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Terrestrial lidar data collected from four large tropical rainforest trees in Floresta Nacional de Caxiuanã
<p>Title<br> -----</p> <p>Terrestrial lidar data collected from four large tropical rainforest trees in Floresta Nacional de Caxiuanã</p> <p>Authors<br> -------</p> <p>A. Burt<br> M. Boni Vicari<br> A. C. L. da Costa<br> I. Coughlin<br> P. Meir<br> L. Rowland<br> M. Disney</p> <p>Contact<br> -------</p> <p>a.burt@ucl.ac.uk</p> <p>License<br> -------</p> <p>These data are distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC BY 4.0) - see the LICENSE file for details.</p> <p>Overview<br> --------</p> <p>Terrestrial lidar data were acquired from four large tropical rainforest trees prior to harvest (diameter range: 0.6-1.2m, height range: 30-46m) in a natural closed forest stand in Floresta Nacional de Caxiuanã, Pará, Brazil (approx. coordinates in the WGS-84 datum: -1.798, -51.435 degrees), during August/October 2018.<br> This dataset includes: i) raw lidar data, ii) tree-level point clouds, and iii) quantitative structural models.<br> A complete description of the four trees, these data, and the companion destructive harvest data can be found in our paper entitled: ‘New insights into large tropical tree mass and structure from direct harvest and terrestrial lidar’.</p> <p>Acquisition<br> -----------</p> <p>Neighbouring vegetation surrounding each tree was removed before data collection.<br> Lidar data were acquired using a RIEGL VZ-400 terrestrial laser scanner.<br> A minimum of 16 scans (upright and tilt) were collected from 8 scan positions around each tree.<br> The angular step between sequentially fired pulses was 0.04 degrees, and the distance between scanner and tree varied.<br> This arrangement provided a 45 degree sampling arc around each tree, and a complete sample of the scene from each position.<br> The laser pulse has a wavelength of 1550nm, a beam divergence of 0.35mrad, and the diameter of the footprint at emission is 7mm.<br> The instrument was in ‘High Speed Mode’ (pulse repetition rate: 300kHZ), ‘Near Range Activation’ was off (minimum measurement range: 1.5m), and waveforms were not stored. </p> <p>Processing<br> ----------</p> <p>i) Individual scans were registered onto a common coordinate system using RIEGL RiSCAN PRO (v2.7.0, http://riegl.com).<br> ii) Tree-level point clouds were extracted from the larger-area point cloud using treeseg (v0.2.0, https://github.com/apburt/treeseg).<br> iii) Points were classified as returns from wood or leaf material using TLSeparation (v1.2.1.5, https://github.com/TLSeparation).<br> iv) Points from buttresses were manually removed using CloudCompare (v2.10.3, https://cloudcompare.org).<br> v) Quantitative structural models were constructed using TreeQSM (v2.3.2, https://github.com/InverseTampere/TreeQSM) via optqsm (v0.1.0, https://github.com/apburt/optqsm). </p> <p>File and directory naming convention<br> ------------------------------------</p> <p>The four trees are identified: CAX-H_T1, CAX-H_T2, CAX-H_T3 and CAX-H_T4.<br> The various files and directories are described as follows: </p> <p>./CAXH-H/<br> ├───CAX-H_T1/ (Directory: tree-level directories)<br> ├───CAX-H_T2/<br> ├───CAX-H_T3/<br> ├───CAX-H_T4/<br> │ ├───2018-10-06.001.riproject/<br> │ │ ├───ScanPos001/ (Directory: individual scan directories containing raw lidar data and other auxiliary files; odd: upright, even: tilt)<br> │ │ ├───ScanPos.../<br> │ │ ├───ScanPos020/<br> │ │ │ ├───181006_194253.rxp (File: measurement data stream)<br> │ │ │ ├───181006_194253.mon.rxp (File: monitoring data stream) <br> │ │ ├───matrix/ (Directory: contains the registration matrices)<br> │ │ │ ├───001.dat<br> │ │ │ ├───....dat<br> │ │ │ ├───020.dat (File: 3x4 matrix used to rotate and translate scan 20 into the coordinate system of scan 1)<br> │ │ ├───clouds/ (Directory: contains tree-level point clouds)<br> │ │ │ ├───CAXH_T4.txt (File: point cloud of CAX-H_T4 as extracted by treeseg)<br> │ │ │ ├───CAXH_T4nb.txt (File: CAXH_T4.txt with buttress points manually removed using CloudCompare)<br> │ │ │ ├───CAXH_T4w.txt (File: CAXH_T4.txt with leafy returns removed using TLSeparation)<br> │ │ │ ├───CAXH_T4l.txt (File: CAXH_T4.txt with woody returns removed using TLSeparation)<br> │ │ │ ├───CAXH_T4wnb.txt (File: CAXH_T4.txt with buttress points manually removed using CloudCompare, and leafy returns removed using TLSeparation)<br> │ │ ├───models/ (Directory: contains quantitative structural models constructed from the tree-level point clouds)<br> │ │ │ ├───CAXH_T4.mat (File: quantitative structural model of CAXH_T4.txt)<br> │ │ │ ├───CAXH_T4nb.mat<br> │ │ │ ├───CAXH_T4w.mat<br> │ │ │ ├───CAXH_T4wnb.mat<br> │ │ │ ├───CAXH_T4.models.dat (File: reports the volume (m3) and standard deviation (m3) of the QSMs)<br> │ │ │ ├───intermediate/ (Directory: contains intermediate QSMs generated by optqsm)<br> │ │ │ │ ├───CAXH_T4/<br> │ │ │ │ ├───CAXH_T4nb/<br> │ │ │ │ ├───CAXH_T4w/<br> │ │ │ │ ├───CAXH_T4wnb/<br> │ │ │ │ │ ├───CAXH_T4wnb-1.mat<br> │ │ │ │ │ ├───CAXH_T4wnb-....mat<br> │ │ │ │ │ ├───CAXH_T4wnb-10.mat</p>
Strong genetic differentiation on a small geographic scale in the Neotropical rainforest understory tree Paypayrola blanchetiana (Violaceae)
Self-incompatible plants as well as common plant species are expected to be especially vulnerable to the deleterious effects of fragmentation on genetic diversity. Paypayrola blanchetiana (Violaceae) is a common, self-incompatible understory tree in the East Brazilian Atlantic forest. Its autochorous seed dispersal and occurrence in dense, well-separated clusters makes it an interesting model for studies of gene flow and genetic structuring on a small geographic scale. A previous study has found remarkably low fruit set and frequent seed abortions in this species in several populations situated in forest fragments. We tested the hypothesis that P. blanchetiana is affected by inbreeding and loss of genetic diversity in a fragmented landscape. Nine nuclear and three plastid microsatellite loci were genotyped for 285 individuals (149 adult trees and 136 saplings) across seven populations in five forest fragments in a 240 km2 sugarcane-rainforest matrix. We found a low to moderate genetic diversity in nuclear loci of P. blanchetiana, population structuring on a small geographical scale and high levels of inbreeding. Haplotype distributions confirmed that seed dispersal is very limited. There were, however, no signs for lower genetic diversity or higher inbreeding in populations situated in the smallest forest fragments. Furthermore, genetic diversity was not lower in the sapling cohort, which was created in post-fragmentation condition. Therefore, we may be witnessing the genetic consequences of this species biology, rather than immediate effects of fragmentation.
Figure 2 from: Gillespie LJ, Cardinal-McTeague WM, Wurdack KJ (2020) Monadelpha (Euphorbiaceae, Plukenetieae), a new genus of Tragiinae from the Amazon rainforest of Venezuela and Brazil. PhytoKeys 169: 119-135. https://doi.org/10.3897/phytokeys.169.59244
Figure 2 Pollen morphology of Monadelpha guayanensisA SEM of pollen grain showing polar view with five colpi B closeup of mesocolpium and two colpi. Source: Stergios & Aymard 9182 (MO). Figure reproduced from Gillespie (1994b) with permission from the Missouri Botanical Garden Press.
Figure 3 from: Gillespie LJ, Cardinal-McTeague WM, Wurdack KJ (2020) Monadelpha (Euphorbiaceae, Plukenetieae), a new genus of Tragiinae from the Amazon rainforest of Venezuela and Brazil. PhytoKeys 169: 119-135. https://doi.org/10.3897/phytokeys.169.59244
Figure 3 Phylogenetic relationships of Monadelpha. Bayesian 50% majority rule consensus tree for the 159-accession (80 taxa) ITS dataset of Tragiinae, demonstrating the distinct phylogenetic placement of Monadelpha (subclade T6/9). Subclade naming system follows Cardinal-McTeague and Gillespie (2016) with minor adjustments. Branches are labeled with Bayesian posterior probabilities (PP) and maximum likelihood bootstrap percentages (MLBP). Bold branches indicate strong support (PP >0.95, MLBP >85) and coloured boxes indicate general distribution (New World = blue, Old World = yellow).
