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opencc-by-4.0Mar 2022View details →

Ficus trees with upregulated or downregulated defence did not impact predation on their neighbours in a tropical rainforest

Trees can emit volatile organic compounds (VOCs) when under attack by herbivores, and these signals can also be detected by natural enemies and neighbouring trees. There is still limited knowledge of intra- and inter-specific communication in diverse habitats. We studied the effects of induced VOC emissions by three Ficus species on predation on the focal Ficus trees in a lowland tropical rainforest in Papua New Guinea. Further we assessed predation across a phylogenetically diverse set of neighbouring tree species. Two of the focal tree species, Ficus pachyrrhachis and F. hispidioides, have strong alkaloid-based constitutive defences while the third one, F. wassa, is lower in constitutive chemical defences. We experimentally manipulated the jasmonic acid signalling pathway by spraying the focal individuals with either methyl jasmonate (MeJA) or diethyldithiocarbamic acid (DIECA). These treatments induce increases or decreases in VOC emissions, respectively. We tested the possible effects of VOC emissions on each focal Ficus tree and two of its neighbours by measuring the predation rate of plasticine caterpillars. We found that predation increased after the MeJA application in only one focal tree species, F. wassa, while the DIECA application had no effect on any of the three focal species. Further, we did not detect an effect of our treatments on predation rates across neighbouring trees. Neither the phylogenetic distance of the neighbouring tree from the focal tree nor the physical distance from the focal tree had any effect on predation rates for any of the three focal Ficus species. These results suggest that even congeneric tree species vary in their response to the MeJA and DIECA treatment and subsequent response to VOC emissions by predators. Our results also suggest that MeJA effects did not spill over to neighbouring trees in highly diverse tropical rainforest vegetation.

opencc-zeroApr 2022View details →

Gene expression plasticity, genetic variation and fatty acid remodelling in divergent populations of a tropical bivalve species: lipid profiles

Ocean warming challenges marine organisms' resilience, especially for species experiencing temperatures close to their upper thermal limits. A potential increase in thermal tolerance might significantly reduce the risk of population decline, which is intrinsically linked to variability in local habitat temperatures. Our goal was to assess the plastic and genetic potential of response to elevated temperatures in a tropical bivalve model, Pinctada margaritifera. We benefit from two ecotypes for which local environmental conditions are characterized by either large diurnal variations in the tide-pools (Marquesas archipelago) or lower mean temperature with stable to moderate seasonal variations (Gambier archipelago). We explored the physiological basis of individual responses to elevated temperature, genetic divergence as well as plasticity and acclimation by combining lipidomic and transcriptomic approaches. We show that P. margaritifera has certain capacities to adjust to long-term elevated temperatures that was thus far largely underestimated. Genetic variation across populations overlaps with gene expression and involves the mitochondrial respiration machinery, a central physiological process that contributes to species thermal sensitivity and their distribution ranges. Our results present evidence for acclimation potential in P. margaritifera and urge for longer term studies to assess populations resilience in face of climate change.

Figure 3. Solanum sanchez-vegae. A in Four New Vining Species of Solanum (Dulcamaroid Clade) from Montane Habitats in Tropical America

Figure 3. Solanum sanchez-vegae. A) portion of stem, B) petiole articulation, C) buds, D) open flower, E) flower cross-section showing stigma detail, F) anthers, G) fruit. A–F drawn from Smith & Sanchez-Vega 7524, G from Hutchison et al. 5738. doi:10.1371/journal.pone.0010502.g003

Figure 1. Solanum aspersum. A in Four New Vining Species of Solanum (Dulcamaroid Clade) from Montane Habitats in Tropical America

Figure 1. Solanum aspersum. A) portion of stem, with details of trichomes, B) young bud, C) open flower, D) fruiting inflorescence, E) young fruit. A–C drawn from MacDougal et al. 4251, D–E from Zak 1857A. doi:10.1371/journal.pone.0010502.g001

Figure 4 in Four New Vining Species of Solanum (Dulcamaroid Clade) from Montane Habitats in Tropical America

Figure 4. Solanum sanchez-vegae. Peru. La Libertad. A. Cano s.n. (photograph courtesy of A. Cano, USM). doi:10.1371/journal.pone.0010502.g004

Figure 5. Solanum sousae. A in Four New Vining Species of Solanum (Dulcamaroid Clade) from Montane Habitats in Tropical America

