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Data from: Environmental constraints on the compositional and phylogenetic beta-diversity of tropical forest snake assemblages
The ongoing biodiversity crisis increases the importance and urgency of studies addressing the role of environmental variation on the composition and evolutionary history of species assemblages, but especially the tropics and ectotherms remain understudied. In regions with rainy summers, coexistence of ectothermic species may be determined by the partitioning of the climatic niche, since ectotherms can rely on water availability and thermoregulatory behaviour to buffer constraints along their climatic niche. Conversely, ectotherms facing dry summers would have fewer opportunities to climatic niche partitioning and other processes rather than environmental filtering would mediate species coexistence. We used 218 snake assemblages to quantify the compositional (CBD) and phylogenetic (PBD) beta-diversity of snakes in the Atlantic Forest (AF) hotspot. We identify two AF regions with distinct climatological regimes: dry summers in the northern-AF and rainy summers in the southern-AF. While accounting for the influence of multiscale spatial processes, we disentangle the relative contribution of thermal, water-related, and topographic conditions in structuring the CBD and PBD of snake assemblages, and determine the extent in which snake assemblages under distinct climatological regimes are affected by environmental filtering. Thermal conditions best explain CBD and PBD of snakes for the whole AF, whereas water-related factors best explain the structure of snake assemblages within a same climatological regime. CBD and PBD patterns are similarly explained by spatial factors but snake assemblages facing dry summers are more affected by spatial processes operating at fine to intermediate spatial scale whereas those assemblages in regions with rainy summers have a stronger signature of coarser-scale processes. As expected, environmental filtering plays a stronger role in southern-AF than northern-AF, and the synergism between thermal and water-related conditions is the key cause behind this difference. Differences in climatological regimes within the tropics may affect processes mediating species coexistence. The role of broad-scale gradients (e.g. temperature, precipitation) in structuring tropical ectothermic assemblages is greater in regions with rainy summers where climatic niche partitioning is more likely. Our findings highlight the potential stronger role of biotic interactions and neutral processes in structuring ectothermic assemblages facing changes towards warmer and dryer climates.
Data from: Long-term recovery of the functional community assembly and carbon pools in an African tropical forest succession
On the African continent, the population is expected to expand fourfold in the next century, which will increasingly impact the global carbon cycle and biodiversity conservation. Therefore, it is of vital importance to understand how carbon stocks and community assembly recover after slash-and-burn events in tropical second-growth forests. We inventoried a chronosequence of 15 1-hectare plots in lowland tropical forest of the central Congo Basin and evaluated changes in aboveground and soil organic carbon stocks and in tree species diversity, functional composition and community-weighted functional traits with succession. We aimed to track long-term recovery trajectories of species and carbon stocks in secondary forests, comparing 5 to 200+ year old secondary forest with reference primary forest. Along the successional gradient, the functional composition followed a trajectory from resource acquisition to resource conservation, except for nitrogen-related leaf traits. Despite a fast initial recovery of species diversity and functional composition, there were still important structural and carbon stock differences between old-growth secondary and pristine forest, which suggests that a full recovery of secondary forests might take much longer than currently shown. As such, the aboveground carbon stocks of 200+ year old forest were only 57% of those in the pristine reference forest, which suggests a slow recovery of aboveground carbon stocks, although more research is needed to confirm this observation. The results of this study highlight the need for more in-depth studies on forest recovery in Central Africa, to gain insight into the processes that control biodiversity and carbon stock recovery.
Data from: Pleistocene climatic changes drive diversification across a tropical savanna
Spatial responses of species to past climate change depend on both intrinsic traits (climatic niche breadth, dispersal rates) and the scale of climatic fluctuations across the landscape. New capabilities in generating and analysing population genomic data, along with spatial modelling, have unleashed our capacity to infer how past climate changes have shaped populations, and by extension, complex communities. Combining these approaches, we uncover lineage diversity across four co-distributed lizards from the Australian Monsoonal Tropics and explore how varying climatic tolerances interact with regional climate history to generate common versus disparate responses to late Pleistocene change. We find more divergent spatial structuring and temporal demographic responses in the drier Kimberley region compared to the more mesic and consistently suitable Top End. We hypothesize that, in general, the effects of species' traits on sensitivity to climate fluctuation will be more evident in climatically marginal regions. If true, this points to the need in climatically marginal areas to craft more species- (or trait-) specific strategies for persistence under future climate change.
