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opencc-zeroJan 2016View details →

Supporting raw data for: The key role of the largest extant neotropical frugivore (Tapirus terrestris) in promoting admixture of plant genotypes across the landscape

These files contain the supporting raw data of the journal article The key role of the largest extant neotropical frugivore (Tapirus terrestris) in promoting admixture of plant genotypes across the landscape. They include the geographical coordinates and genotypes (microsatellites) of 259 palm (Syagrus romanzoffiana) individuals analyzed in the mentioned study, as well as an example of one input file for conducting data analysis with the software COLONY 2.0. A text file (´Readme') describing this archived supporting data in further detail is also provided.

opencc-by-4.0Aug 2022View details →

Text-fig. 1. a: Po Plain and foothills of the Northern Apennine in Northern Italy (inset) with the location of Oriolo (black star) and other Early and Middle Pleistocene plant localities, Enza and Stirone. Red lines indicate the frontal thrust arcs (modified from Martinetto et al. 2015). b: The "La Salita" section, Oriolo and chronology of the two "Sabbie gialle" cycles based on large mammals and palaeomagnetic correlation (modified from Toniato et al. 2017; IMMS 2020* [Italian Mediterranean Marine Stages] updated from Cohen and Gibbars 2020; GTS 2021* [Global Time Scale] updated from Head et al. 2021). c: Quarry "La Salita", Oriolo, in 1987. Main unconformities (U) separating the two "Sabbie gialle" cycles and terrestrial deposits on top are shown. Leaf symbols indicate the positions of some of the layers rich in fossil leaves (photo by G. B. Vai, modified). d: Surroundings of Faenza with the location of Oriolo and adjacent coeval sites yielding plant macrofossils. in The Late Early Pleistocene Flora Of Oriolo, Faenza (Italy): Assembly Of The Modern Forest Biome

Text-fig. 1. a: Po Plain and foothills of the Northern Apennine in Northern Italy (inset) with the location of Oriolo (black star) and other Early and Middle Pleistocene plant localities, Enza and Stirone. Red lines indicate the frontal thrust arcs (modified from Martinetto et al. 2015). b: The "La Salita" section, Oriolo and chronology of the two "Sabbie gialle" cycles based on large mammals and palaeomagnetic correlation (modified from Toniato et al. 2017; IMMS 2020* [Italian Mediterranean Marine Stages] updated from Cohen and Gibbars 2020; GTS 2021* [Global Time Scale] updated from Head et al. 2021). c: Quarry "La Salita", Oriolo, in 1987. Main unconformities (U) separating the two "Sabbie gialle" cycles and terrestrial deposits on top are shown. Leaf symbols indicate the positions of some of the layers rich in fossil leaves (photo by G. B. Vai, modified). d: Surroundings of Faenza with the location of Oriolo and adjacent coeval sites yielding plant macrofossils.

Linked collectors and determiners for: NEON Biorepository Terrestrial Plant Collection (Canopy Foliage).

Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Terrestrial Plant Collection (Canopy Foliage)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/f0b88eb8-cfc1-4989-861d-30521645ce11">https://bionomia.net/dataset/f0b88eb8-cfc1-4989-861d-30521645ce11</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/f0b88eb8-cfc1-4989-861d-30521645ce11">https://gbif.org/dataset/f0b88eb8-cfc1-4989-861d-30521645ce11</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: NEON Biorepository Terrestrial Plant Collection (Leaf Tissue).

Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Terrestrial Plant Collection (Leaf Tissue)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/edc4ab0b-1ad7-4e53-a741-4423d0196a06">https://bionomia.net/dataset/edc4ab0b-1ad7-4e53-a741-4423d0196a06</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/edc4ab0b-1ad7-4e53-a741-4423d0196a06">https://gbif.org/dataset/edc4ab0b-1ad7-4e53-a741-4423d0196a06</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: NEON Biorepository Terrestrial Plant Collection (Herbarium Vouchers).

Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Terrestrial Plant Collection (Herbarium Vouchers)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/3fed506c-d04f-4cd4-b373-bd602572f39b">https://bionomia.net/dataset/3fed506c-d04f-4cd4-b373-bd602572f39b</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/3fed506c-d04f-4cd4-b373-bd602572f39b">https://gbif.org/dataset/3fed506c-d04f-4cd4-b373-bd602572f39b</a>. Formatted as a Frictionless Data package.

opencc-by-4.0Aug 2017View details →

Text-fig. 8. Palaeogene terrestrial fossiliferous deposits of Africa. Note the position of the Tunisian Oligocene deposits, and their obvious interest in terms of geographic position and age (data for the Palaeogene of North Africa are from Tabuce et al. 2000, 2001, 2011, Delmer et al. 2006, Coster et al. 2012, Yans et al. 2014, Solé et al. 2016). Note that Nakwai (Kenya) is no longer considered to be Oligocene. in Arsinoitherium (Embrithopoda) And Other Large Mammals And Plants From The Oligocene Of Tunisia

Text-fig. 8. Palaeogene terrestrial fossiliferous deposits of Africa. Note the position of the Tunisian Oligocene deposits, and their obvious interest in terms of geographic position and age (data for the Palaeogene of North Africa are from Tabuce et al. 2000, 2001, 2011, Delmer et al. 2006, Coster et al. 2012, Yans et al. 2014, Solé et al. 2016). Note that Nakwai (Kenya) is no longer considered to be Oligocene.

dryad40/100

Data from: Water controls the divergent responses of terrestrial plant photosynthesis under nitrogen enrichment

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publicAug 2024View details →

Pattern and driver of the compositional variations in a tropical cloud forest: Comparing vascular epiphytes with terrestrial woody plants

β-diversity patterns (the compositional variations across sites) and their drivers are the major concerns of biodiversity research and conservation practices, whereas such information remains scarce for vascular epiphytes, especially in tropical forest communities. This study aimed to reveal the pattern and driving process of the compositional variations of vascular epiphytes in a tropical cloud forest on Hainan island, southern China, and their differences from those of terrestrial woody plants. To this end, we quantified their between-habitat compositional variations and distinguished the underlying components of β-diversity (nestedness and turnover). We then examined the relative roles of niche-based and neutral processes in driving the compositional variations by using a null model approach. Our results showed that the between-habitat compositional variations were significant for both plant assemblages and stronger in vascular epiphytes than in terrestrial woody plants. The turnover component of β-diversity was significantly stronger in terrestrial woody plants, accounting for 73.16%–80.08% of the variations. By contrast, the nestedness component was significantly stronger in vascular epiphytes and characterized 46.82%–67.5% of the variations. Besides, the compositional variations of both plant assemblages, especially terrestrial woody plants, were generally poorly fitted by the simulated niche-based scenarios but well fitted by the simulated neutral scenarios. Overall, the compositional variations of both plant assemblages were significant and mainly due to dispersal limitation, albeit to varying degrees. Hence, further studies of these plant assemblages at local scales should not be ideologically limited to the niche-based framework. Moreover, the stronger nestedness observed in vascular epiphytes suggests the greater importance of prioritizing conservation efforts in the species-rich habitats for these plants.

opencc-by-4.0Jun 2024View details →

zenodo36/100

Code and data for: Evolutionary assembly of the plant terrestrialization toolkit from protein domains

