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7,883 results for “Tropic”
Data from: Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers
Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, FST = 0.34). Most loci showed only population-specific deviations from Hardy–Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability.
Data from: Life on the edge: a comparative study of eco-physiological adaptations of frogs to tropical semiarid environments
A key goal of ecology and evolution is to understand the relative contributions of environment and history in determining the geographic distribution of organisms. For the Neotropical lowlands, where temperatures are similar across landscapes, we hypothesize that water balance may be a critical but understudied factor in determining the distribution of species. Amphibians are especially sensitive to variation in precipitation due to their permeable skin. Here we focused on lowland frogs of north-western South America and investigated variation among 17 species in potentially important ecologically relevant performance variables related to water balance, and tested for possible adaptations to semiarid conditions within species. We studied frogs from coastal xeric, savannah and wet forest biomes under common laboratory conditions and quantified rates of evaporative water loss, rates of water uptake, and variation in water-searching behavior and performance. We found significant differences in all three performance variables among species, even after accounting for shared evolutionary history. A phylogenetic ANCOVA showed that categorizing species by ecological habits (terrestrial vs. arboreal) explained much of the eco-performance trait variation among species. Secondarily, environment explained additional variation, e.g., coastal xeric species showed reduced rates of water loss and terrestrial savannah amphibians showed lower rates of water uptake. Conspecific frog populations from different biomes exhibited similar performance. We compare our results with previous studies and conclude that ecological habit is the principle factor that predicts eco-physiological trait variation and the possible geographic distribution of lowland Neotropical frogs.
Data from: Nurse-based restoration of degraded tropical forests with tussock grasses: experimental support from the Andean cloud forest
1. The degradation of the Andean cloud forest raises strong biological conservation issues and threatens the sustainability of a crucial water resource. The idea that nurse-based restoration can accelerate the recovery of these forests is underexplored, despite its promise as a restoration technique. Recent conceptual models predict that facilitation among plants may be an important mechanism, but there is a lack of strong empirical support. We gathered experimental data to test this prediction and explore the relevance of using nurse-based forest restoration in these environments. 2. A 20-month factorial experimental design in the Andean tropical cloud forest was established. We measured the survival and estimated the biomass production of transplanted seedlings of a keystone canopy forest species, Ceroxylon echinulatum (Arecaceae), in a deforested area in the presence/absence of herbivory, a potential nurse plant (the tussock grass Setaria sphacelata, Poaceae), and artificial shade. 3. The joint effects of deforestation and herbivory led to the death of all seedlings, whereas most seedlings survived in the adjacent forest, which was used as the control. The presence of nurse plants led to significantly higher survival and growth of Ceroxylon seedlings throughout the experiment, regardless of herbivore presence. 4. The nurse effects were explained by a reduction of the relative abiotic stress experienced by the seedlings outside the forest, i.e. the consistently decreasing maximum vapour pressure deficit. Furthermore, nurse tussocks delayed and reduced the effects of herbivory by offering physical protection and a refuge for seedlings against detection by herbivores. However, the effects of herbivory and abiotic stress on facilitation were not additive. 5. Synthesis and applications: Facilitation in degraded cloud forest can be intense as soon as the beneficiary plants are driven away from their physiological optimum (relative abiotic stress) and/or are confronted by herbivory. Using pre-established exotic tussock grasses as a nurse-based restoration technique in degraded cloud forest is a low-cost, non-detrimental (to biodiversity) option, especially in the absence of nurse trees and shrubs. The success of this method requires transplanting seedlings at the base of tussocks.