Data from: Impact of a hurricane on the herpetofaunal assemblages of a successional chronosequence in a tropical dry forest
Land‐use change is the main cause of deforestation and degradation of tropical forest in Mexico. Frequently, these lands are abandoned leading to a mosaic of natural vegetation in secondary succession. Further degradation of the natural vegetation in these lands could be exacerbated by stochastic catastrophic events such as hurricanes. Information on the impact of human disturbance parallel to natural disturbance has not yet been evaluated for faunal assemblages in tropical dry forests. To evaluate the response of herpetofaunal assemblages to the interaction of human and natural disturbances, we used information of pre‐ and post‐hurricane herpetofaunal assemblages inhabiting different successional stages (pasture, early forest, young forest, intermediate forest, and old growth forest) of dry forest. Herpetofaunal assemblages were surveyed in all successional stages two years before and two years after the hurricane Jova that hit the Pacific Coast of Mexico on October 2011. We registered 4093 individuals of 61 species. Overall, there were only slight effects of successional stage, hurricane Jova or the interaction between them on abundance, observed species richness and diversity of the herpetofauna. However, we found marked changes in estimated richness and composition of frogs, lizards, and snakes among successional stages in response to hurricane Jova. Modifications in vegetation structure as result of hurricane pass promoted particular changes in each successional stage and taxonomic group (anurans, lizards, and snakes). Secondary forests at different stages of succession may attenuate the negative effects of an intense, short‐duration, and low‐frequency natural disturbance such as hurricane Jova on successional herpetofaunal trajectories and species turnover.
Data from: Understanding the mechanisms of anti-tropical divergence in the seabird White-faced Storm-petrel (Procellariiformes: Pelagodroma marina) using a multi-locus approach
Analytical methods that apply coalescent theory to multilocus data have improved inferences of demographic parameters that are critical to understanding population divergence and speciation. In particular, at the early stages of speciation, it is important to implement models that accommodate conflicting gene trees, and benefit from the presence of shared polymorphisms. Here, we employ eleven nuclear loci and the mitochondrial control region to investigate the phylogeography and historical demography of the pelagic seabird White-faced Storm-petrel (Pelagodroma marina) by sampling subspecies across its antitropical distribution. Groups are all highly differentiated: global mitochondrial ΦST = 0.89 (P < 0.01) and global nuclear ΦST varies between 0.22 and 0.83 (all P < 0.01). The complete lineage sorting of the mitochondrial locus between hemispheres is corroborated by approximately half of the nuclear genealogies, suggesting a long-term antitropical divergence in isolation. Coalescent-based estimates of demographic parameters suggest that hemispheric divergence of P. marina occurred approximately 840 000 ya (95% HPD 582 000–1 170 000), in the absence of gene flow, and divergence within the Southern Hemisphere occurred 190 000 ya (95% HPD 96 000–600 000), both probably associated with the profound palaeo-oceanographic changes of the Pleistocene. A fledgling sampled in St Helena (tropical South Atlantic) suggests recent colonization from the Northern Hemisphere. Despite the great potential for long-distance dispersal, P. marina antitropical groups have been evolving as independent, allopatric lineages, and divergence is probably maintained by philopatry coupled with asynchronous reproductive phenology and local adaptation.