Figure 5. Solanum sousae. A) portion of stem with flowering inflorescence, B) flower, C) flower cross section, D) anthers, E) portion of stem with fruiting inflorecence. A–D drawn from Ventura 2212, E from Maya J. 3938. doi:10.1371/journal.pone.0010502.g005

Figure 2. Solanum luculentum. A in Four New Vining Species of Solanum (Dulcamaroid Clade) from Montane Habitats in Tropical America

Figure 2. Solanum luculentum. A) portion of stem with flowering inflorescence, B) detail of stem with peeling bark, C) buds, D) open long-styled flower with anthers removed, E) long-styled flower cross-section, F) anthers, G) short-styled flower cross-section, H) fruiting inflorescence from putatively pistillate individual. A–B drawn from Nee & Callejas 32546, C–F from Steyermark et al. 127855, G from Steyermark & Dunsterville 100777, H from Killip & Smith 15952. doi:10.1371/journal.pone.0010502.g002

opencc-by-4.0Jul 2021View details →

Multi-taxa environmental DNA inventories reveal distinct taxonomic and functional diversity in urban tropical forest fragments

Urban expansion and associated habitat transformation drives shifts in biodiversity, with declines in taxonomic and functional diversity. Forests fragments within urban landscapes offer a number of ecosystem services, and help to maintain biodiversity and ecosystem functions. Here, we focus on a tropical forest environment, and on the soil biota. Using eDNA metabarcoding, we compare forest fragments within the city of Cayenne, French Guiana, with a neighbouring continuous undisturbed forest. We wished to determine if urban forest fragments conserve high levels of alpha and beta diversity as well as similar functional composition for plants, soil animals, fungi and bacteria. We found that alpha diversity is similar across habitats for plants and fungi, lower in urban forests for metazoans and higher for bacteria. We also found that urban forests communities differ from undisturbed forests in their taxonomic composition, with urban forests exhibiting greater turnover between fragments potentially caused by ecological drift and limited dispersal. However, their functional composition exhibited limited differences, with an enrichment of palms, arbuscular mycorrhizal fungi and bacteria and a depletion of climber plants and termites. Thus, although urban forest fragments do shelter soil biodiversity that differs from native forests, the losses of soil functions may be relatively limited. This study demonstrates the strong potential of a multi-taxa eDNA approach for rapid inventories across taxonomic kingdoms, in particular for cryptic soil diversity. It also demonstrates the key role of urban forest fragments in conserving biodiversity and ecosystem function, and points to a need for more systematic monitoring of these areas in urban management plans. For each of the 16 samples per plot, 15 g of soil was used for eDNA analyses. Extracellular DNA was extracted as described previously (Zinger et al., 2016; 2019), where each soil sample is added to 15ml of saturated phosphate buffer (Na2HPO4; 0.12m; pH ≈8) in 50ml Falcon tubes. This is placed in an agitator for 15 minutes, before a 2ml aliquot of the soil/phosphate buffer mixture is pipetted into an Eppendorf tube and centrifuged for five minutes at 13000 rcf. 500μL of the resulting supernatant is then recovered and used for the next extraction steps that are carried out with a commercial kit for soil DNA (NucleoSpin® Soil; Macherey-Nagel, Düren, Germany), skipping the lysis step and following manufacturer’s instructions. The DNA extract was recovered in 100 μL and diluted 10 times before being used as PCR template.  For each plot one DNA extraction negative control was performed adding up 17 extractions per plot. PCR amplifications were then conducted for four DNA molecular markers, with primers targeting either Viridiplantae (subsequently referred to as plants), Eukaryotes, Fungi or Bacteria (Table 1). For each marker, PCR amplification of samples occurred across 12 plates. Each PCR reaction was performed in a total volume of 20 μl and comprised 10 μl of AmpliTaq Gold Master Mix (Life Technologies, Carlsbad, CA, USA), 5.84 μl of Nuclease-Free Ambion Water (Thermo Fisher Scientific, Massachusetts, USA), 0.25 μM of each primer, 3.2 μg of BSA (Roche Diagnostic, Basel, Switzerland), and 2 μl of DNA template that was before 10-fold diluted to reduce the amounts of PCR inhibitors. Thermocycling conditions for each primer pair are indicated in Table 1.  A negative extraction control per site and a negative PCR control per PCR plate were amplified and sequenced in parallel with the regular samples. Positive controls were also included and consisted of mock communities of plants and fungi DNA (no mock communities were built for bacteria or eukaryotes here), which were used to guide choices in our data curation process. Two PCR replicates were performed for each sample and control. Amplification was conducted using a double indexing system strategy (Binladen et al. 2007) using a system of 32 by 36 octamers with at least five differences between them located at the 5’ end of each primer (Coissac 2012). In doing so, each PCR product had a unique combination of tags for both forward and reverse primers, allowing for the retrieval of sequence data for each sample. Ten wells per PCR plate were left empty to act as sequencing controls (non-used tag combinations) for downstream data curation (see below). PCR products were pooled and sequencing libraries were constructed using the Illumina TruSeq NanoPCRFree kit following the supplier’s instructions (Illumina Inc., San Diego, California, USA), except that the ligation product was not PCR amplified to limit tag-jump biases (Taberlet et al 2018). The libraries were then sequenced on different Illumina platforms (San Diego, CA, USA) depending on the marker considered (Table S1), using the paired-end technology. Bioinformatic analyses were performed on the GenoToul bioinformatics platform (Toulouse, France), with the OBITOOLS package (Boyer et al. 2016). First, ‘illuminapairedend’ was used to assemble