Highlighting convergent evolution in morphological traits in response to climatic gradient in African tropical tree species: the case of genus Guibourtia Benn
<ol> <li><span>Adaptive evolution is a major driver of organism diversification but the links between phenotypic traits and environmental niche remains little documented in tropical trees. Moreover, trait-niche relationships are complex because a correlation between the traits and environmental niches displayed by a sample of species may result from (1) convergent evolution if different environmental conditions have selected different sets of traits, and/or (2) phylogenetic inertia if niche and morphological differences between species are simply function of their phylogenetic divergence, in which case the trait-niche correlation does not imply any direct causal link. Here, we aim to assess the respective roles of phylogenetic inertia and convergent evolution in shaping the differences of botanical traits and environmental niches among congeneric African tree species that evolved in different biomes. </span></li> <li><span>This issue was addressed with the tree genus <i>Guibourtia </i>Benn. (Leguminosae, Detarioideae) which contains 13 African species occupying various forest habitat types, from rain forest to dry woodlands, with different climate and soil conditions. To this end, we combined morphological data with ecological niche modelling and used a highly resolved plastid phylogeny of the 13 African <i>Guibourtia</i> species. </span></li> <li><span>First, we demonstrated phylogenetic signals in both morphological traits (Mantel test between phylogenetic and morphological distances between species: r=0.24, p=0.031) and environmental niches (Mantel test between phylogenetic and niche distances between species: r=0.23, p=0.025). Second, we found a significant correlation between morphology and niche, at least between some of their respective dimensions (Mantel's r=0.32, p=0.013), even after accounting for phylogenetic inertia (Phylogenetic Independent Contrast: r=0.69, p=0.018). This correlation occurred between some leaflet and flower traits and solar radiation, relative humidity, precipitations and temperature range. </span></li> <li><span>Our results demonstrate the convergent evolution of some morphological traits in response to climatic factors in congeneric tree species and highlight the action of selective forces, along with neutral ones, in shaping the divergence between congeneric tropical plants.</span></li> </ol>
Ancient tropical extinctions at high latitudes contributed to the latitudinal diversity gradient
<p class="Style1PCI"><span><span><span><span>Global biodiversity currently peaks at the equator and decreases toward the poles. Growing fossil evidence suggest this hump-shaped latitudinal diversity gradient (LDG) has not been persistent through time, with similar diversity across latitudes flattening out the LDG during past greenhouse periods. However, when and how diversity declined at high latitudes to generate the modern LDG remains an open question. Although diversity-loss scenarios have been proposed, they remain mostly undemonstrated. We outline the 'asymmetric gradient of extinction and dispersal' framework that contextualizes previous ideas behind the LDG under a time-variable scenario. Using phylogenies and fossils of Testudines, Crocodilia and Lepidosauria, we find that the hump-shaped LDG could be explained by (1) disproportionate extinctions of high-latitude tropical-adapted clades when climate transitioned from greenhouse to icehouse, and (2) equator-ward biotic dispersals tracking their climatic preferences when tropical biomes became restricted to the equator. Conversely, equivalent diversification rates across latitudes can account for the formation of an ancient flat LDG. The inclusion of fossils in macroevolutionary studies allows revealing time-dependent extinction rates hardly detectable from phylogenies only. This study underscores that the prevailing evolutionary processes generating the LDG during greenhouses differed from those operating during icehouses.</span></span></span></span></p>
Data from: What can multiple phylogenies say about the latitudinal diversity gradient? A new look at the tropical conservatism, out-of-the-tropics, and diversification rate hypotheses
We reviewed published phylogenies and selected 111 phylogenetic studies representing mammals, birds, insects, and flowering plants. We then mapped the latitudinal range of all taxa to test the relative importance of the tropical conservatism, out of the tropics, and diversification rate hypotheses in generating latitudinal diversity gradients. Most clades originated in the tropics, with diversity peaking in the zone of origin. Transitions of lineages between latitudinal zones occurred at 16–22% of the tree nodes. The most common type of transition was range expansions of tropical lineages to encompass also temperate latitudes. Thus, adaptation to new climatic conditions may not represent a major obstacle for many clades. These results contradict predictions of the tropical conservatism hypothesis (i.e., few clades colonizing extratropical latitudes), but support the out-of-the-tropics model (i.e., tropical originations and subsequent latitudinal range expansions). Our results suggest no difference in diversification between tropical and temperate sister lineages; thus, diversity of tropical clades was not explained by higher diversification rates in this zone. Moreover, lineages with latitudinal stasis diversified more compared to sister lineages entering a new latitudinal zone. This preserved preexisting diversity differences between latitudinal zones and can be considered a new mechanism for why diversity tends to peak in the zone of origin.