Evolutionary assembly of the plant terrestrialization toolkit from protein domains <ul> <li>We want to trace the evolutionary predisposition the green lineage had at the time of terrestrialization.</li> <li>Terrestrialization is a complete change in environment from water, and these acted like new and/or intensified stress factors on the green lineage.</li> <li>Thus, in order to trace the evolutionary predisposition which led to successful overcoming of challenges of a new environment, we carefully annotate, dissect and analyse the stress proteome of the extant Green lineage.</li> </ul> Key Concepts <ul> <li>Already existing Concept: <ul> <li>Orthology</li> </ul> </li> <li>New/Redefined Concept <ul> <li>Embryophytic Domain: Protein domain which has an Embryophytic ancestor, that is, present in at least one Bryophyte species and at least one Tracheophyte species</li> <li>Latent Genetic Potential (LGP): Key (functional) Embryophytic protein domains having Last Common Ancestor (LCA) prior to the LCA of protein with corresponding function</li> </ul> </li> </ul> Data: (Figure 1 A) <ul> <li>We take 6 species from Cholorophyte algae lineage, 7 from Streptophyte algae lineage, 5 from Bryophyte lineage and 14 from Tracheophyte lineage. 5 species from Cyanobacteria were taken as an outgroup lineage.</li> </ul> Stress-annotation (Figure 1B) <ul> <li>First 57,796 orthogroups were obtained from 37 proteome. This is computed by using OrthoFinder2.</li> <li>Next we need to annotate stress-related proteins across our dataset. Following are existing ways of annotation: <ul> <li>Extensive experiments have been done on A.thaliana and P.patens in the green lineage. Thus, we stress-annotated 37 proteomes using TAIR10 and PEATmoss respectively. From this method, we stress-annotated 4,902 orthogroups</li> <li>Eggnogmapper is a known tool with an extensive database used for gene ontology purposes. We stress-annotated 17,349 orthogroups.</li> </ul> </li> <li>In order to avoid experimental bias and tool-based randomness we overlap the two methods to have our final stress-annotation. We finally filtered 2,475 stress-annotated orthogroups from 57,796 orthogroups.</li> </ul> Overview of Stress-annotation (Figure 1C, 1D) <ul> <li>To have an overview of stress-annotation, overlaps of stress-annotated protein domains, proteins and orthogroups across our dataset lineages and various response to stresses are shown.</li> </ul> Distribution of Stress-annotation (Figure 2) <ul> <li>Using the overlap annotation approach explained earlier, the stress-annotated orthogroups and corresponding protein domains are in Figure 2A. A standard pattern is observed in both, that is, the unique number of stress orthogroups and protein domains increase from Cyanobacteria to Tracheophytes. The number of proteins and average number of protein domains also increases similarly.</li> <li>Top 10 bursts of protein domains from one lineage to the next is shown in Figure 2B.</li> </ul> Changes in stress-annotation with respect to Protein Domains (Figure 3) <ul> <li>Figure 3 is a 4-dimensional plot with the following parameters: Species(37), Protein Domains (100), Number of Orthgogroups with Protein Domain (size of circle), Number of Proteins with Protein Domain (Color of circle). The plot is sorted from top to bottom based on the number of orthogroups, and the top 100 protein domains are chosen for the plot.</li> <li>This plot is used to express an overview of the most significant occurances of sub- and neo-functionalizations. Here, each orthogroup is considered to be a protein family. 2 protein families can have an overlapping number of functions. That is why there are more than 1 orthogroup which have the same protein domain.</li> </ul> Assembling LGP from protein domains (Figure 4) - refer to Key Concepts to understand LGP <ul> <li>In Figure 1A, we show 2 categories (x/y) of orthogroups at each node (a,b,c,d,e,f). The number y for example at node b indicates the number of orthogroups (4) in Tracheophyta+Bryophyta+Zygnemaotphyceae that have LGP (or key Embryophytic protein domains) in Charophyceae. The number x at node b indicates the number of orthogroups (131) in Tracheophyta+Bryophyta+Zygnemaotphyceae that have LGP in all the rest of the lineages (Charophyceae+Klebsormidiophyceae+Chlorokybophyceae+Mesostigmatophyceae+Chlorophytes) in the figure.</li> <li>Since we are concerned about the LGP for Land Plants (Embryophytes), we look at node a. Next, we functionally annotate 96 orthogroups. 50 annotations that occur the most number of times is shown in Figure 4B.</li> <li>In Figure 4C, we can see in which species the key Embryophytic Domains are present whose proteins and protein families are only seen in Embryophytes.</li> </ul> Thus, from the final figure we can trace the LGP present at the time of terrestrialization in the LCA of Land Plants. Database files: These are intermediate files used in code for different figures. Following is the link to access them:<a href="https://data.mendeley.com/datasets/mnrn7j7hrw/draft?a=b981b40f-01a8-48ff-9d6a-151f6223810c" rel="nofollow">https://data.mendeley.com/datasets/mnrn7j7hrw/draft?a=b981b40f-01a8-48ff-9d6a-151f6223810c</a> [OR]<a href="https://owncloud.gwdg.de/index.php/s/dH3Y4MAHSfbmhrA" rel="nofollow">https://owncloud.gwdg.de/index.php/s/dH3Y4MAHSfbmhrA</a>