paired-end reads. This algorithm is based on an exact alignment algorithm that considers the quality scores at all positions during the assembly process. Subsequently, we used the ‘ngsfilter’ command to identify and remove the primers and tags on each read, and assign reads to their respective samples. This program was used with its default parameters tolerating two mismatches for each of the two primers and no mismatch for the tags. Following this, sequencing reads were dereplicated using the ‘obiuniq’ command. Sequences of low quality (containing Ns or with paired-end alignment scores below 50) were excluded using the ‘obigrep’ command. The same command was used to exclude sequences represented by only one read (singletons) as they are more likely to be molecular artefacts (Taberlet et al. 2018). Sequences outside of the preset range were also discarded (Table 1). To remove PCR/sequencing errors as well as intraspecific variability, we built OTUs (Operational Taxonomic Units) using the ‘sumaclust’ clustering algorithm (Mercier et al. 2013), which considers the most abundant sequence of each cluster as the cluster representative.  OTUs were set at a sequence similarity threshold of 97% for eukaryotes, fungi and bacteria following the standards in microbial ecology, but this was lowered to 95% for plants since the eDNA target region is shorter (typically around 50 base pairs), where one mismatch inherently results in a lower percentage of similarity. To assign a taxon to plant and fungal OTUs, we built two reference sequence databases, one global, using the ecoPCR programme (Ficetola et al. 2010) and the plant / fungi specific markers on the European Molecular Biology Laboratory (EMBL; release 141), a second local, generated from specimens of fungi (Jaouen et al. 2019) and plants (see Zinger et al. 2019) collected in French Guiana. OTUs were then assigned a taxonomy, using OBITOOL’s ecotag programme (Boyer et al. 2016), which performs a global alignment of each OTU sequence (the query) against each reference. The reference taxon assigned to each OTU corresponds to the Last Common Ancestor of all the best-match sequences for the query. For taxonomic assignment of bacteria and eukaryote OTUs, the SILVA taxonomic database was used (version 1.3; Quast et al., 2012). Classification was performed by a local nucleotide BLAST search against the non-redundant version of the SILVA SSU Ref dataset (release 132; http://www.arb-silva.de) using blastn (version 2.2.30+; http://blast.ncbi.nlm.nih.gov/Blast.cgi) with standard settings (Camacho et al., 2009).  Eukaryote derived metazoan OTUs were then further assigned a taxonomy for Phyla identified at the Arthropoda, Annelida and Nematoda level using reference sequence databases built as above for these groups using the ecoPCR programme on EMBL release 141. Datasets were subsequently filtered to remove contaminants as well as artefacts such as PCR chimeras and remaining sequencing errors, following Zinger et al. (2019) and using routines now implemented in the metabaR R package (Zinger et al 2020b), in R version 3.6.1 (R Development Core Team, 2013). The filtering process consisted of four steps: (i) a negative control-based filtering. OTUs whose maximum abundance was found in extraction/PCR negative controls were removed from the dataset, as they were likely to be reagent/aerosol contaminants, better amplified in the absence of competing DNA fragments as it is the case in biological samples. (ii) a reference-based filtering. OTUs which are too dissimilar from sequences available in reference databases are potential chimeras generated during sequencing and amplification. In this study, we chose to set similarity thresholds at 95% for plants, 80% for bacteria and eukaryotes and due to the marker being more polymorphic, 65% for fungi. For plants and fungi, the remaining assignment was then verified with the local database, to confirm if assigned taxa also occurred in the local dataset, with preference given to local assignment. In addition, we removed all taxa that are not targeted by the primer used. (iii) an abundance-based filtering. This procedure targets incorrect assignment of a few numbers of sequences corresponding to true OTUs occurring to the wrong sample, a phenomenon called “tag-switching” (Esling et al. 2015), “tag jumps” (Schnell et al. 2015) or “cross-talk” (Edgar 2018). It consists in setting OTUs abundances to 0 in samples where their abundance represents < 0.03% of the total OTU abundance in the entire dataset. (iv) Finally, we conducted a PCR-based filtering by considering any PCR reaction that yielded less than 100 reads for plants, 1000 reads for fungi, bacteria and eukaryotes as non-functional, and removed them from the dataset. Data provided consists of 4 x OTU tables for each of the markers used to target different components of the soil biota, with rows representing each OTU, and columns the features of the OTU within the dataset, namely their id code, the number of read counts in the analysed dataset, their similarity score against the taxonomic dataset used to identify them, and when possible, a functional group assignment used in the manuscript. Details of these can be found above and in the manuscript and supplementary information. For each of the four datasets, we also provide a .rds file, corresponding to the processed dataset used in manuscript preparation. This is in the format of a metabaR list which includes PCR, Sample, Read count and the seperately provided OTU datasets. To facilitate interpretation, please refer to Zinger, L., Lionnet, C., Benoiston, A.S., Donald, J., Mercier, C. and Boyer, F., 2021. metabaR: an R package for the evaluation and improvement of DNA metabarcoding data quality. Methods in Ecology and Evolution, 12(4), pp.586-592. For the fungal (ITS) data, we also provide :  - the R1/R2 raw fastq files of the samples used in the paper + experimental controls - a tsv file containing the tag combinations corresponding to the samples/PCR replicates, to enable demultiplexing of data. - a csv file containing the description of each sample.