Data from: Abiotic constraints on the activity of tropical lizards
Many tropical ectotherms are considered vulnerable to anthropogenic climate change because they have evolved to become thermal specialists. Indeed, several recent studies have suggested that even small increases in mean operative temperature may lead to a reduction in activity and the subsequent extinction of populations. Within the tropics, lizards are considered particularly vulnerable due to the potential for climate change to directly impact physiology and alter community interactions. However, models usually focus on the effects of mean operative temperature at the expense of other climate variables that may also affect lizard physiology. We used daily variation in operative temperature, humidity, and wind speed to examine how changes in climate influence activity in two species of lizards from the island of Cayo Menor, Honduras. Anolis lemurinus is a forest species, whereas A. allisoni is an open-habitat species. We conducted daily surveys for active lizards in habitat typical to each species, while simultaneously measuring operative thermal environments with physical models. The effects of the thermal environment were considered in the context of the thermal sensitivity of sprint speed for each species, and compared with the effects of the hydric (humidity) and convective (wind) environments. When all surveys were combined into a single analysis, the activity of the forest species Anolis lemurinus was positively correlated with wind speed, the spatial heterogeneity of operative temperature, and the mismatch between mean operative temperature and the optimal temperature for sprint performance. Mean operative temperature did significantly effect Anolis lemurinus activity, but only when it was above their thermal optimum. Activity of the open-habitat species A. allisoni was negatively correlated with wind speed, but was not related to any other climate variable. Whereas the mismatch between mean operative temperature and the thermal optimum for performance predicted the activity level of the forest species in ways partially consistent with its use in models for the response of lizards to climate change, the effects of the abiotic environment were habitat-dependent. Our results suggest that successfully predicting the biological impacts of climate change will require holistic models that account for more than changes in mean temperature alone.
Data from: Taxonomic and functional ant diversity along a secondary successional gradient in a tropical forest
The taxonomic diversity (TD) of tropical flora and fauna tends to increase during secondary succession. This increase may be accompanied by changes in functional diversity (FD), although the relationship between TD and FD is not well understood. To explore this relationship, we examined the correlations between the TD and FD of ants and forest age in secondary forests at the α- and β-diversity levels using single- and multi-trait-based approaches. Our objectives were to understand ant diversity patterns and to evaluate the role of secondary forests in the conservation of biodiversity and in the resilience of tropical forests. Ant assemblages were sampled across a chronosequence in the Lacandon region, Mexico. All species were characterized according to 12 functional ecomorphological traits relevant to their feeding behavior. We found that TD and FD were related to forest age at the alpha level, but not at the beta level. α-functional richness and divergence increased linearly with species richness and diversity, respectively. Also, the relationship between taxonomic and functional turnover was linear and positive. Our results indicated that functional traits were complementary across the chronosequence. The increase in FD was mainly driven by the addition of rare species with relevant traits. The older secondary forests did not recover all of the functions of old growth forest but did show a tendency to recovery. Because older successional stages support more TD and FD, we suggest developing agriculture and forestry management practices that facilitate rapid post-agricultural succession and thereby better preserve the functionality of tropical forests.
Extinction-immigration dynamics lag behind environmental filtering in shaping the composition of tropical dry forests within a changing landscape
The impact of rapid habitat loss and fragmentation on biodiversity is a major issue. However, we still lack an integrative understanding of how these changes influence biodiversity dynamics over time. In this study, we investigate the effects of these changes in terms of both niche-based and neutral dynamics. We hypothesize that habitat loss has delayed effects on neutral immigration-extinction dynamics, while edge effects and environmental heterogeneity in habitat patches have rapid effects on niche-based dynamics. We analyzed taxonomic and functional composition of 100 tree communities in a tropical dry forest landscape of New-Caledonia subject to habitat loss and fragmentation. We designed an original, process-based simulation framework, and performed Approximate Bayesian Computation to infer the influence of niche-based and neutral processes. Then, we performed partial regressions to evaluate the relationships between inferred parameter values of communities and landscape metrics (distance to edge, patch area, and habitat amount around communities), derived from either recent or past (65 yrs ago) aerial photographs, while controlling for the effect of soil and topography. We found that landscape structure influences both environmental filtering and immigration. Immigration rate was positively related to past habitat amount surrounding communities. In contrast, environmental filtering was mostly affected by present landscape structure and mainly influenced by edge vicinity and topography. Our results highlight that landscape changes have contrasting spatio-temporal influences on niche-based and neutral assembly dynamics. First, landscape-level habitat loss and community isolation reduce immigration and increase demographic stochasticity, resulting in slow decline of local species diversity and extinction debt. Second, recent edge creation affects environmental filtering, incurring rapid changes in community composition by favoring species with edge-adapted strategies. Our study brings new insights about temporal impacts of landscape changes on biodiversity dynamics. We stress that landscape history critically influences these dynamics and should be taken into account in conservation policies.