Figure 1 from: Gillespie LJ, Cardinal-McTeague WM, Wurdack KJ (2020) Monadelpha (Euphorbiaceae, Plukenetieae), a new genus of Tragiinae from the Amazon rainforest of Venezuela and Brazil. PhytoKeys 169: 119-135. https://doi.org/10.3897/phytokeys.169.59244
Figure 1 Illustration of Monadelpha guayanensis. A habit showing staminate inflorescence B staminate flower C habit showing infructescence D pistillate flower E mericarp of dehisced capsule with enclosed seed F seed, lateral view with hilum at top. Sources: A, B based on Stergios & Aymard 9182 (MO) C–F based on Stergios & Aymard 9182 (NY). Illustration by Cathy Pasquale reproduced from Gillespie (1994b) with permission from the Missouri Botanical Garden Press.
FIGURE 4 in A new genus and species ofAgraeciini (Orthoptera: Tettigoniidae: Conocephalinae) from Amazon Rainforest
FIGURE 4. Distribution map of Wuyjugu pizai.
Supplementary material 2 from: Basset Y, Donoso DA, Hajibabaei M, Wright MTG, Perez KHJ, Lamarre GPA, De León LF, Palacios-Vargas JG, Castaño-Meneses G, Rivera M, Perez F, Bobadilla R, Lopez Y, Ramirez JA, Barrios H (2020) Methodological considerations for monitoring soil/litter arthropods in tropical rainforests using DNA metabarcoding, with a special emphasis on ants, springtails and termites. Metabarcoding and Metagenomics 4: e58572. https://doi.org/10.3897/mbmg.4.58572
Appendix S2
FIGURE 14. Male Tico gen. n in A new genus and two new species of planthopper in the tribe Cenchreini (Hemiptera: Auchenorrhyncha: Derbidae) from lowland tropical rainforest in Costa Rica
FIGURE 14. Male Tico gen. n. pseudosororius sp. n. wing venation; black = vein, green = cell.
FIGURE 6. Male Tico gen. n in A new genus and two new species of planthopper in the tribe Cenchreini (Hemiptera: Auchenorrhyncha: Derbidae) from lowland tropical rainforest in Costa Rica
FIGURE 6. Male Tico gen. n. emmettcarri sp. n. wing venation; black = vein, green = cell.
Genotyping by sequencing data of five legume tree species widespread in the rainforests of West and Central Africa
<p>Although today the forest cover is continuous in Central Africa this may have not always been the case, as the scarce fossil record in this region suggests that arid conditions might have significantly reduced tree density during the Ice Ages. Our aim was to investigate whether the dry ice-age periods left a genetic signature on tree species that can be used to infer the date of the past fragmentation of the rainforest. We sequenced reduced representation libraries of 182 samples representing five widespread Legume trees and seven outgroups. Phylogenetic analyses identified an early divergent lineage for all species in West Africa (Upper Guinea), and two clades in Central Africa: Lower Guinea-North and Lower Guinea-South. As the structure separating the Northern and Southern clades -congruent across species- cannot be explained by geographic barriers, we tested other hypotheses with demographic model testing using ∂a∂I. The best estimates indicate that the two clades split between the Upper Pliocene and the Pleistocene, a date compatible with forest fragmentation driven by ice-age climatic oscillations. Furthermore, we found remarkably older split dates for the shade-tolerant tree species with non-assisted seed dispersal than for light-demanding species with long-distance wind dispersal. Different recolonisation abilities after recurrent cycles of forest fragmentation seem to explain why species with long-distance dispersal show more recent genetic admixture between the two clades than species with limited seed dispersal. Despite their old history, our results depict the African rainforests as a dynamic biome where tree species have expanded relatively recently after the last glaciation.</p>
Data from: Realistic heat pulses protect frogs from disease under simulated rainforest frog thermal regimes
Recent emergences of fungal diseases have caused catastrophic global losses of biodiversity. Temperature is one of the most important factors influencing host-fungus associations but the effects of temperature variability on disease development are rarely examined. The chytrid pathogen Batrachochytrium dendrobatidis (Bd) has had severe effects on populations of hundreds of rainforest-endemic amphibian species but we know little about the effects of rainforest-specific host body temperature cycles on infection patterns. To address this challenge, we used body temperature regimes experienced in nature by frogs in the Australian Wet Tropics to guide a controlled experiment investigating the effects of body temperature fluctuations on infection patterns in a model host (Litoria spenceri), with emphasis on exposing frogs to realistic 'heat pulses' that only marginally exceed the thermal optimum of the fungus. We then exposed cultured