opencc-by-4.0May 2022View details →

Global and tropical band averages for a selection of CMIP5 and CMIP6 models: piControl and abrupt-4xCO2 experiments (compressed)

This dataset provides post-processed spatial averages for a selection of 55 CMIP5 and CMIP6 models. The experiments contained in this dataset are only the pre-industrial controls (piControl) and the experiments with a four-fold increase in the atmospheric CO$_{2}$ concentration in relation to the pre-industrial level (abrupt-4xCO2). The spatial averages are global and tropical bands from x°S to x°N, where the x value is between 5 and 40 in increments of 5°. This dataset was created to study climate sensitivity in general and the effect of stratospheric circulation changes on the tropical equilibrium climate sensitivity. It contains the following variables: <ul> <li>incoming (d) short-wave (SW, s) radiative flux (RF, r) at the top of the atmosphere (TOA, t): rsdt</li> <li>outgoing (u) SW RF at TOA: rsut</li> <li>outgoing long-wave (LW, l) RF at TOA: rlut</li> <li>net (n) RF at TOA: rnt*</li> <li>incoming SW RF at the surface (s): rsds</li> <li>outgoing SW RF at the surface: rsus</li> <li>incoming LW RF at the surface: rlds</li> <li>outgoing LW RF at the surface: rlus</li> <li>net RF at the surface: rns*</li> <li>sensible heat flux (hfs) at the surface: hfss</li> <li>latent heat flux (hfl) at the surface: hfls</li> <li>surface temperature (t): ts</li> <li>atmospheric temperature: ta</li> <li>specific humidity: hus</li> <li>zonal component of wind: ua</li> <li>meridional component of wind: va</li> <li>lagrangian tendency of pressure (vertical component of wind in pressure per time dimensions): wap</li> <li>surface pressure: ps</li> <li>geopotential height: zg</li> </ul> *rnt and rns were calculated for the creation of this dataset using the model output rlut rsut, rsds, rsus, rlds, rlus. This version updates the previous version by providing the dataset in a compressed tarball. Use `tar -xzvf CMIP_data.tar.gz` to extract and decompress.

