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Data from: Habitat fragmentation differentially shapes neutral and immune gene variation in a tropical bird species

Habitat fragmentation is a major cause of biodiversity loss, responsible for an alteration of intraspecific patterns of neutral genetic diversity and structure. Although neutral genetic variation can be informative for demographic inferences, it may be a poor predictor of adaptive genetic diversity and thus of the consequences of habitat fragmentation on selective evolutionary processes. In this context, we contrasted patterns of genetic diversity and structure of neutral loci (microsatellites) and immune genes (i.e., toll-like receptors) in an understorey bird species, the wedge-billed woodcreeper Glyphorynchus spirurus. The objectives were (1) to investigate forest fragmentation effects on population genetic diversity, (2) to disentangle the relative role of demography (genetic drift and migration) and selection, and (3) to assess whether immunogenetic patterns could be associated with variation of ectoparasite (i.e., ticks) pressures. Our results revealed an erosion of neutral genetic diversity and a substantial genetic differentiation among fragmented populations, resulting from a decrease in landscape connectivity and leading to the divergence of distinct genetic pools at a small spatial scale. Patterns of genetic diversity observed for TLR4 and TLR5 were concordant with neutral genetic patterns, whereas those observed for TLR3 and TLR21 were discordant. This result underlines that the dominant evolutionary force shaping immunogenetic diversity (genetic drift vs. selection) may be different depending on loci considered. Finally, tick prevalence was higher in fragmented environments. We discussed the hypothesis that pathogen selective pressures may contribute to maintain adaptive genetic diversity despite the negative demographic effect of habitat fragmentation on neutral genetic diversity.

Thermal adaptations to extreme freeze-thaw cycles in the high tropical Andes

Temperature plays a key role in the biology of ectotherms, including anurans, which are found at higher elevations in the tropics than anywhere in the temperate zone. High-elevation tropical environments are characterized by extreme daily thermal fluctuation including high daily maxima and nightly freezing. Our study investigated the contrasting operative temperatures of the anurans Telmatobius marmoratus and Pleurodema marmoratum in different environmental contexts at the same elevation and biome above 5200 meters. Telmatobius marmoratus avoids extremes of daily temperature fluctuation by utilizing thermally buffered aquatic habitat at all life stages, with minimal operative temperature variation (range: 4.6–8.0°C). Pleurodema marmoratum, in contrast, experienced operative temperatures from -3.5 to 44°C and has one of the widest thermal breadths reported for any tropical frog, from >32°C (critical thermal maximum) to surviving freezing periods of 1 hr and 6 hr down to -3.0°C. Our findings expand experimental evidence of frost tolerance in amphibians to the widespread Neotropical family Leptodactylidae, the first such evidence of frost tolerance in a tropical amphibian. Our study identifies three strategies (wide thermal tolerance breadth, use of buffered microhabitats, and behavioral thermoregulation), which allow these tropical frogs to withstand the current wide daily thermal fluctuation above 5000 masl and which may help them adapt to future climatic changes.

Data from: Phenolics lie at the center of functional versatility in the responses of two phytochemically diverse tropical trees to canopy thinning

Saplings in the shade of the tropical understorey face the challenge of acquiring sufficient carbon for growth as well as defence against intense pest pressure. A minor increase in light availability via canopy thinning may allow for increased investment in chemical defence against pests, but it may also necessitate additional biochemical investment to prevent light-induced oxidative stress. The shifts in secondary metabolite composition that increased sun exposure may precipitate in such tree species present an ideal milieu for evaluating the potential of a single suite of phenolic secondary metabolites to be used in mitigating both abiotic and biotic stressors. To conduct such an evaluation, we exposed saplings of two unrelated species to a range of light environments and compared changes in their foliar secondary metabolome alongside corresponding changes in the abiotic and biotic activity of their secondary metabolite suites. Among the numerous classes of secondary metabolites found in both species, phenolics accounted for the majority of increases in antioxidant and UV-absorbing properties as well as activity against an invertebrate herbivore and a fungal pathogen. Our results support the hypothesis that phenolics contribute to the capacity of plants to resist co-occurring abiotic and biotic stressors in resource-limited conditions.