Bd to an expanded array of heat pulse treatments and measured parameters of population growth to help resolve the role of host immunity in our in vivo results. Infections developed more slowly in frogs exposed to daily 4-h heat pulses of 26°C or 29°C than in frogs in constant temperature treatments without heat pulses (control). Frogs that experienced heat pulses were also less likely to exceed infection intensities at which morbidity and mortality become likely. Ten of 11 (91%) frogs from the daily 29°C heat pulse treatment even cleared their infections after approximately nine weeks. Cultured Bd also grew more slowly when exposed to heat pulses than in constant-temperature control treatments, suggesting that mild heat pulses have direct negative effects on Bd growth in nature, but precluding us from determining whether there was a concurrent benefit of heat pulses to host immunity. Our results suggest that even in habitats where average temperatures may be suitable for fungal growth and reproduction, infection risk or the outcome of existing infections may be heavily influenced by short but frequent exposures to temperatures that only slightly exceed the optimum for the fungus. Our findings provide support for management interventions that promote warm microenvironments for hosts, such as small-scale removal of branches overhanging critical habitat or provision of artificial heat sources.
Data from: Testing hypotheses for genealogical discordance in a rainforest lizard
Genealogical discordance, or when different genes tell distinct stories although they evolved under a shared history, often emerges from either coalescent stochasticity or introgression. In this study, we present a strong case of mito-nuclear genealogical discordance in the Australian rainforest lizard species complex of Saproscincus basiliscus and S. lewisi. One of the lineages that comprises this complex, the Southern S. basiliscus lineage, is deeply divergent at the mito- chondrial genome but shows markedly less divergence at the nuclear genome. By placing our results in a comparative context and reconstructing the lineages' demography via multi-locus and coalescent-based Approximate Bayesian Computation (ABC) methods, we test hypotheses for how coalescent variance and introgression contribute to this pattern. These analyses suggest that the observed genealogical discordance likely results from introgression. Further, to generate such strong discordance, introgression probably acted in concert with other factors promoting asymmetric gene flow between the mitochondrial and nuclear genomes, such as selection or sex-biased dispersal. This study offers a framework for testing sources of genealogical discordance and suggests that historical introgression can be an important force in shaping the genetic diversity of species and their populations.
Data from: Trade-offs for butterfly alpha and beta diversity in human-modified landscapes and tropical rainforests
The accelerating expansion of human populations and associated economic activity across the globe have made maintaining large, intact natural areas increasingly challenging. The difficulty of preserving large intact landscapes in the presence of growing human populations has led to a growing emphasis on landscape approaches to biodiversity conservation with a complementary strategy focused on improving conservation in human-modified landscapes. This, in turn, is leading to intense debate about the effectiveness of biodiversity conservation in human-modified landscapes and approaches to better support biodiversity in those landscapes. Here, we compared butterfly abundance, alpha richness, and beta diversity in human-modified landscapes [urban, sugarcane] and natural, forested areas to assess the conservation value of human-modified landscapes within the Wet Tropics bioregion of Australia. We used fruit-baited traps to sample butterflies and analyzed abundance and species richness in respective land uses over a one-year period. We also evaluated turnover and spatial variance components of beta diversity to determine the extent of change in temporal and spatial variation in community composition. Forests supported the largest numbers of butterflies, but were lowest in each, alpha species richness, beta turnover, and the spatial beta diversity. Sugarcane supported higher species richness, demonstrating the potential for conservation at local scales in human-modified landscapes. In contrast, beta diversity was highest in urban areas, likely driven by spatial and temporal variation in plant composition within the urban landscapes. Thus, while improving conservation on human-modified landscapes may improve local alpha richness, conserving variation in natural vegetation is critical for maintaining high beta diversity.