opencc-zeroMay 2022View details →

Data from: Global plant ecology of tropical ultramafic ecosystems

This is a compiled geospatial dataset in ESRI polygon shapefile format of ultramafic soils of the neotropics showing the location of ultramafic soils in Guatemala, Cuba, Dominican Republic, Puerto Rico, Costa Rica, Colombia, Argentina, Chile, Venezuela, Ecuador, Brazil, Suriname, French Guiana, and Bolivia. The data are derived from seven geospatial datasets. Original datasets were subset to include only ultramafic areas, datasets were assigned a common projection (WGS84), attribute tables were reconciled to a common set of fields, and the datasets were combined. The dataset includes three components: 1) a geospatial dataset in ESRI polygon shapefile format of ultramafic soils of the neotropics showing the location of ultramafic soils in Guatemala, Cuba, Dominican Republic, Puerto Rico, Costa Rica, Colombia, Argentina, Chile, Venezuela, Ecuador, Brazil, Suriname, French Guiana, and Bolivia. 2) A regional-specific bibliography for all tropical ultramafic regions discussed in the original manuscript (Garnica-Diaz et al. 2022), and 3) an updated list in .csv format of major ultramafic outcrops worldwide including their latitude and longitude coordinates.

opencc-by-4.0May 2022View details →

Microspines in tropical climbing plants: a small-scale fix for life in an obstacle course

This dataset is associated to the original research article "Microspines in tropical climbing plants: a small-scale fix for life in an obstacle course" published in the Journal of Experimental Botany.  <table> <tbody> <tr> <td>Variable</td> <td>Description</td> <td>Type of variable</td> <td>Units</td> </tr> <tr> <td>sample</td> <td>Sample identifiier</td> <td>Nominal Variable</td> <td> </td> </tr> <tr> <td>sp_code</td> <td>Species identifier</td> <td>Nominal Variable</td> <td> </td> </tr> <tr> <td>sp</td> <td>Species latin name</td> <td>Nominal Variable</td> <td> </td> </tr> <tr> <td>direction</td> <td>Friction test direction</td> <td>Categorical variable</td> <td> </td> </tr> <tr> <td>static_force</td> <td>Force needed to induce motion of the stem segment</td> <td>Continuous variable</td> <td>mN</td> </tr> <tr> <td>sliding_force</td> <td>Force needed to maintain the stem segment in motion</td> <td>Continuous variable</td> <td>mN</td> </tr> <tr> <td>sliding_dist</td> <td>Distance spanned by the stem segment during test</td> <td>Continuous variable</td> <td>mm</td> </tr> <tr> <td>nPeaks</td> <td>Number of force peaks detected during test</td> <td>Discrete variable</td> <td>mN</td> </tr> <tr> <td>peak_frequ</td> <td>Peak frequency during sliding (NPeaks/sliding_dist)</td> <td>Continuous variable</td> <td>peaks.mm-1</td> </tr> <tr> <td>diam</td> <td>Diameter of the tested segment</td> <td>Continuous variable</td> <td>mm</td> </tr> </tbody> </table>

opencc-zeroDec 2021View details →

Data from: Occupancy winners in tropical protected forests: a pantropical analysis

The structure of forest mammal communities appears surprisingly consistent across the continental tropics, presumably due to convergent evolution in similar environments. Whether such consistency extends to mammal occupancy, despite variation in species characteristics and context, remains unclear. Here we ask whether we can predict occupancy patterns and, if so, whether these relationships are consistent across biogeographic regions. Specifically, we assessed how mammal feeding guild, body mass and ecological specialization relate to occupancy in protected forests across the tropics. We used standardized camera-trap data (1,002 camera-trap locations and 2-10 years of data) and a hierarchical Bayesian occupancy model. We found that occupancy varied by regions, and certain species characteristics explained much of this variation. Herbivores consistently had the highest occupancy. However, only in the Neotropics did we detect a significant effect of body mass on occupancy: large mammals had lowest occupancy. Importantly, habitat specialists generally had higher occupancy than generalists, though this was reversed in the Indo-Malayan sites. We conclude that habitat specialization is key for understanding variation in mammal occupancy across regions, and that habitat specialists often benefit more from protected areas, than do generalists. The contrasting examples seen in the Indo-Malayan region likely reflect distinct anthropogenic pressures.