Local adaptation constrains drought tolerance in a tropical foundation tree
<p>1. Plant species with broad climatic ranges might be more vulnerable to climate change than previously appreciated due to intraspecific variation in climatic stress tolerance. In tropical forests, drought is increasingly frequent and severe, causing widespread declines and altering community dynamics. Yet, little is known about whether foundation tropical trees vary in drought tolerance throughout their distributions, and how intraspecific variation in drought tolerance might contribute to their vulnerability to climate change. 2. We tested for local adaptation in seedling emergence and establishment with a full-factorial reciprocal transplant experiment including 27 populations and 109,350 seeds along a 3500 mm precipitation gradient for a widespread tropical foundation tree, Metrosideros polymorpha, in Hawaii. To more precisely relate seedling performance to soil moisture, we conducted a complementary greenhouse experiment to test responses of the same focal populations to simulated drought. 3. In the reciprocal transplant experiment, we observed significant variation among populations and sites in germination and seedling establishment rates. Overall, there was a significant link between historical rainfall of populations and their performance under current rainfall at the study sites consistent with local adaptation. In particular, populations from historically wet sites demonstrated lower germination rates in currently dry sites compared to wet field sites, while populations from historically dry sites germinated well across all sites, with particularly high germination in dry sites. In the greenhouse, seedlings from wet populations survived fewer days without water, and succumbed at wetter soil conditions than populations from historically dry sites, corroborating results from the field experiment. 4. <em>Synthesis. </em>While climate change models project the greatest drying trends for historically dry areas in Hawaii, even moderate drying of wet sites could significantly reduce M. polymorpha recruitment given the sensitivity of seedlings to slight changes in water regimes. Thus, although M. polymorpha demonstrates high seedling drought tolerance in some populations, providing evidence of resilience at the species-scale, there are nonetheless vulnerable populations likely to decline under climate change. Our approach demonstrates that even trees with high dispersal can show significant clines in drought tolerance, and suggests that similar intraspecific variation might be an important consideration for other tropical tree species.</p>
Data from: Nonrandom, diversifying processes are disproportionately strong in the smallest size classes of a tropical forest
A variety of ecological processes influence diversity and species composition in natural communities. Most of these processes, whether abiotic or biotic, differentially filter individuals from birth to death, thereby altering species' relative abundances. Nonrandom outcomes could accrue throughout ontogeny, or the processes that generate them could be particularly influential at certain stages. One long-standing paradigm in tropical forest ecology holds that patterns of relative abundance among mature trees are largely set by processes operating at the earliest life cycle stages. Several studies confirm filtering processes at some stages, but the longevity of large trees makes a rigorous comparison across size classes impossible without long-term demographic data. Here, we use one of the world's longest-running, plot-based forest dynamics projects to compare nonrandom outcomes across stage classes. We considered a cohort of 7,977 individuals in 186 species that were alive in 1971 and monitored in 13 mortality censuses over 42 y to 2013. Nonrandom mortality with respect to species identity occurred more often in the smaller rather than the larger size classes. Furthermore, observed nonrandom mortality in the smaller size classes had a diversifying influence; species richness of the survivors was up to 30% greater than expected in the two smallest size classes, but not greater than expected in the larger size classes. These results highlight the importance of early life cycle stages in tropical forest community dynamics. More generally, they add to an accumulating body of evidence for the importance of early-stage nonrandom outcomes to community structure in marine and terrestrial environments.
Data from: The geographical and institutional distribution of ecological research in the tropics
We reviewed 1333 papers published in Biotropica and the Journal of Tropical Ecology from 1995 to 2004. Only 62 percent of tropical countries were represented in our survey, with 62 percent of the publications based on research conducted in only ten countries. Sixty-two percent of papers had lead authors that were based at institutions outside the country where the research was conducted. Cross-national collaboration was limited, accounting for only 28 percent of papers with multiple authors. To evaluate if our choice of focal journals could have biased our results, we also reviewed 652 papers published in Ecology, Oecologia, Conservation Biology, and Biological Conservation for five randomly selected years from the same time period. While some differences in authorship and the geographic distribution of research existed, the results from these journals generally mirrored patterns observed in the two focal ones—almost 54 percent of publications were based on research conducted in only ten countries, and most studies had lead authors from a developed country. The results of our review suggest that the geographical distribution of research in the tropics is unequal, and that some important regions remain understudied. The results also suggest a need for a greater focus on establishing collaborative relationships with scientists from tropical countries.
Data from: Hot dogs: high ambient temperatures impact reproductive success in a tropical carnivore
Climate change imposes an urgent need to recognise and conserve the species likely to be worst affected. However, while ecologists have mostly explored indirect effects of rising ambient temperatures on temperate and polar species, physiologists have predicted direct impacts on tropical species. The African wild dog (Lycaon pictus), a tropical species, exhibits few of the traits typically used to predict climate change vulnerability. Nevertheless, we predicted that wild dog populations might be sensitive to weather conditions, because the species shows strongly seasonal reproduction across most of its geographical range. We explored associations between weather conditions, reproductive costs, and reproductive success, drawing on long-term wild dog monitoring data from sites in Botswana (20°S, 24 years), Kenya (0°N, 12 years), and Zimbabwe (20°S, 6 years). High ambient temperatures were associated with reduced foraging time, especially during the energetically costly pup-rearing period. Across all three sites, packs which reared pups at high ambient temperatures produced fewer recruits than did those rearing pups in cooler weather; at the non-seasonal Kenya site such packs also had longer inter-birth intervals. Over time, rising ambient temperatures at the (longest-monitored) Botswana site coincided with falling wild dog recruitment. Our findings suggest a direct impact of high ambient temperatures on African wild dog demography, indicating that this species, which is already globally endangered, may be highly vulnerable to climate change. This vulnerability would have been missed by simplistic trait-based assessments, highlighting the limitations of such assessments. Seasonal reproduction, which is less common at low latitudes than at higher latitudes, might be a useful indicator of climate change vulnerability among tropical species.
