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opencc-by-4.0Jan 2022View details →

Figure 4 in Uvariopsis dicaprio (Annonaceae) a new tree species with notes on its pollination biology, and the Critically Endangered narrowly endemic plant species of the Ebo Forest, Cameroon

Figure 4 Global distribution of Uvariopsis dicaprio, together with U. korupensis and U. submontana. Full-size DOI: 10.7717/peerj.12614/fig-4

opencc-by-4.0Jan 2022View details →

Figure 1 in Uvariopsis dicaprio (Annonaceae) a new tree species with notes on its pollination biology, and the Critically Endangered narrowly endemic plant species of the Ebo Forest, Cameroon

Figure 1 Uvariopsis dicaprio. Cauliflorous inflorescences on trunk. Photo Lorna MacKinnon. Full-size DOI: 10.7717/peerj.12614/fig-1

opencc-by-4.0Jan 2022View details →

Figure 2 in Uvariopsis dicaprio (Annonaceae) a new tree species with notes on its pollination biology, and the Critically Endangered narrowly endemic plant species of the Ebo Forest, Cameroon

Figure 2 Uvariopsis dicaprio. Trunk apex with cauliflorous flowers and canopy. Photo Lorna MacKinnon. Full-size DOI: 10.7717/peerj.12614/fig-2

opencc-zeroMar 2022View details →

The implications of incongruence between gene tree and species tree topologies for divergence time estimation

Phylogenetic analyses are increasingly being performed with datasets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences on divergence time estimation has not been fully investigated. Using a series of simulation experiments and empirical analyses, we demonstrate that when topological incongruence between gene trees and the species tree is not accounted for, the temporal duration of branches in regions of the species tree that are affected by incongruence is underestimated, whilst the duration of other branches is considerably overestimated. This effect becomes more pronounced with higher levels of topological incongruence. We show that this pattern results from erroneous estimation of the number of substitutions along branches in the species tree, although the effect is modulated by the assumptions inherent to divergence time estimation, such as those relating to the fossil record or among-branch-substitution-rate variation. By only analysing loci with gene trees that are topologically congruent with the species tree, or only taking into account the branches from each gene tree that are topologically congruent with species tree, we demonstrate that the effects of topological incongruence can be ameliorated. Nonetheless, even when topologically congruent gene trees or topologically congruent branches are selected, error in divergence time estimates remains. This stems from temporal incongruences between divergence times in species trees and divergence times in gene trees, and more importantly, the difficulty of incorporating necessary assumptions for divergence time estimation.

opencc-by-4.0May 2022View details →

Decomposition, topology, properties, and graphs of woody crown networks of 15 tree species of Cerrado vegetation

Data of decomposition, topology, properties, and the corresponding graphs of 15 adult tree species of Cerrado vegetation, sensu stricto physiognomy. The woody crown networks (WCN) representations in a bidimensional space were obtained by drawing followed the methodology described by Prado et al. (2020, Prado, C.H.B.A., Trovão, D.M.B.M., Souza, J.P., 2020. A network model for determining the woody crown's decomposition, topology, and properties. Journal of Theoretical Biology, v. 499, p. 110318. https://doi.org/<a href="https://www.x-mol.com/paperRedirect/1258515479077781504">10.1016/j.jtbi.2020.110318</a>.). The branching regions were the nodes, and the woody crown segments connecting the nodes or merely emerging from them were the connectors. Those trees grew under natural conditions in a most common (sensu stricto) physiognomy of Cerrado vegetation, in a reservoir of 86 ha, located at 850 m above sea level in São Carlos city, São Paulo state, Brazil, at 21°58'- 22°00'S and 47°51'-47°52'W. Following the Köppen climatic classification, this region is between Aw and Cwa, a tropical climate with dry winter and wet summer. The rainy season occurs between October-March, and the dry season between April and September.

opencc-by-4.0May 2022View details →

Polymorphism-aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes

Supplementary files of Polymorphism-aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes by Borges, Boussau, Höhna, Pereira and Kosiol

opencc-zeroJun 2022View details →

Great tits (Parus major) flexibly learn that herbivore-induced plant volatiles indicate prey location – an experimental evidence with two tree species