Data from: Frost maintains forests and grasslands as alternate states in a montane tropical forest-grassland mosaic; but alien tree invasion and warming can disrupt this balance
1. Forest-grassland mosaics, with abrupt boundaries between the two vegetation types, occur across the globe. Fire and herbivory are widely considered primary drivers that maintain these mosaics by limiting tree establishment in grasslands, while edaphic factors and frosts are generally considered to be secondary factors that reinforce these effects. However, the relative importance of these drivers likely varies across systems. In particular, although frost is known to occur in many montane tropical mosaics, experimental evidence for its role as a driving factor is limited. 2. We used replicated in-situ transplant and warming experiments to examine the role of microclimate (frost and freezing temperatures) and soil in influencing germination and seedling survival of both native forest trees and alien invasive Acacia trees in grasslands of a tropical montane forest-grassland mosaic in the Western Ghats of southern India. 3. Seed germination of both native and alien tree species was higher in grasslands regard-less of soil type, indicating that germination was not the limiting stage to tree establishment. However, irrespective of soil type, native seedlings in grasslands incurred high mortality fol-lowing winter frosts and freezing temperatures relative to native seedlings in adjoining forests where freezing temperatures did not occur. Seedling survival through the tropical winter was thus a primary limitation to native tree establishment in grasslands. In contrast, alien Acacia seedlings in grasslands incurred much lower levels of winter mortality. Experimental night-time warming in grasslands significantly enhanced over-winter survival of all tree seedlings, but increases in recruitment were much greater for alien Acacia than for native tree seedlings. 4. Synthesis: Our results provide evidence for a primary role for frost and freezing temperatures in limiting tree establishment in grasslands of this tropical forest-grassland mosaic. Future increases in temperature are likely to release trees from this limitation and favour tree expansion into grasslands, with rates of expansion of non-native Acacia likely to be much greater than that of native trees. We suggest that studies of frost limitation to plant establishment are needed across a range of tropical ecosystems to re-evaluate the general importance of frost as a driver of vegetation transitions in the tropics.
Agouti reintroduction recovers seed dispersal of a large-seeded tropical tree
<p>The aim of animal reintroductions has mainly been species recovery; only few reintroduction initiatives focus on ecosystem restoration. Therefore, reintroduction consequences on ecological interactions are seldom assessed. We used the interaction between a reintroduced population of agoutis (<i>Dasyprocta leporina</i>) and a vulnerable tropical endemic tree (<i>Joannesia princeps</i>) to examine reintroduction effects on seed dispersal and seedling establishment. To test the outcomes of this interaction we tracked seeds of <i>J. princeps</i> in two adjacent forest areas with and without reintroduced agoutis. We also assessed if dispersal distances affected seedling survival. To determine seed fate and dispersal distance we used spool-and-line tracking, together with camera traps to identify dispersers. Agoutis were the only species removing <i>J. princeps</i> seeds, thus dispersal only occurred where agoutis had been reintroduced; in the area without agoutis, all seeds remained intact on the soil, even one year after the experiment's beginning. At the reintroduction area, most seeds were preyed upon by agoutis but 7% remained dispersed and 2% germinated after ten months. Only seeds buried by agoutis were able to germinate. Most dispersed seeds were disperse 15 m or farther and longer dispersal distances benefited <i>J. princeps</i>, since seedlings farther from a conspecific adult tree had greater survival probability. Agoutis were also seen burying seeds of two other plant species; these mammals have the potential to benefit dozens of large-seeded species in our study system<span>. </span>Agouti reintroduction thus exemplifies the value of trophic rewilding programs to re-establish ecological interactions and restore ecosystem functioning.</p>
Data from: Nurse species and indirect facilitation through grazing drive plant community functional traits in tropical alpine peatlands
Facilitation among plants mediated by grazers occurs when an unpalatable plant extends its protection against grazing to another plant. This type of indirect facilitation impacts species coexistence and ecosystem functioning in a large array of ecosystems worldwide. It has nonetheless generally been understudied so far in comparison with the role played by direct facilitation among plants. We aimed at providing original data on indirect facilitation at the community scale to determine the extent to which indirect facilitation mediated by grazers can shape plant communities. Such experimental data are expected to contribute to refining the conceptual framework on plant–plant–herbivore interactions in stressful environments. We set up a 2-year grazing exclusion experiment in tropical alpine peatlands in Bolivia. Those ecosystems depend entirely on a few, structuring cushion-forming plants (hereafter referred to as "nurse" species), in which associated plant communities develop. Fences have been set over two nurse species with different strategies to cope with grazing (direct vs. indirect defenses), which are expected to lead to different intensities of indirect facilitation for the associated communities. We collected functional traits which are known to vary according to grazing pressure (LDMC, leaf thickness, and maximum height), on both the nurse and their associated plant communities in grazed (and therefore indirect facilitation as well) and ungrazed conditions. We found that the effect of indirectly facilitated on the associated plant communities depended on the functional trait considered. Indirect facilitation decreased the effects of grazing on species relative abundance, mean LDMC, and the convergence of the maximum height distribution of the associated communities, but did not affect mean height or cover. The identity of the nurse species and grazing jointly affected the structure of the associated plant community through indirect facilitation. Our results together with the existing literature suggest that the "grazer–nurse–beneficiary" interaction module can be more complex than expected when evaluated in the field.