The response of carbon assimilation and storage to long-term drought in tropical trees is dependent on light availability

1) Whether tropical trees acclimate to long-term drought stress remains unclear. This uncertainty is amplified if drought stress is accompanied by changes in other drivers such as the increases in canopy light exposure that might be induced by tree mortality or other disturbances. 2) Photosynthetic capacity, leaf respiration, non-structural carbohydrate (NSC) storage and stomatal conductance were measured on 162 trees at the world's longest running (15 yr) tropical forest drought experiment. We test whether surviving trees have altered strategies for carbon storage and carbon use in the drier and elevated light conditions present following drought-related tree mortality. 3) Relative to control trees, the surviving trees experiencing the drought treatment showed functional responses including: i) moderately reduced photosynthetic capacity; ii) increased total leaf NSC; and iii) a switch from starch to soluble sugars as the main store of branch NSC. This contrasts with earlier findings at this experiment of no change in photosynthetic capacity or NSC storage. The changes detected here only occurred in the subset of drought-stressed trees with canopies exposed to high radiation and were absent in trees with less-exposed canopies, and also in the community average. In contrast to previous results acquired through less intensive species sampling from this experiment, we also observe no species-average drought-induced change in leaf respiration. 4) Our results suggest that long-term responses to drought stress are strongly influenced by a tree's full-canopy light environment and therefore that disturbance-induced changes in stand density and dynamics are likely to substantially impact tropical forest responses to climate change. We also demonstrate that, while challenging, intensive sampling is essential in tropical forests to avoid sampling biases caused by limited taxonomic coverage.

opencc-zeroOct 2020View details →

Contrasting effects of host tree isolation on population connectedness in two tropical epiphytic bromeliads

Premise of the study Conversion of primary forests to pastures is a major cause of habitat fragmentation in the tropics. Fragmentation is expected to impede gene flow for many plant species that are restricted to remaining forest fragments. Epiphytes may be especially vulnerable to this effect of forest fragmentation because they depend on host trees. However, trees that remain in pastures may enhance connectivity across the landscape for epiphyte species that can thrive on such trees. To investigate this possibility, we studied the genetic structures of two such species on isolated pasture trees and surrounding forest, in relation to their local abundances in different habitat types and aspects of their reproductive biology including pollen and seed dispersal agents, and looked for evidence of increased or diminished gene flow. Methods We used microsatellite markers to assess geographic patterns of genetic diversity and differentiation in two epiphytic bromeliads, Catopsis nitida and Werauhia tonduziana, in the Monteverde region of Costa Rica. Key results About 85% of the FST value for Catopsis nitida was found among pastures within regions, while for Weruahia tonduziana, about 80% of the FST value was contributed by differences between regions, indicating much more gene flow within regions, relative to C. nitida. Conclusions Although there was substantial genetic differentiation among epiphyte populations, those on isolated pasture trees were not substantially less diverse than those in adjacent forests, suggesting that pasture trees may serve as "stepping stones" that help these species maintain their genetic connectedness and diversity at larger geographic scales.

opencc-zeroDec 2015View details →

Data from: Species-habitat relationships and ecological correlates of butterfly abundance in a transformed tropical landscape

Tropical butterfly conservation strategies often focus on total and/or common species richness to assess the conservation value of a patch or habitat. However, such a strategy overlooks the unique dynamics of rare species. We evaluated the species-habitat relationships of 209 common, intermediate, and rare butterfly species (including morphospecies) across four habitat types (mature, degraded, or fragmented forest, and urban parks) and two patch sizes (<400 ha, ≥400 ha) in Singapore. Common species richness was consistent across habitat types. Intermediate species richness declined by more than 50 percent in urban parks (relative to all forest habitats), and rare species richness was reduced by 50 percent in degraded and fragmented forest and by 90 percent in urban parks (relative to mature forest). Large patches had comparable overall richness to small patches, but they supported more rare species and three times as many habitat-restricted species over a similar area. Importantly, a number of rare species were confined to single small patches. Mixed-effects regression models were constructed to identify habitat and ecological/life history variables associated with butterfly abundance. These models revealed that species with greater habitat specialization, rare larval host plants, few larval host plant genera, and narrow global geographic ranges were more likely to be rare species. Overall, these results demonstrate that the richness of habitat-restricted and rare species do not follow the same spatial distribution patterns as common species. Therefore, while conserving mature forests is key, effective butterfly conservation in a transformed landscape should take into account rare and habitat-restricted species.