Data from: The insect-focused classification of fruit syndromes in tropical rainforests: an inter-continental comparison
We propose a new classification of rainforest plants into eight fruit syndromes, based on fruit morphology and other traits relevant to fruit-feeding insects. This classification is compared with other systems based on plant morphology or traits relevant to vertebrate fruit dispersers. Our syndromes are based on fruits sampled from 1,192 plant species at three Forest Global Earth Observatory plots: Barro Colorado Island (Panama), Khao Chong (Thailand) and Wanang (Papua New Guinea). The three plots differed widely in fruit syndrome composition. Plant species with fleshy, indehiscent fruits containing multiple seeds were important at all three sites. However, in Panama a high proportion of species had dry fruits, while in New Guinea and Thailand, species with fleshy drupes and thin mesocarps were dominant. Species with dry, winged seeds that do not develop as capsules were important in Thailand, reflecting the local importance of Dipterocarpaceae. These differences can also determine differences among frugivorous insect communities. Fruit syndromes and colours were phylogenetically flexible traits at the scale studied, as only three of the eight seed syndromes, and one of the 10 colours, showed significant phylogenetic clustering at either genus or family levels. Plant phylogeny was, however, the most important factor explaining differences in overall fruit syndrome composition among individual plant families or genera across the three study sites.
Data from: Trade-offs in juvenile growth potential vs. shade tolerance among subtropical rainforest trees on soils of contrasting fertility
Plant adaptation to gradients of light availability involves a well-studied functional trade-off, as does adaptation to gradients of nutrient availability. However, little is known about how these two major trade-offs interact, and thus, it remains unclear whether and how the nature of the growth–shade tolerance trade-off differs on soils of contrasting fertility. We asked whether juvenile growth–shade tolerance trade-offs differed in slope and elevation between tree assemblages on nutrient-rich basalt and nutrient-poor rhyolite soils in an Australian subtropical rain forest. We measured the growth of, and the range of light environments occupied by, juveniles (40–120 cm tall) of eight basalt specialists, six rhyolite specialists, and one generalist that was common on both substrates. In situ minimum light requirements were estimated from the 5th percentile of the distribution of naturally regenerated juveniles in relation to daily light transmittance. Stem growth was measured for 12–16 months across a wide range of light environments to estimate the light compensation point of growth of each species. Light compensation points of growth showed nearly a 1 : 1 correspondence with in situ minimum light requirements of species, indicating that whole-plant carbon balance is a key driver of ecological success in low light. Minimum light requirements were negatively correlated with relative growth rate in low light, but correlated positively with growth in high light. Soil type had no effect on either the slope or the elevation of this trade-off, all species aligning around a common growth–shade tolerance trade-off, but our results do show a wider range of growth rates and shade tolerance on the nutrient-rich basalt soil than on the nutrient-poor rhyolite. Our results suggest that adaptation to light availability involves fundamentally similar trade-offs on these two substrates of differing fertility. However, a wider range of growth rates and shade tolerance on the nutrient-rich basalt soil than on the nutrient-poor rhyolite may help to explain the higher species richness and greater structural complexity of forest stands on the former substrate.
FIGURE 1 in A third species of the rare frog genus Holoaden (Terrarana, Strabomantidae) from a montane rainforest area of southeastern Brazil
FIGURE 1. Holoaden pholeter sp. nov., holotype (MNRJ 51475, adult female, SVL 44.6 mm), in life.
FIGURE 2 in New species of Crotonia (Acari: Oribatida) from Tasmania Rainforest, and the habitat preferences of Crotoniidae
FIGURE 2. Crotonia pyemaireneri sp. nov. Female a) dorsal; b) ventral; c) caudal apophyses.
FIGURE 3. Crotonia ovata Olszanowski, 2000, male a in New species of Crotonia (Acari: Oribatida) from Tasmania Rainforest, and the habitat preferences of Crotoniidae
FIGURE 3. Crotonia ovata Olszanowski, 2000, male a) dorsal; b) ventral.
FIGURE 1 in New species of Crotonia (Acari: Oribatida) from Tasmania Rainforest, and the habitat preferences of Crotoniidae
FIGURE 1. Crotonia tasmaniana sp. nov. Female a) dorsal; b) ventral
FIGURE 2 in A new mid-altitude rainforest species of Typhlops (Serpentes: Typhlopidae) from Madagascar with notes on the taxonomic status of T. boettgeri Boulenger, T. microcephalus Werner, and T. capensis Rendahl
FIGURE 2. Typhlops andasibensis sp. nov., lateral view of head of paratype, ZSM 53/2005.
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