Data from: Distance-decay differs among vertical strata in a tropical rainforest
1. Assemblage similarity decays with geographic distance—a pattern known as the distance-decay relationship. While this pattern has been investigated for a wide range of organisms, ecosystems, and geographical gradients, whether these changes vary more cryptically across different forest strata (from ground to canopy) remains elusive. 2. Here, we investigated the influence of ground vs arboreal assemblages to the general distance-decay relationship observed in forests. We seek to explain differences in distance-decay relationships between strata in the context of the vertical stratification of assemblage composition, richness, and abundance. 3. We surveyed for a climate sensitive model organism, amphibians, across vertical rainforest strata in Madagascar. For each tree, we defined assemblages of ground-dwelling, understory, or canopy species. We calculated horizontal distance-decay in similarity across all trees, and across assemblages of species found in different forest strata (ground, understory, and canopy). 4. We demonstrate that within stratum comparisons exhibit a classic distance-decay relationship for canopy and understory communities but no distance-decay relationships for ground communities. We suggest that differences in horizontal turnover between strata may be due to local scale habitat and resource heterogeneity in the canopy, or the influence of arboreal traits on species dispersal and distribution. 5. Synthesis: Biodiversity patterns in horizontal space were not consistent across vertical space, suggesting that canopy fauna may not play by the same set of 'rules' as their conspecifics living below them on the ground. Our study provides compelling evidence that the above-ground amphibian assemblage of tropical rainforests is the primary driver of the classical distance-decay relationship.
Data from: Small but not isolated: a population genetic survey of the tropical tree Cariniana estrellensis (Lecythidaceae) in a highly fragmented habitat
Here, we explore the mating pattern and genetic structure of a tropical tree species, Cariniana estrellensis, in a small population in which progeny arrays (n=399), all adults (n=28) and all seedlings (n=39) were genotyped at nine highly informative microsatellite loci. From progeny arrays we were able to identify the source tree for at least 78% of pollination events. The gene immigration rates, mainly attributable to pollen, were high, varying from 23.5 to 53%. Although gene dispersal over long distance was observed, the effective gene dispersal distances within the small population were relatively short, with mean pollination distances varying from 69.9 to 146.9 m, and seed dispersal distances occurring up to a mean of 119.6 m. Mating system analyses showed that C. estrellensis is an allogamous species (tm=0.999), with both biparental inbreeding (tm−ts=−0.016) and selfing rates (s=0.001) that are not significantly different from zero. Even though the population is small, the presence of private alleles in both seedlings and progeny arrays and the elevated rates of gene immigration indicate that the C. estrellensis population is not genetically isolated. However, genetic diversity expressed by allelic richness was significantly lower in postfragmentation life stages. Although there was a loss of genetic diversity, indicating susceptibility of C. estrellensis to habitat fragmentation, no evidence of inbreeding or spatial genetic structure was observed across generations. Overall, C. estrellensis showed some resilience to negative genetic effects of habitat fragmentation, but conservation strategies are needed to preserve the remaining genetic diversity of this population.