Small mammals reduce distance-dependence and increase seed predation risk in tropical rainforest fragments

Seed predation and reduced predation risk with distance from conspecific trees are important influences on tree regeneration in tropical forests. Shifts in animal communities, such as an increase in rodents and other small mammals due to forest fragmentation, could alter patterns of seed predation and affect tree regeneration and community dynamics in forest fragments. We performed a field experiment on four native rainforest tree species in the Western Ghats, India, to test whether fragmentation increases seed predation by mammals and alters the distance-dependence of seed predation. We monitored seed predation within open and mammal-exclosure plots, near and far from the canopies of conspecific trees, in contiguous and fragmented forests. Seed predation of Cullenia exarillata, Ormosia travancorica, and Syzygium rubicundum was markedly higher in forest fragments, and more so within open plots than exclosures, while the predominantly insect-predated Acronychia pedunculata experienced similar predation in contiguous forests and fragments. Seed predation of C. exarillata and S. rubicundum was unrelated to distance from conspecific trees in open plots in both contiguous forests and fragments, in contrast to exclosures that showed marked near versus far differences in seed predation. Our findings suggest that by increasing overall seed predation risk and imposing similar seed predation risk near and far from adults variably across the tree species, small mammals could alter processes that shape tree diversity and species composition in fragmented tropical rainforests.

Functional assembly of tropical montane tree islands in the Atlantic Forest is shaped by stress-tolerance, bamboo-presence and facilitation

Aims: Amidst the Campos de Altitude (Highland Grasslands) in the Brazilian Atlantic Forest, woody communities grow either clustered in tree islands or interspersed within the herbaceous matrix. The functional ecology, diversity and biotic processes shaping these plant communities are largely unstudied. We characterised the functional assembly and diversity of these tropical montane woody communities and investigated how they fit within Grime's CSR (C – competitor, S – stress-tolerant, R – ruderal) scheme, what functional trade-offs they exhibit and how traits and functional diversity vary in response to bamboo presence/absence. Methods: To characterize the functional composition of the community, we sampled five leaf traits and wood density along transects covering the woody communities both inside tree islands and outside (i.e. isolated woody plants in the grasslands community) . Then, we used Mann Whitney test, t-test and variation partitioning to determine the effects of inside vs outside tree island and bamboo presence on community weighted means, woody species diversity and functional diversity. Results: We found a general SC/S strategy with drought-related functional trade-offs. Woody plants in tree islands had more acquisitive traits than those within the grasslands. Trait variation was mostly taxonomically than spatially driven, and species composition varied between inside and outside tree islands. Leaf thickness, wood density and foliar water uptake were unrelated to CSR-strategies, suggesting independent trait dimensions and multiple drought-coping strategies within the predominant S-strategy. Islands with bamboo presence showed lower Simpson diversity, lower functional dispersion, lower foliar water uptake and greater leaf thickness than in tree islands without bamboo. Conclusions: The observed functional assembly hints towards large-scale environmental abiotic filtering shaping stress-tolerant community strategy, and small-scale biotic interactions driving small-scale trait variation. We recommend experimental studies with fire, facilitation treatments, eco-physiological and recruitment traits to elucidate on tree island expansion and communities response to climate change.

The symmetry spectrum in a hybridising, tropical group of rhododendrons

Many diverse plant clades possess bilaterally symmetrical flowers and specialized pollination syndromes suggesting these traits may promote diversification. We examine the evolution of diverse floral morphologies and the association with diversification history in a species-rich tropical radiation of Rhododendron. We used restriction-site associated DNA sequencing on 114 taxa from Rhododendron sect. Schistanthe to reconstruct phylogenetic relationships, infer colonization of Southeast Asia and examine hybridization. We then captured and quantified floral variation using geometric morphometric analyses which we interpret in a phylogenetic context. We uncovered phylogenetic complexity caused by introgression within and between clades. Morphometric analyses revealed flower symmetry to be a morphological continuum without a clear transition from radial to bilateral symmetry. The largest radiation of tropical Rhododendron species is associated with an expansion into novel floral morphological space as species diversified in New Guinea about 6 million years ago. Our results showed that the recent radiation of tropical Rhododendron is a consequence of hybridization, genetic isolation caused by mountain building, and the evolution of floral novelty. Floral variation evolved via changes to multiple components of the corolla that are only recognized in geometric morphometrics with both front and side views of flowers.

