampal synapses testifies to its probable mnemonic role. Arguably, the place cell representation should, if it is to support spatial learning, be modifiable according to known principles of synaptic reorganization. The present article reviews evidence that the place cell representation is indeed plastic, and that its plasticity depends on the same neurobiological mechanisms known to underlie experimentally induced synaptic plasticity. Inferences are drawn regarding the architecture of the spatial representation and the principles by which it is modified. Spatial learning is promising to be the first kind of memory which is completely understood at all levels, from molecular through circuitry to behaviour and beyond.

Heterogeneous modulation of place cell firing by changes in context

Hippocampal place cells show spatially localized activity that can be modulated by both geometric information (e.g., the distances and directions of features in the environment) and nongeometric information (e.g., colors, odors, and possibly behaviors). Nongeometric information may allow the discrimination of different spatial contexts. Understanding how nongeometric (or contextual) information affects hippocampal activity is important in light of proposals that the hippocampus may play a role in constructing a representation of spatial context. We investigated the contextual modulation of place cell activity by recording hippocampal place cells while rats foraged in compound contexts comprising black or white color paired with lemon or vanilla odor. Some cells responded to the color or odor changes alone, but most responded to varying combinations of both. Thus, we demonstrate, for the first time, that there is a heterogeneous input by contextual inputs into the hippocampus. We propose a model of contextual remapping of place cells in which the geometric inputs are selectively activated by subsets of contextual stimuli. Because it appears that different place cells are affected by different subsets of contextual stimuli, the representation of the entire context would require activity at the population level, supporting a role for the hippocampus in constructing a representation of spatial context.

Preserved performance in a hippocampal-dependent spatial task despite complete place cell remapping

The spatially localized firing of hippocampal place cells is thought to underlie the navigational function of the hippocampus. Performance on a spatial task learned using a particular place cell map should therefore deteriorate if the map is disrupted. To test this prediction, we trained rats on a hippocampal-dependent spatial task in a black box and tested them in a white box. Although the change from black to white induced remapping of most place cells, navigational performance remained essentially intact. Furthermore, place cell activity was also unrelated to specific aspects of the task such as tone onset, response, or goal location. Together, these results imply that the spatial information needed to solve this navigation task is represented outside the hippocampus and suggest that the place cells encode some other aspect, such as the spatial context.

Immigration and the ephemerality of a natural population bottleneck: evidence from molecular markers

Population bottlenecks are often invoked to explain low levels of genetic variation in natural populations, yet few studies have documented the direct genetic consequences of known bottlenecks in the wild. Empirical studies of natural population bottlenecks are therefore needed, because key assumptions of theoretical and laboratory studies of bottlenecks may not hold in the wild. Here we present microsatellite data from a severe bottleneck (95% mortality) in an insular population of song sparrows (Melospiza melodia). The major findings of our study are as follows: (i) The bottleneck reduced heterozygosity and allelic diversity nearly to neutral expectations, despite non-random survival of birds with respect to inbreeding and wing length. (ii) All measures of genetic diversity regained pre-bottleneck levels within two to three years of the crash. This rapid recovery was due to low levels of immigration. (iii) The rapid recovery occurred despite a coincident, strong increase in average inbreeding. These results show that immigration at levels that are hard to measure in most field studies can lead to qualitatively very different genetic outcomes from those expected from mutations only. We suggest that future theoretical and empirical work on bottlenecks and metapopulations should address the impact of immigration.