Data from: Reproductive behaviour indicates specificity in resource use: phylogenetic examples from temperate and tropical insects
Specificity (= the degree of ecological specialisation) is one of the fundamental concepts of the science of ecology. Ambiguities on how to define and measure specificity have however complicated respective research efforts. Here we propose that, in insects, a behavioural trait –adult oviposition latency in captivity without a favourable host plant – correlates with a species' specificity in larval host use. In the absence of a suitable host, monophagous insects are expected to wait for a long time before commencing oviposition, with the long waiting time corresponding to careful host location behaviour in nature. Polyphagous insects, in contrast, should be selected for an increased oviposition rate at the expense of the quality of oviposition substrate encountered and will on average have a short latency time. Using experimentally derived data on oviposition latency, we performed a phylogenetically informed analysis based on Bayesian inference to show that this variable correlates with host specificity (larval diet breadth) in a sample of North-European species of geometrid moths. A closely related index – the probability to lay any eggs on an unfavourable substrate – shows an analogous pattern. To provide an example of how these indices can be applied, we compare our sample of geometrid moths from Northern Europe with a sample from equatorial Africa. A comparative analysis based on an original phylogenetic reconstruction found no differences between the two study sites in parameters of oviposition behaviour. We conclude that behavioural tests can provide information about ecological interactions when the latter cannot be directly recorded. Our example study also hints at the possibility that host specificity of herbivores is not necessarily higher in a tropical region compared to a temperate one.
Elevational contrast in predation and parasitism risk to caterpillars in a tropical rainforest
<p>Invertebrate predators and parasitoids are among the most important natural enemies of insect herbivores. Yet, the strength of natural enemy pressure along an altitudinal gradient and interactions between groups of natural enemies (such as predation on parasitized prey) are not well known. Various methods are used to reveal mortality factors of herbivores. Predation pressure is usually assessed through exposure of artificial prey. However, this method cannot provide information about the attacks of parasitoids, or their eventual interactions with predators. Further, artificial or dead prey might not attract predators because they do not show expected host behavior, and this method mostly cannot distinguish between predation and scavenging. For the first time in a tropical rainforest, we quantified mortality factors along an altitudinal gradient using exposure of live caterpillars. We exposed a total of 800 live caterpillars of <i>Talanga excelsalis moresbyensis</i> Strand (Lepidoptera: Crambidae) on saplings of <i>Ficus copiosa</i> Steud. (Moraceae) at two elevations in primary tropical rain forest in Papua New Guinea (200 and 1 200 m a.s.l.). We exposed the caterpillars in two treatments: exposed to and protected from invertebrate predators and parasitoids. Disappearance of caterpillars was significantly higher in the exposed treatment. Further, caterpillar disappearance was significantly higher in lowlands than in highlands (43 vs. 12%). We consider the vast majority of the disappearance to be due to predation, as migration of the caterpillars from the focal trees was not observed (except one caterpillar). This estimate of invertebrate predation rate corresponds with studies which used artificial caterpillar models. No significant difference in parasitism rate between the two elevations was observed (12 vs. 13%). The combination of the disappearance and parasitism rate patterns means that larval parasitoids face stronger pressure from invertebrate predators through higher predation of their hosts in the lowlands than in the highlands.</p>
Data from: Molecular profiling of diatom assemblages in tropical lake sediments using taxon-specific PCR and Denaturing High-Performance Liquid Chromatography (PCR-DHPLC)
Here we present a protocol to genetically detect diatoms in sediments of the Kenyan tropical Lake Naivasha, based on taxon-specific PCR amplification of short fragments (approx. 100 bp) of the small subunit ribosomal (SSU) gene and subsequent separation of species-specific PCR products by PCR-based DHPLC. An evaluation of amplicons differing in primer specificity to diatoms and length of the fragments amplified demonstrated that the number of different diatom sequence types detected after cloning of the PCR products critically depended on the specificity of the primers to diatoms and the length of the amplified fragments whereby shorter fragments yielded more species of diatoms. The DHPLC was able to discriminate between very short amplicons based on the sequence difference, even if the fragments were of identical length. and if the amplicons differed only in a small number of nucleotides. Generally the method identified the dominant sequence types from mixed amplifications. A comparison with microscopic analysis of the sediment samples revealed that the sequence types identified in the molecular assessment corresponded well with the most dominant species. In summary, the PCR-based DHPLC protocol offers a fast, reliable, and cost-efficient possibility to study DNA from sediments and other environmental samples with unknown organismic content, even for very short DNA fragments.