Data from: Mating system variability in a mouthbrooding cichlid fish from a tropical lake
Intraspecific variability in mating behavior and disparities between social and reproductive behavior add complexity to the description of animal mating systems. A previously published field study on a population of the maternally mouthbrooding cichlid fish Ctenochromis horei in the north of Lake Tanganyika suggested mate monopolization by the most dominant male. In the present study, genetic reconstructions of paternity in a population in the south of the lake provided no evidence for male mate monopolization, as none of the inferred sires had offspring in more than one brood. The ability to reconstruct sire genotypes from offspring alleles was confirmed by computer simulations. Multiple paternity occurred in several broods and was significantly more frequent in the sample taken in the rainy season than in the dry season sample (100% of broods versus 12.5%, respectively; p = 0.0014). The data suggest geographic and temporal variation in the mating behavior of C. horei despite its continuous year-round reproduction, invariable brood care behavior and habitat-specific distribution in the relatively constant and confined environment of a tropical lake. Moreover, our data show that inferences on the distribution of male reproductive success, if based on each geographical or temporal data set alone, would fail to describe the potential for sexual selection in this species.
Data from: Nitrogen saturation in humid tropical forests after 6 years of nitrogen and phosphorus addition: hypothesis testing
Nitrogen (N) saturation hypothesis suggests that when an ecosystem reaches N-saturation, continued N input will cause increased N leaching, nitrous oxide (N2O) emission, and N mineralization and nitrification rates. It also suggests that a different element will become the main limiting factor when N saturation has been reached. Although this hypothesis has been tested in temperate forests, whether they can be directly applied to N-saturated tropical forests remain poorly addressed. To test this hypothesis, soil inorganic N, soil N mineralization and nitrification rate, soil N2O emission rate and nitrate (inline image) leaching rate were measured in an N-saturated old-growth tropical forest in southern China, after 6 years of N and P addition. We hypothesized that N addition would stimulate further N saturation, but P addition might alleviate N saturation. As expected, our results showed that six continuous years of experimental N addition did cause further N saturation, which was indicated by significant increases in soil inorganic N concentration, N2O emission and nitrate (inline image) leaching. However, in contrast to our expectations, N addition significantly decreased in situ rates of net N mineralization and nitrification, which could be related to associated changes in enzyme activity and microbial community composition. On the other hand, P addition mitigated N saturation, as expected. Soil inorganic N concentration, N2O emission and inline image leaching decreased significantly after P addition, but the net rates of N mineralization and nitrification were significantly increased. Our results provide a new understanding of the N saturation hypothesis, suggesting that the effects of long-term N deposition on net N mineralization and nitrification rates in N-saturated tropical forests can be negative and that P addition can alleviate N saturation in such tropical systems.
Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical-temperate congener pair
<p>The biotic interactions hypothesis posits that biotic interactions are more important drivers of adaptation closer to the equator, evidenced by "stronger" contemporary interactions (e.g. greater interaction rates) and/or patterns of trait evolution consistent with a history of stronger interactions. Support for the hypothesis is mixed, but few studies span tropical and temperate regions while experimentally controlling for evolutionary history. Here, we integrate field observations and common garden experiments to quantify the relative importance of pollination and herbivory in a pair of tropical-temperate congeneric perennial herbs. <i>Phytolacca rivinoides</i> and <i>P. americana</i> are pioneer species native to the Neotropics and the eastern USA, respectively. We compared plant-pollinator and plant-herbivore interactions between three tropical populations of <i>P. rivinoides </i>from Costa Rica and three temperate populations of <i>P. americana</i> from its northern range edge in Michigan and Ohio. For some metrics of interaction importance, we also included three subtropical populations of <i>P. americana</i> from its southern range edge in Florida. This approach confounds species and region but allows us, uniquely, to measure complementary proxies of interaction importance across a tropical-temperate range in one system. To test the prediction that lower-latitude plants are more reliant on insect pollinators, we quantified floral display and reward, insect visitation rates, and self-pollination ability (autogamy). To test the prediction that lower-latitude plants experience more herbivore pressure, we quantified herbivory rates, herbivore abundance, and leaf palatability. We found evidence supporting the biotic interactions hypothesis for most comparisons between <i>P. rivinoides</i> and north-temperate <i>P. americana</i> (floral display, insect visitation, autogamy, herbivory, herbivore abundance, and young-leaf palatability). Results for subtropical <i>P. americana</i> populations, however, were typically not intermediate between <i>P. rivinoides</i> and north-temperate <i>P. americana</i>, as would be predicted by a linear latitudinal gradient in interaction importance. Subtropical young-leaf palatability was intermediate, but subtropical mature leaves were the least palatable, and pollination-related traits did not differ between temperate and subtropical regions. These nonlinear patterns of interaction importance suggest future work to relate interaction importance to climatic or biotic thresholds. In sum, we found that the biotic interactions hypothesis was more consistently supported at the larger spatial scale of our study.</p>
Data from: Phylogeny of genus Cupuladria (Bryozoa: Cheilostomata) in the Neogene of tropical America
We used 57 morphometric characters to discriminate 17 extant and fossil Cupuladria species and analyzed their phylogenetic relationships in relation to extant Discoporella species. Data were gathered from 496 extant and fossil Cupuladria specimens ranging in age from early Miocene to Recent and distributed from the Caribbean to tropical eastern Pacific. A first series of discriminant analyses distinguished three morphological groups: Cupuladria with vicarious avicularia, Cupuladria without vicarious avicularia, and Discoporella. Further discriminant analyses identified 17 species of Cupuladria. Cladistic analyses of these three groups yielded four equally parsimonious trees. All of the consensus trees exhibited the same topology, dividing the 25 tropical American cupuladriids into four distinct monophyletic clades, including Discoporella, and are consistent with previous molecular phylogenies except that there are no molecular data for the CV2 clade. Diversification of species was higher in the CV1 and CV2 clades than CNV clade, and involved mostly Caribbean species. Cupuladria with vicarious clade 1 (CV1) includes: C. monotrema, C. pacificiensis, C. exfragminis, C. cheethami, C. biporosa, and four new species: C. pervagata, C. floridensis, C. colonensis and C. dominicana. Cupuladria with vicarious clade 2 (CV2) includes: C. multesima, C. incognita, and three new species C. collyrida, C. veracruxiensis and C. planissima. Cupuladria clade without vicarious (CNV) includes: C. surinamensis, C. panamensis, and one new species C. gigas. The stratigraphic occurrence of species is consistent with cladogram topology within clades. However hypothesized cladistic relations among clades are the reverse of their stratigraphic occurrence with younger clade CNV appearing as the hypothetical ancestor of the two older clades CV1 and CV2. More extensive collections of early to middle Miocene specimens of Cupuladria and Discoporella will be required to resolve this apparent paradox.
Data from: Predation risk perception, food density and conspecific cues shape foraging decisions in a tropical lizard
When foraging, animals can maximize their fitness if they are able to tailor their foraging decisions to current environmental conditions. When making foraging decisions, individuals need to assess the benefits of foraging while accounting for the potential risks of being captured by a predator. However, whether and how different factors interact to shape these decisions is not yet well understood, especially in individual foragers. Here we present a standardized set of manipulative field experiments in the form of foraging assays in the tropical lizard Anolis cristatellus in Puerto Rico. We presented male lizards with foraging opportunities to test how the presence of conspecifics, predation-risk perception, the abundance of food, and interactions among these factors determines the outcome of foraging decisions. In Experiment 1, anoles foraged faster when food was scarce and other conspecifics were present near the feeding tray, while they took longer to feed when food was abundant and when no conspecifics were present. These results suggest that foraging decisions in anoles are the result of a complex process in which individuals assess predation risk by using information from conspecific individuals while taking into account food abundance. In Experiment 2, a simulated increase in predation risk (i.e., distance to the feeding tray) confirmed the relevance of risk perception by showing that the use of available perches is strongly correlated with the latency to feed. We found Puerto Rican crested anoles integrate instantaneous ecological information about food abundance, conspecific activity and predation risk, and adjust their foraging behavior accordingly.