opencc-zeroOct 2020View details →

Negative trait-based association between abundance of nitrogen fixing trees and long-term tropical forest biomass accumulation

1. Plant functional traits are thought to drive biomass production and biogeochemical cycling in tropical forests, but it remains unclear how nitrogen (N)-fixing legumes influence the functional traits of neighboring trees and forest-wide biomass dynamics. Further, the degree to which effects of N-fixers are density-dependent and may depend on stem size and spatial scale remain largely unknown. 2. Here, we examine 30-years of stem demography data for ~20,000 trees in a lowland tropical forest in Trinidad that span a wide range of functional traits thought to drive aboveground biomass (AGB) dynamics. 3. These forests show positive but decreasing long-term net AGB accumulation resulting from constant average productivity but increasing mortality of non-fixing trees over time. We find that high abundance of N-fixing trees is associated with compositional shifts in non-fixer functional traits that confer lower competitive performance and biomass accumulation. Across tree size classes, most interactions between N-fixers and non-fixers were negative, density dependent, and strongest at smaller spatial scales. 4. Synthesis. Overall, our findings suggest that local trait-based interactions between N-fixing and non-fixing trees can influence long-term carbon accumulation in tropical forests.

opencc-by-4.0Nov 2020View details →

Nits tropicals a la fase de maduració de la vinya a la D.O. Empordà (Baix Empordà) a llarg del segle XXI als escenaris de canvi climàtic RCP 8.5 i RCP4.5 (format SHP)

Arxius del shapefile (format SHP de Esri) amb la distribució espacial del valor mitjà de les nits tropicals a la fase de maduració de la vinya a la D.O. Empordà (Baix Empordà) als escenaris de canvi climàtic  RCP 8.5 i RCP4.5 projectat per a les dècades dels anys 2030, 2050, 2070 i 2090 i el període Control (1972-2005). A més, un arxiu Word amb les metadades del shapefile.

opencc-zeroOct 2020View details →

Thermal niche traits of high alpine plant species and communities across the tropical Andes and their vulnerability to global warming

<a name="_Hlk10643461">Aim</a> The Climate Variability Hypothesis (CVH) predicts that locations with reduced seasonal temperature variation select for species with narrower thermal ranges. Here we (1) test the CVH by assessing the effect of latitude and elevation on the thermal ranges of Andean vascular plant species and communities, and (2) assess tropical alpine plants vulnerability to warming based on their thermal traits. Location Tropical Andes Taxon Vascular plants Methods Temperature data for 505 vascular plant species from alpine communities on 49 summits, were extracted from 29,627 geo-referenced occurrences. Species thermal niche traits (TNTs) were estimated using bootstrapping for: minimum temperature, optimum (mean) temperature, and breadth (maximum-minimum). Plant community-weighted scores were estimated using the TNTs of their constituent species. CVH was tested for species, biogeographic species groups and communities. Vulnerability to global warming was assessed for species, biogeographic species groups and communities. Results Species restricted to the equator showed narrower thermal niche breadth than species whose ranges stretch far from the equator, however, no difference in niche breadth was found across summits' elevation. Biogeographic species groups distributed close to the equator and restricted to alpine regions showed narrower niche breadth than those with broader ranges. Community weighted-scores of thermal niche breadth were positively related to distance from equator but not to elevation. Based on their TNTs, species restricted to equatorial latitudes and plant communities dominated by these species were identified as the most vulnerable to the projected 1.5 °C warming, due to a potentially higher risk of losing thermal niche space. Main conclusions Our study confirms that the CVH applies to high tropical Andean plant species and communities, where latitude had a strong effect on the thermal niche breadth. TNTs are identified as suitable indicators of species' vulnerability to warming and are suggested to be included in long-term biodiversity monitoring in the Andes.