Data from: Diversity in tropical ecosystems: the species richness and turnover of moths in Malaysian rainforests
As a contribution to accurate estimation of arthropod alpha and beta diversities in tropical forests, we present results of some of the largest moth samples ever collected in the Malaysian region. To estimate alpha diversity, light traps were run at three geographically distinct locations. We generated individual-based and coverage-based rarefaction curves to estimate sampling sufficiency and alpha diversity of the locations. Despite a large number of moths collected (67 282 individuals, from three locations), none of the rarefaction curves reached asymptote. The species accumulation curves based on the Chao1 richness estimator at each location suggested that, even when sampling yielded over 30 000 individuals, Chao1 could not reliably estimate the observed number of species. In one of the three locations, moths were collected systematically by light traps in 1979–1980 and 2000–2001. Despite over 160 trapping nights and 16 500 individuals collected in total, the estimated total number of species (2262) was well below the general collection conducted at the same location over a 35-year period [3921 species (1975–2013)]. Beta diversity was investigated using the samples collected at one location on two occasions over a 20-year period. The faunal composition has changed over the 20-year period, possibly as a result of extensive land-use change around the study location. We estimated the minimum sampling effort required to detect such changes by calculating type II errors. Unlike alpha diversity estimation, we found that only four replicate samples, each with only two trapping nights, would be sufficient to reliably detect changes in assemblage composition.
Data from: Loss of animal seed dispersal increases extinction risk in a tropical tree species due to pervasive negative density dependence across life stages
Overhunting in tropical forests reduces populations of vertebrate seed dispersers. If reduced seed dispersal has a negative impact on tree population viability, overhunting could lead to altered forest structure and dynamics, including decreased biodiversity. However, empirical data showing decreased animal-dispersed tree abundance in overhunted forests contradict demographic models which predict minimal sensitivity of tree population growth rate to early life stages. One resolution to this discrepancy is that seed dispersal determines spatial aggregation, which could have demographic consequences for all life stages. We tested the impact of dispersal loss on population viability of a tropical tree species, Miliusa horsfieldii, currently dispersed by an intact community of large mammals in a Thai forest. We evaluated the effect of spatial aggregation for all tree life stages, from seeds to adult trees, and constructed simulation models to compare population viability with and without animal-mediated seed dispersal. In simulated populations, disperser loss increased spatial aggregation by fourfold, leading to increased negative density dependence across the life cycle and a 10-fold increase in the probability of extinction. Given that the majority of tree species in tropical forests are animal-dispersed, overhunting will potentially result in forests that are fundamentally different from those existing now.
Data from: Ecological and phylogenetic predictors of mobbing behavior in a tropical dry forest
Mobbing represents a well-known anti-predatory behavior, where potential prey display aggressively against a predator. Despite considerable experimental and descriptive work, no models predict species participation in mobbing assemblages. Here, we aimed to understand why some bird species engage in this behavior, while others do not, and what factors can be used to predict mobbing engagement within an avian community. We investigated whether certain functional traits, such as body size, foraging guild, foraging mode, and strata, as well species abundance and evolutionary relatedness, are important mobbing predictors. To address these goals, we simulated the presence of the Ferruginous Pygmy-Owl (Glaucidium brasilianum) by broadcasting its voice in 230 experiments conducted in 115 points, systematically distributed in a dry forest of northeastern Brazil. We compared these results to 162 avian surveys (point counts) conducted in the same area. Our avian surveys detected 108 bird species (local avian community), whereas our playback experiments attracted 72 species (mobbing assemblage). In general, small, canopy insectivorous or frugivorous birds dominated the mobs. The best mobbing predictors were body mass and guild, whereas species abundance, foraging mode, and strata were not retained in the best models. We found a strong phylogenetic component in body mass and mobbing propensity (almost 90% of the species and individuals participating in the mobs were passerines). At the community level, we found significant differences in the functional and phylogenetic structure of the mobbing assemblage in relation to the avian community. Our results suggest that mobbing behavior is tightly associated to predation risk and the capacity of individual species to find and detect predators, and that functional and phylogenetic features can predict species participation in this complex animal behavior.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.