Data from: Diversity and composition of tropical butterflies along an Afromontane agricultural gradient in the Jimma Highlands, Ethiopia
Afromontane landscapes are typically characterized by a mosaic of smallholder farms and the biodiversity impacts of these practices will vary in accordance to local management and landscape context. Here, we assess how tropical butterfly diversity is maintained across an agricultural landscape in the Jimma Highlands of Ethiopia. We used transect surveys to sample understory butterfly communities within degraded natural forest, semi-managed coffee forest (SMCF), exotic timber plantations, open woodland, croplands and pasture. Surveys were conducted in 29 one-hectare plots and repeated five times between January and June 2013. We found that natural forest supports higher butterfly diversity than all agricultural plots (measured with Hill's numbers). SMCF and timber plantations retain relatively high abundance and diversity, but these metrics drop off sharply in open woodland, cropland and pasture. SMCF and timber plantations share the majority of their species with natural forest and support an equivalent abundance of forest-dependent species, with no increase in widespread species. There was some incongruence in the responses of families and sub-families, notably that Lycaenidae are strongly associated with open woodland and pasture. Adult butterflies clearly utilize forested agricultural practices such as SMCF and timber plantations, but species diversity declines steeply with distance from natural forest suggesting that earlier life-stages may depend on host plants and/or microclimatic conditions that are lost under agricultural management. From a management perspective, the protection of natural forest remains a priority for tropical butterfly conservation, but understanding functioning of the wider landscape mosaic is important as SMCF and timber plantations may act as habitat corridors that facilitate movement between forest fragments.
Data from: Tropical ancient DNA from bulk archaeological fish bone reveals the subsistence practices of a historic coastal community in southwest Madagascar
Taxonomic identification of archaeological fish bones provides important insights into the subsistence practices of ancient coastal peoples. However, it can be difficult to execute robust morphological identification of fish bones from species-rich fossil assemblages, especially from post-cranial material with few distinguishing features. Fragmentation, weathering and burning further impede taxonomic identification, resulting in large numbers of unidentifiable bones from archaeological sites. This limitation can be somewhat mitigated by taking an ancient DNA (aDNA) bulk-bone metabarcoding (BBM) approach to faunal identification, where DNA from non-diagnostic bone fragments is extracted and sequenced in parallel. However, a large proportion of fishing communities (both past and present) live in tropical regions that have sub-optimal conditions for long-term aDNA preservation. To date, the BBM method has never been applied to fish bones before, or to fossils excavated from an exposed context within a tropical climate. Here, we demonstrate that morphologically indistinct bulk fish bone from the tropics can be identified by sequencing aDNA extracted from 100 to 300 ya archaeological midden material in southwest Madagascar. Despite the biases of the approach, we rapidly obtained family, genus, and species-level assemblage information, and used this to describe a subset of the ichthyofauna exploited by an 18th century fishing community. We identified 23 families of fish, including benthic, pelagic, and coral-dwelling fishes, suggesting a reliance on a variety of marine and brackish habitats. When possible, BBM should be used alongside osteological approaches to address the limitations of both; however, this study highlights how genetic methods can nevertheless be a valuable tool for helping resolve faunal assemblages when morphological identification is hindered by taphonomic processes, lack of adequate comparative collections, and time constraints, and can provide a temporal perspective on fish biodiversity in the context of accelerated exploitation of the marine environment.
Data from: Immediate impact of a hurricane on the structure of a tropical butterfly community
More intense and frequent hurricanes may lead to long-lasting effects to tropical ecosystems. Here we describe the immediate impact on the butterfly community of a lowland forest in Belize, following Hurricane Earl. Species richness and abundance increased post-hurricane, likely driven by convergence of the organisation between the canopy and understory communities.