Predicting tropical tree mortality with leaf spectroscopy

Do tropical trees close to death have a distinct change to their leaf spectral signature? Tree mortality rates have been increasing in tropical forests globally, reducing the global carbon sink. Upcoming hyperspectral satellites could be used to predict regions close to experiencing extensive tree mortality during periods of stress, such as drought. Here we show, for a tropical rainforest in Borneo, how imminent tropical tree mortality impacts leaf physiological traits and reflectance. We measured leaf reflectance (400-2500 nm), light saturated photosynthesis (Asat), leaf dark respiration (Rdark), leaf mass area (LMA) and % leaf water across five campaigns in a six-month period during which there were two causes of tree mortality: a major natural drought and a co-incident tree stem girdling treatment. We find that prior to mortality, there were significant (P<0.05) leaf spectral changes in the red (650-700 nm), the NIR (1000 -1400 nm) and SWIR bands (2000-2400 nm) and significant reductions in the potential carbon balance of the leaves (increased Rdark and reduced Asat). We show that the partial least squares regression technique can predict mortality in tropical trees across different species and functional groups with medium precision but low accuracy (r2 of 0.65 and RMSE/mean of 0.58). However, most tree death in our study was due to girdling, which is not a natural form of death. More research is needed to determine if this spectroscopy technique can be applied to tropical forests in general.

RAD-seq reveals patterns of diversification, hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees

A common pattern observed in temperate tree clades is that species are often morphologically distinct and partially interfertile but maintain species cohesion despite ongoing hybridization where ranges overlap. Although closely related species commonly occur in sympatry in tropical ecosystems, little is known about patterns of hybridization within a clade over time, and the implications of this hybridization for the maintenance of species boundaries. In this study, we focused on a clade of sympatric trees in the genus Diospyros in the Mascarene islands and investigated whether species are genetically distinct, whether they hybridize, and how patterns of hybridization are related to the time since divergence among species. We sampled multiple populations from each of 12 Mascarene Diospyros species, generated genome-wide SNP data using 2bRADseq, and conducted population genomic and phylogenomic analyses. We found that Mascarene Diospyros species diverged millions of years ago and are largely genetically distinct from one another. Although hybridization was observed between closely related species belonging to the same subclade, more distantly related species showed little evidence of interspecific hybridization. Phylogenomic analyses also suggested that introgression occurred during the evolutionary history of the clade. This suggests that, as diversification progressed, interspecific hybridization also occurred among species, but became infrequent as lineages diverged from one another and evolved reproductive barriers. Species now co-exist in partial sympatry, and experience limited hybridization between close relatives. Additional research is needed to better understand the role introgression may have played in adaptation and diversification of Mascarene Diospyros, and its relevance for conservation.

Data from: Drivers of assemblage-wide calling activity in tropical anurans and the role of temporal resolution