1. When searching for food, great tits (Parus major) can use herbivore-induced plant volatiles (HIPVs) as an indicator of arthropod presence. Their ability to detect HIPVs was shown to be learned, and not innate, yet the flexibility and generalization of learning remains unclear. 2. We studied if, and if so how, naïve and trained great tits (Parus major) discriminate between herbivore-induced and non-induced saplings of Scotch elm (Ulmus glabra) and cattley guava (Psidium cattleyanum). We chemically analysed the used plants and showed that their HIPVs differed significantly and overlapped only in a few compounds. 3. Birds trained to discriminate between herbivore-induced and non-induced saplings preferred the herbivore-induced saplings of the plant species they were trained to. Naïve birds did not show any preferences. Our results indicate that the attraction of great tits to herbivore-induced plants is not innate, rather it is a skill that can be acquired through learning, one tree species at a time. 4. We demonstrate that the ability to learn to associate HIPVs with food reward is flexible, expressed to both tested plant species, even if the plant species has not coevolved with the bird species (i.e. guava). Our results imply that the birds are not capable of generalising HIPVs among tree species but suggest that they either learn to detect individual compounds or associate whole bouquets with food rewards.

opencc-zeroJul 2022View details →

Data from: Improving quartet graph construction for scalable and accurate species tree estimation from gene trees

Summary methods are one of the dominant approaches for estimating species trees from genome-scale data. However, they can fail to produce accurate species trees when the input gene trees are highly discordant due to gene tree estimation error as well as biological processes, like incomplete lineage sorting. Here, we introduce a new summary method TREE-QMC that offers improved accuracy and scalability under these challenging scenarios. TREE-QMC builds upon the algorithmic framework of QMC (Snir and Rao 2010) and its weighted version wQMC (Avni et al. 2014). Their approach takes weighted quartets (four-leaf trees) as input and builds a species tree in a divide-and-conquer fashion, at each step constructing a graph and seeking its max cut. We improve upon this methodology in two ways. First, we address scalability by providing an algorithm to construct the graph directly from the input gene trees. By skipping the quartet weighting step, TREE-QMC has a time complexity of O(n^3 k) with some assumptions on subproblem sizes, where n is the number of species and k is the number of gene trees. Second, we address accuracy by normalizing the quartet weights to account for "artificial taxa," which are introduced during the divide phase so that solutions on subproblems can be combined during the conquer phase. Together, these contributions enable TREE-QMC to outperform the leading methods (ASTRAL-III, FASTRAL, wQFM) in an extensive simulation study. We also present the application of these methods to an avian phylogenomics data set.

opencc-by-4.0Jul 2022View details →

Bark and sapwood allometry for fourteen North American tree species

Measurements of sapwood and bark thickness for fourteen North American tree species, based on visual inspection of 651 tree cores. The recorded values include: species name, stem diameter at the breast height (1.3 m above the ground surface; DBH in cm), bark thickness (cm), and sapwood thickness (cm). A detailed documentation of this dataset as well as the site description where the samples were collected are provided in the associated publication (https://doi.org/10.1016/j.agrformet.2022.109092).

opencc-by-4.0Apr 2022View details →

Figure 2. Mitotype tree and distribution maps for 98 in Integrative taxonomy reveals cryptic diversity in North American Lasius ants, and an overlooked introduced species

Figure 2. Mitotype tree and distribution maps for 98 DNA-barcodes belonging to 7 mitotypes of the ant Lasius niger (blue, n = 70) and 15 mitotypes of L. ponderosae sp. nov. (red, n = 28). The red dashed line delimits the expected natural range of L. ponderosae sp. nov.53 Maps have been created using the free R-package "ggmap" v3.0.0 (https://github.com/dkahle/ggmap) in R v4.1.1. Map tiles by Stamen Design, under CC BY 3.0.

opencc-zeroAug 2022View details →

Evidence of climate-driven selection on tree traits and trait plasticity across the climatic range of a riparian foundation species

Selection on quantitative traits by heterogeneous climatic conditions can lead to substantial trait variation across a species range. In the context of rapidly changing environments, however, it is equally important to understand selection on trait plasticity. To evaluate the role of selection in driving divergences in traits and their associated plasticities within a widespread species, we compared molecular and quantitative trait variation in Populus fremontii (Fremont cottonwood), a foundation riparian distributed throughout Arizona. Using SNP data and genotypes from 16 populations reciprocally planted in three common gardens, we first performed QST-FST analyses to detect selection on traits and trait plasticity. We then explored the environmental drivers of selection using trait-climate and plasticity-climate regressions. Three major findings emerged: 1) There was significant genetic variation in traits expressed in each of the common gardens and in the phenotypic plasticity of traits across gardens, both of which were heritable. 2) Based on QST-FST comparisons, there was evidence of selection in all traits measured; however, this result varied from no effect in one garden to highly significant in another, indicating that detection of past selection is environmentally dependent. We also found strong evidence of divergent selection on plasticity across environments for two traits. 3) Traits and/or their plasticity were often correlated with population source climate (R2 up to 0.77 and 0.66, respectively). These results suggest that steep climate gradients across the Southwest have played a major role in shaping the evolution of divergent phenotypic responses in populations and genotypes now experiencing climate change.