Data from: Multilocus phylogeography reveals nested endemism in a gecko across the monsoonal tropics of Australia
Multilocus phylogeography can uncover taxonomically unrecognized lineage diversity across complex biomes. The Australian monsoonal tropics includes vast, ecologically intact savanna-woodland plains interspersed with ancient sandstone uplands. Though recognized in general for its high species richness and endemism, the biodiversity of the region remains underexplored due to its remoteness. This is despite a high rate of ongoing species discovery, especially in wetter regions and for rock-restricted taxa. To provide a baseline for ongoing comparative analyses, we tested for phylogeographic structure in an ecologically generalized and widespread taxon, the gecko Heteronotia binoei. We apply coalescent analyses to multilocus sequence data (mitochondrial DNA and eight nuclear DNA introns) from individuals sampled extensively and at fine scale across the region. The results demonstrate surprisingly deep and geographically nested lineage diversity. Several intraspecific clades previously shown to be endemic to the region were themselves found to contain multiple, short-range lineages. To infer landscapes with concentrations of unique phylogeographic diversity, we probabilistically estimate the ranges of lineages from point data and then, combining these estimates with the nDNA species tree, estimate phyloendemism across the region. Highest levels of phyloendemism occur in northern Top End, especially on islands, across the topographically complex Arnhem escarpment, and across the sandstone ranges of the western Gulf region. These results drive home that deep phylogeographic structure is prevalent in tropical low-dispersal taxa, even ones that are ubiquitous across geography and habitats.
Data from: Comparing forest structure and biodiversity on private and public land: secondary tropical dry forests in Costa Rica
Secondary forests constitute a substantial proportion of tropical forestlands. These forests occur on both public and private lands and different underlying environmental variables and management regimes may affect post‐abandonment successional processes and resultant forest structure and biodiversity. We examined whether differences in ownership led to differences in forest structure, tree diversity, and tree species composition across a gradient of soil fertility and forest age. We collected soil samples and surveyed all trees in 82 public and 66 private 0.1‐ha forest plots arrayed across forest age and soil gradients in Guanacaste, Costa Rica. We found that soil fertility appeared to drive the spatial structure of public vs. private ownership; public conservation lands appeared to be non‐randomly located on areas of lower soil fertility. On private lands, areas of crops/pasture appeared to be non‐randomly located on higher soil fertility areas while forests occupied areas of lower soil fertility. We found that forest structure and tree species diversity did not differ significantly between public and private ownership. However, public and private forests differed in tree species composition: 11 percent were more prevalent in public forest and 7 percent were more prevalent in private forest. Swietenia macrophylla, Cedrela odorata, and Astronium graveolens were more prevalent in public forests likely because public forests provide stronger protection for these highly prized timber species. Guazuma ulmifolia was the most abundant tree in private forests likely because this species is widely consumed and dispersed by cattle. Furthermore, some compositional differences appear to result from soil fertility differences due to non‐random placement of public and private land holdings with respect to soil fertility. Land ownership creates a distinctive species composition signature that is likely the result of differences in soil fertility and management between the ownership types. Both biophysical and social variables should be considered to advance understanding of tropical secondary forest structure and biodiversity.
Data from: Impacts and recovery from Severe Tropical Cyclone Yasi on the Great Barrier Reef
Full recovery of coral reefs from tropical cyclone (TC) damage can take decades, making cyclones a major driver of habitat condition where they occur regularly. Since 1985, 44 TCs generated gale force winds (≥17 metres/second) within the Great Barrier Reef Marine Park (GBRMP). Of the hurricane strength TCs (≥H1—Saffir Simpson scale; ≥ category 3 Australian scale), TC Yasi (February, 2011) was the largest. In the weeks after TC Yasi crossed the GBRMP, participating researchers, managers and rangers assessed the extent and severity of reef damage via 841 Reef Health and Impact Surveys at 70 reefs. Records were scaled into five damage levels representing increasingly widespread colony-level damage (1, 2, 3) and reef structural damage (4, 5). Average damage severity was significantly affected by direction (north vs south of the cyclone track), reef shelf position (mid-shelf vs outer-shelf) and habitat type. More outer-shelf reefs suffered structural damage than mid-shelf reefs within 150 km of the track. Structural damage spanned a greater latitudinal range for mid-shelf reefs than outer-shelf reefs (400 vs 300 km). Structural damage was patchily distributed at all distances, but more so as distance from the track increased. Damage extended much further from the track than during other recent intense cyclones that had smaller circulation sizes. Just over 15% (3,834 km2) of the total reef area of the GBRMP is estimated to have sustained some level of coral damage, with ~4% (949 km2) sustaining a degree of structural damage. TC Yasi likely caused the greatest loss of coral cover on the GBR in a 24-hour period since 1985. Severely impacted reefs have started to recover; coral cover increased an average of 4% between 2011 and 2013 at re-surveyed reefs. The in situ assessment of impacts described here is the largest in scale ever conducted on the Great Barrier Reef following a reef health disturbance.
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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.