1. Temporal scale in animal communities is often associated with seasonality, despite the large variation in species activity during a diel cycle. A gap thus remains in understanding the dynamics of short-term activity in animal communities. 2. Here we assessed calling activity of tropical anurans and addressed how species composition varied during night activity in assemblages along gradients of local and landscape environmental heterogeneity. 3. We investigated 39 anuran assemblages in the Pantanal wetlands (Brazil) with passive acoustic monitoring during the peak of one breeding season and first determined changes in species composition between night periods (early, mid, and late) using two temporal resolutions (1-hour and 3-hour intervals). Then, we addressed the role of habitat structure (local and landscape heterogeneity variables from field-based and remote sensing metrics) and ecological context (species richness and phylogenetic relatedness) in determining changes in species composition (i) between night periods and (ii) across days. 4. Nocturnal calling activity of anuran assemblages varied more within the 1-hour resolution than the 3-hour resolution. Differences in species composition between early and late-night periods were related to local habitat structure and phylogenetic relatedness, while a low variation in compositional changes across days was associated with low-heterogeneous landscapes. None of these relationships were observed using the coarser temporal resolution (3-hour). 5. Our findings on the variation of calling activity in tropical anuran assemblages suggest potential trades-off mediated by fine-temporal partitioning. Local and landscape heterogeneity may provide conditions for spatial partitioning, while the relatedness among co-signaling species provides cues on the ecological overlap of species with similar requirements. These relationships suggest a role of niche dimensional complementarity on the structuring of these anuran assemblages over fine temporal scales. We argue that fine-temporal differences between species in breeding activity can influence the outcome of species interaction and that addressing temporal scaling issues can improve our understanding of dynamics of animal communities.

Data from: Elevation and leaf litter interact in determining the structure of ant communities on a tropical mountain

Tropical mountains encompass a wide range of environmental conditions and are useful models for studying drivers of community structure. Invertebrate species richness and abundance show various elevational patterns. However, the drivers of these differences are not well understood, although microhabitat complexity is potentially important. We studied ground-dwelling ants using pitfall trapping and hand collection on Mt. Wilhelm (Papua New Guinea) from 169 to 3,795 m a.s.l. We tested for the effects of elevation and leaf litter depth (as a measure of microhabitat complexity) on ant abundance, species richness and composition. We sampled 118 species, with ants present up to 2,331 m a.s.l. Species richness peaked at mid-elevation (~700 m), but the elevational pattern for abundance varied depending on sampling scale. Leaf litter depth negatively affected abundance once elevation had been accounted for, while elevation and litter depth had an interactive effect on species richness. Species richness was positively related to litter depth at lower elevations, but negatively above ~700 m. Species composition varied with elevation and less strongly with leaf litter depth. We speculate that in the lowlands, litter depth rather than temperature limits ant communities. At high elevations, the deeper litter decreases temperature of the litter layer, and temperature becomes limiting. At mid elevations, temperature is not yet too low, and litter is still relatively deep, hence generating a mid-elevation peak in ant richness. Our results may explain differing richness-elevation patterns of litter arthropods around the world, and provide testable predictions for future studies on this topic.

opennotspecifiedDec 2020View details →

FIGURE 1. A–B in First record of hybridization in Caranx Lacepède, 1801 (Carangidae: Perciformes) in the Tropical Eastern Pacific Ocean

FIGURE 1. A–B. Specimen of C. melampygus x C. sexfasciatus, 576 mm SL (UCR 3209-001), captured at Isla Montuosa, Pacific coast of Panama (7.467472, -82.266556; 30 m depth). (A) Fresh and (B) after preservation. C–D. Preserved specimens, representatives of the parental species: (C) C. melampygus (UCR 0423-027, 153 mm SL) and (D) C. sexfasciatus (UCR 3112- 003, 122 mm SL). Scale bar=50 mm.

opennotspecifiedDec 2020View details →

FIGURE 2 in First record of hybridization in Caranx Lacepède, 1801 (Carangidae: Perciformes) in the Tropical Eastern Pacific Ocean

FIGURE 2. Consensus tree of selected members of Caranx. Topology inferred combining the information of five different models: Neighbor-Joining (NJ), Bayesian Inference (BI), Maximum-Likelihood (ML), Minimum Evolution (ME) and Maximum Parsimony (MP) for a total of 19 (626-bp) COX1 sequences. Numbers at nodes represent support values in percentage (posterior probability for BI) for each one of the five models, respectively. The tree is rooted with Nematistius pectoralis.