opencc-zeroJun 2024View details →

Evolutionary assembly of the plant terrestrialization toolkit from protein domains

Land plants (embryophytes) came about in a momentous evolutionary singularity: plant terrestrialization. This event marks not only the conquest of land by plants but also the massive radiation of embryophytes into a diverse array of novel forms and functions. The unique suite of traits present in the earliest land plants is thought to have been ushered in by a burst genomic novelty. Here, we asked the question of how these bursts were possible. For this, we used phylostratigraphy to explore the (i) initial emergence and (ii) reshuffling of domains to give rise to hallmark environmental response genes of land plants. We pinpoint that a quarter of the embryophytic stress physiology is specific to the lineage, yet a significant portion of this novelty arises not de novo but from re-shuffling and recombining of pre-existing domains. Our data suggest that novel combinations of old genomic substrates shaped the plant terrestrialization toolkit, including hallmark processes in signaling, biotic interactions, and specialized metabolism.

zenodo36/100

Data and Code for "No general support of functional diversity enhancing resilience across terrestrial plant communities"

The data and code provided here is to support the study "No general support of functional diversity enhancing resilience across terrestrial plant communities"  This repository contains the following files:  The code to reproduce main analysisi and graphs in R and HTML format <ul> <li>RcodeNoGeneralSupport.R</li> <li>RcodeNoGeneralSupport.html</li> </ul> The data to be used for the different analyses <ul> <li>ResilienceFDIndices.csv</li> <li>ResilienceFDIndices-BiomassH.csv</li> <li>ResilienceFDIndices-BiomassW.csv</li> <li>ResilienceFDIndices-CompositionW.csv</li> <li>ResilienceFDIndices-Herbaceous.csv</li> <li>ResilienceFDIndices-woody.csv</li> <li>ResilienceSR.csv</li> <li>ResilienceSR-BiomassH.csv</li> <li>ResilienceSR-BiomassW.csv</li> <li>ResilienceSR-CompositionW.csv</li> <li>ResilienceSR-herbaceous.csv</li> <li>ResilienceSR-woody.csv</li> </ul> The detailed information for each variable in each data set <ul> <li>README.txt</li> </ul>

opencc-by-4.0Jan 2024View details →

opencc-zeroJan 2023View details →

Datasets from: Local- and landscape-scale drivers of terrestrial herbaceous plant diversity along a tropical rainfall gradient in Western Ghats, India

This data set contains information on local- and landscape-level terrestrial herbaceous plant diversity and critical abiotic factors along a 36-km East-West transect in Mudumalai Tiger Reserve, Tamil Nadu India. Understory angiosperms with no above-ground wood (secondary cambial growth) were considered as herbaceous plants.

zenodo36/100

Datasets of eponyms for South American plants and Mozambican terrestrial vertebrates

Two datasets containing information on the Eponyms of South American plants and Mozambique's terrestrial vertebrates.

opencc-by-4.0Apr 2023View details →

publicJun 2024View details →

Evolutionary assembly of the plant terrestrialization toolkit from protein domains

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publicApr 2020View details →

Impacts of global environmental change drivers on non-structural carbohydrates in terrestrial plants

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