The evolutionary history and mechanistic basis of female ornamentation in a tropical songbird

Ornamentation, such as the showy plumage of birds, is widespread among female vertebrates, yet the evolutionary pressures shaping female ornamentation remain uncertain. In part this is due to a poor understanding of the mechanistic route to ornamentation in females. To address this issue, we evaluated the evolutionary history of ornament expression in a tropical passerine bird, the White-shouldered Fairywren, whose females, but not males, strongly vary between populations in occurrence of ornamented black-and-white plumage. We first use phylogenomic analysis to demonstrate that female ornamentation is derived and that female ornamentation evolves independently of changes in male plumage. We then use exogenous testosterone in a field experiment to induce partial ornamentation in naturally unornamented females. By sequencing the transcriptome of experimentally induced ornamented and natural feathers, we identify genes expressed during ornament production and evaluate the degree to which female ornamentation in this system is associated with elevated testosterone, as is common in males. We reveal that some ornamentation in females is linked to testosterone and that sexes differ in ornament-linked gene expression. Lastly, using genomic-outlier analysis we identify a candidate melanogenesis gene that lies in a region of high genomic divergence among populations that is also differentially expressed in feather follicles of different female plumages. Taken together, these findings are consistent with sex-specific selection favoring the evolution of female ornaments and demonstrate a key role for testosterone in generating population divergence in female ornamentation through gene regulation. More broadly, our work highlights similarities and differences in how ornamentation evolves in the sexes.

opencc-zeroJul 2022View details →

Data from: Out of the tropics: Macroevolutionary size trends in an old insect order are shaped by temperature and predators

Global body size distributions are shaped by selection pressures arising from biotic and abiotic factors such as temperature, predation and parasitism. Here, we investigated the ecological and evolutionary drivers of global latitudinal size gradients in an old insect order (Odonata; dragonflies and damselflies). Phylogenetic comparative analyses revealed that global size variation of extant taxa is negatively influenced by both regional avian diversity and temperature. Interestingly, fossil data show that the relationship between wing size and latitude has shifted: latitudinal size trends had initially negative slopes but became shallower or positive following the emergence of birds 150 MYA. These changing size-latitude trends over geological time were likely driven by bird predation and high dispersal ability of large dragonflies. Our results therefore suggest that latitudinal size gradients were shaped by temperature but also by predators driving the dispersal of large-sized clades out of the tropics and in to the temperate zone.

opencc-zeroAug 2022View details →

Tropical–temperate comparisons in insect seed predation vary between study levels and years

The biotic interaction hypothesis, which states the species interaction becomes stronger in the tropics, is deeply rooted in classic ecological literature and widely accepted to contribute to the latitudinal gradients of biodiversity. Tests in latitudinal insect-plant interaction have emphasized leaf-eating insects on a single or a few plant species rather than within an entire community and mixed accumulating evidence, leaving the biotic interaction hypothesis disputed. We aimed to test the hypothesis by quantifying seed predation by insects in a pair of tropical and temperate forest communities with similar elevations. We applied a consistent study design to sample pre-dispersal seeds with systematically set seed traps in 2019-2020 and examined internally feeding insects. The intensity of seed predation was measured and further applied to tropical versus temperate comparison at two levels (cross-species and community-wide). Our results showed every latitudinal pattern associated with different study levels and years, i.e., negative (greater granivory in the tropics in community-wide comparison in 2020), positive (less granivory in the tropics in community-wide and cross-species comparison in 2019), and missing (similar level of granivory in the tropics in cross-species comparisons in 2020). The cross-species level analyses ignore differences among species in seed production and weaken or even lose the latitudinal trend detected by community-wide comparisons. The between-year discrepancy in tropical-temperate comparisons relates to the highly variable annual seed composition in the temperate forest due to mast seeding of dominant species. Our study highlights that long-term community-level researches across biomes are essential to assess the latitudinal biotic interaction hypothesis.

opencc-by-4.0Apr 2022View details →

Simulated tropical stratospheric upwelling and O$_{3}$ interactions with the 1D RCE model konrad

Model output of the control and CO$_{2}$-doubling experiments with the 1D radiative-convective equilibrium (RCE) model `konrad`. The model output consists of temperature, atmospheric composition, radiative flux, heating rate profiles, time series of the convective top, surface temperature, and the net radiative flux at the top of the atmosphere. It also includes metadata such as the parameters used for each run. The experiments varied the relative humidity profile, the representation of O$_{3}$ chemistry, and, more importantly, a parameterization of the cooling due to the tropical stratospheric upwelling caused by the Brewer-Dobson Circulation. With the dataset, one can study the effects the tropical stratospheric upwelling on the tropical equilibrium climate sensitivity.