Data from: Life-history dimensions indicate non-random assembly processes in tropical island tree communities

Community assembly processes on islands are often non-random. The mechanisms behind non-random assembly, however, are generally difficult to disentangle. Functional diversity in combination with a null model approach that accounts for differences in species richness among islands can be used to test for non-random assembly processes, but has been applied rarely to island communities. By linking functional diversity of trees on islands with a null model approach, we bridge this gap and test for the role of stochastic vs. non-random trait-mediated assembly processes in shaping communities by studying functional diversity-area relationships. We measured 11 plant functional traits linked to species dispersal and resource acquisition strategies of 57 tree species on 40 tropical islands. We grouped traits into four life-history dimensions representing (i) dispersal ability, (ii) growth strategy, (iii) light acquisition, and (iv) nutrient acquisition. To test for non-random assembly processes, we used null models that account for differences in species richness among the islands. Our results reveal contrasting responses of the four life-history dimensions to island area. The dispersal and the growth strategy dimensions were underdispersed on smaller islands, whereas the light acquisition dimension was overdispersed. The nutrient acquisition dimension did not deviate from null expectations. With increasing island area, shifts in the strength of non-random assembly processes increased the diversity of dispersal and acquisition strategies in island communities. Our results suggest that smaller islands may be more difficult to colonize and provide more limited niche space compared to larger islands, whose tree communities are likely determined by stochastic processes and higher niche diversity. Our null model approach highlights that analysing the functional diversity of different life-history dimensions provides a powerful framework to unravel community assembly processes on islands. These complex, non-random assembly processes are masked by measures of functional diversity that do not account for differences in species richness between islands.

Data from: Impacts of habitat on butterfly dispersal in tropical forests, parks and grassland patches embedded in an urban landscape

Dispersal distances of 17 species of butterflies in tropical Singapore were significantly greater in forest than in urban habitat. Butterflies in urban plots frequently moved within suitable habitat (park/grassland) patches but rarely crossed non-habitat patches suggesting potential isolation and a need for urban corridors.

Heterogeneous agroecosystems support high diversity and abundance of trap nesting bees and wasps amongst tropical crops

Land-use intensification for agricultural purposes modifies the structure of natural environments in various ways and at different spatial scales. These modifications can affect ecological processes and the community structure of multi-environment users such as solitary bees and wasps. Understanding the role of distinct habitat descriptors in promoting such changes is one of the major challenges of empirical studies. In this study, we use a multi-scale approach to evaluate how landscape compositional and configurational heterogeneity, vegetation structural complexity, and the proportion of agricultural landscape composition affect communities of bees and wasps that nest in pre-existing cavities in remnants of native vegetation bordering agroecosystems. We selected 25 sampling points along a gradient of amount of surrounding agriculture and landscape diversity within natural physiognomies located in Chapada Diamantina, Bahia, Brazil. Through model selection using Akaike's information criterion, we verified the complementary roles of landscape heterogeneity and local vegetation in structuring these hymenopteran communities. Abundance in the groups showed different tendencies depending on the descriptors employed, pointing to the importance of evaluating within-group specificity. Furthermore, bees and wasps presented differential responses to landscape composition, but they did not differ in relation to configurational complexity. In more heterogeneous landscapes or sites with more complex local vegetation, the proportion of agriculture had a positive influence on the response evaluated. Efficient management of agricultural landscapes therefore requires increased landscape heterogeneity and conservation or restoration of native vegetation remnants at the local scale.

Supplementary material 3 from: Duron Q, Cornulier T, Vidal E, Bourguet E, Ruffino L (2020) Combining live and lethal trapping to inform the management of alien invasive rodent populations in a tropical montane forest. NeoBiota 63: 101-125. https://doi.org/10.3897/neobiota.63.53811

Mean distances (± se) of trapped rats from the edge of the removal area during the four trapping sessions

Supplementary material 4 from: Duron Q, Cornulier T, Vidal E, Bourguet E, Ruffino L (2020) Combining live and lethal trapping to inform the management of alien invasive rodent populations in a tropical montane forest. NeoBiota 63: 101-125. https://doi.org/10.3897/neobiota.63.53811

Distances (in meters) travelled between rats' home range centers in the CMR area and their recapture in the removal area for 27 individuals