opencc-by-4.0Sep 2022View details →

A deep learning dataset for savanna tree species in Northern Australia

We present a baseline deep learning dataset of 2547 polygons for 36 tree species in Northern Australia. Polygons were drawn on imagery that was collected using Remotely Piloted Aircraft System (RPAS). The dataset consists of: <ul> <li>7 orthomosaics </li> <li>7 shape files with polygon annotations </li> <li>1 training dataset in COCO format</li> <li>1 validation dataset in COCO format</li> </ul> Training and validation datasets were derived from the orthomosaics by tiling each image at 1024x1024 pixel size with 512 pixel step size (overlap).  To perform deep learning model training with this dataset go to https://github.com/ajansenn/SavannaTreeAI for more information.

Fig. 16. – Diospyros quadrangularis G.E. Schatz & Lowry. A in Taxonomic studies of Diospyros (Ebenaceae) from the Malagasy region. VI. New species of large trees from Madagascar

Fig. 16. – Diospyros quadrangularis G.E. Schatz & Lowry. A. Branch; B. Fruiting branch with stem cross-sections; C. Detail of leaf (adaxial surface); D. Fruits.

Fig. 18. – Diospyros taikintana G.E. Schatz & Lowry. A in Taxonomic studies of Diospyros (Ebenaceae) from the Malagasy region. VI. New species of large trees from Madagascar

Fig. 18. – Diospyros taikintana G.E. Schatz & Lowry. A. Branch with flower buds; B. Branch with fruits; C. Detail of leaf venation (abaxial surface); D. Detail of flower bud with subtending bracts; E. Fruit (seen from side); F. Fruit (seen from above).

Fig. 14. – Diospyros melanocarpa G.E. Schatz & Lowry. A in Taxonomic studies of Diospyros (Ebenaceae) from the Malagasy region. VI. New species of large trees from Madagascar

Fig. 14. – Diospyros melanocarpa G.E. Schatz & Lowry. A. Branch in fruit; B. Fruit; C. Fruit (seen from above); D. Detail of leaf (adaxial surface). [A–D: Service Forestier 18343, P] [Drawing: Alain Jouy]

Fig. 15. – Diospyros mimusops G.E. Schatz & Lowry. A in Taxonomic studies of Diospyros (Ebenaceae) from the Malagasy region. VI. New species of large trees from Madagascar

Fig. 15. – Diospyros mimusops G.E. Schatz & Lowry. A. Branch with fruit; B. Branch with male inflorescences; C. Detail of leaf (abaxial surface); D. Schematic section of male flower; E. Fruit.

Fig. 13 in Taxonomic studies of Diospyros (Ebenaceae) from the Malagasy region. VI. New species of large trees from Madagascar

Fig. 13. – Photographs of Diospyros L. species. A. Diospyros malandy H.N. Rakouth, R. Randrianaivo, G.E. Schatz & Lowry,

Fig. 17. – Diospyros rakotovaoi G.E. Schatz & Lowry. A in Taxonomic studies of Diospyros (Ebenaceae) from the Malagasy region. VI. New species of large trees from Madagascar

Fig. 17. – Diospyros rakotovaoi G.E. Schatz & Lowry. A. Branch with fruits; B. Detail of leaf (abaxial surface); C. Branch with male inflorescences; D. Fruiting calyx (seen from below); E. Male flower; F. Schematic section of male flower.

Fig. 12. – Diospyros malandy H.N. Rakouth, R. Randrianaivo, G.E. Schatz & Lowry. A in Taxonomic studies of Diospyros (Ebenaceae) from the Malagasy region. VI. New species of large trees from Madagascar

Fig. 12. – Diospyros malandy H.N. Rakouth, R. Randrianaivo, G.E. Schatz & Lowry. A. Branch in fruit; B. Detail of leaf (adaxial surface); C. Fruit; D. Fruiting calyx (seen from below).

Fig. 10. – Diospyros grandiflora G.E. Schatz & Lowry. A in Taxonomic studies of Diospyros (Ebenaceae) from the Malagasy region. VI. New species of large trees from Madagascar

Fig. 10. – Diospyros grandiflora G.E. Schatz & Lowry. A. Branch in fruit; B. Branch with female flowers; C. Schematic section of female flower; D. Corolla of female flower; E. Fruit.