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opencc-by-4.0Dec 2023View details →

Dataset for: Climate and shared evolutionary history drive trait variation among species of Neotropical understory monocots

Dataset and p-values form phylogenetically generalized least square models accompanying the manuscript "Climate and shared evolutionary history drive trait variation among species of Neotropical understory monocots".

opencc-by-4.0Sep 2022View details →

Shared biophysical mechanisms determine early biofilm architecture development across different bacterial species

These data are the numerical values that underlie the Figures 1 - 4, and the Supplementary Figures 1 - 10 for the article "Shared biophysical mechanisms determine early biofilm architecture development across different bacterial species" by the same authors. The content of the data files is organized according to the figures and figure panels of this article.

opencc-zeroMar 2021View details →

FIG. 2 in Mallomonas vietnamica Gusev, Kezlya & Tran, sp. nov. (Synurales, Chrysophyceae), a new species, that shares some features with fossil taxa

FIG. 2. — Mallomonas vietnamica Gusev, Kezlya & Tran sp. nov. scanning electron microscopy images (SEM: A-J): A-D, scales with recessed domes, shifted to the right part of the scales, oriented at different angles to the longitudinal axis (Fig. 2A is a representative scale from the holotype specimen); E-F, undersurface view of the scales; G, long straight bristle; H, J, tips of bristles with teeth; I, foot of the bristle. Scale bars: A, B, D, I, 1 μm; C, E, F, H, J, 2 μm; G, 10 μm.

opencc-by-4.0Aug 2024View details →

Data from: Strategies of resource sharing in clonal plants: A conceptual model and an example of contrasting strategies in two closely related species

These experimental data were collected to quantify amount of C and N translocated between mother and daughter ramets of two stoloniferous species. Data includes concentrations of 13-C and 15-N in plants samples originating from pulse-chase labelling, absolute amounts of the labels present, as well as dry mass of the samples. Details are described in the relevant paper.

Fig. 1 in Ghost species and optimal diversity: shared patterns between two tropical mountains within Auchenorrhyncha (Insecta: Hemiptera)

Fig. 1. Regressions between altitude and Abundance (a), Richness (b), Simpson (c), Shannon (d), on Doi Inthanon (Thailand) during the studied period (April/May). Lines are represented when regressions were significant (p<0.05).

Fig. 5 in Ghost species and optimal diversity: shared patterns between two tropical mountains within Auchenorrhyncha (Insecta: Hemiptera)

Fig. 5. Altitudinal clustering for Doi Inthanon's whole-year trapping, using Neighbor Joining on Jaccard's dissimilarity index. Dominant families (in terms of abundances) are named on branches. Tips correspond to trap elevations.

Fig. 3 in Ghost species and optimal diversity: shared patterns between two tropical mountains within Auchenorrhyncha (Insecta: Hemiptera)

Fig. 3. Regressions between altitude and Abundance (a), Richness (b), Simpson (c), Shannon (d), on Doi Inthanon (Thailand) during the whole Twin Peaks project (2014). Lines are represented when regressions were significant (p<0.05).

Fig. 4 in Ghost species and optimal diversity: shared patterns between two tropical mountains within Auchenorrhyncha (Insecta: Hemiptera)

Fig. 4. Altitudinal clustering for Doi Inthanon (a) and Mount Wilhelm (b), using Neighbor Joining on Jaccard's dissimilarity index. Dominant families (in terms of abundances) are named on branches. Tips correspond to trap altitudes. On one specific branch (in (b)), "Equal" means that no families were particularly dominant.

Fig. 2 in Ghost species and optimal diversity: shared patterns between two tropical mountains within Auchenorrhyncha (Insecta: Hemiptera)

Fig. 2. Regressions between altitude and Abundance (a), Richness (b), Simpson (c), Shannon (d), on Mount Wilhelm (Papua New Guinea) in 2012. Lines are represented when regressions were significant (p<0.05).

opencc-by-4.0May 2023View details →

Humans share features of Alzheimer's neuropathology with other mammalian species

Summary of relevant publications describing Aβ and tau neuropathology in carnivores collated into tables. Table 1. Alzheimer-like neuropathology in carnivore species. Occurrence of Aβ deposits in plaques in the brain and vessels (CAA) plaques and tauopathy (including NFTs and the earlier pTau) in select carnivore (Carnivora) species (primarily focusing on cats and dogs) compared to humans. The age of occurrence and prevalence of these pathologies is reported for each study. Supplementary Table 1 (S1). Occurrence and distribution of plaque and tangle types in carnivore species. Extended version of Table 1 to include the type of plaques, CAA (Aβ residues), and Tau pathology and their distribution across the cerebral cortex and other areas of the brain.  For more information about the classification of mature versus early-stage plaques, see the 'Table legend and Key' tab in the extended table workbook (S1).  Summary of the key findings from the data collated in Table 1 and S1: Dogs, but not cats, have Alzheimer-like mature senile plaques. Other felids (Felidae), such as cheetahs and Tsushima leopard cats, also do not have mature plaques, but other carnivore species, such as sea lions, did display this type of senile plaques. Cats have less cerebral amyloid angiopathy (CAA) in the meninges than dogs and humans. However, there were a higher number of observations of hyperphosphorylated tau in the cat studies we collated than in those studying dogs. Nonetheless, dogs and cats had a similar number of positive reports for neurofibrillary tangles (NFTs), and these were found to be at a lower prevalence than that in humans.

opencc-by-4.0Dec 2015View details →

Fig. 5 in How many species of whipworms do we share? Whipworms from man and other primates form two phylogenetic lineages

Fig. 5. Neighbor joining tree (by AsaturA, which is designed to deal with amino acid saturation) as inferred from cox1 amino acid sequences using an extended data set. Numbers above branches indicate NJ bootstrap support (1000 replicates)/ML bootstrap support (1 000 replicates)/MP bootstrap support (1 000 replicates). Sequences newly reported in this study are bold typed. Tree is rooted to Anatrichosoma haycocki Spratt, 1982 (AJ288160).

opencc-by-4.0Dec 2015View details →

Fig. 4. Unrooted maximum parsimony cox1 in How many species of whipworms do we share? Whipworms from man and other primates form two phylogenetic lineages

Fig. 4. Unrooted maximum parsimony cox1 tree of the genus Trichuris Roederer, 1761 as inferred from partial cox1 amino acid se- quences. Numbers above branches indicate MP bootstrap support (1 000 replicates)/ML bootstrap support (1 000 replicates)/NJ bootstrap support (1 000 replicates). Sequences newly reported in this study are bold typed.

opencc-by-4.0Dec 2015View details →

Fig. 2 in How many species of whipworms do we share? Whipworms from man and other primates form two phylogenetic lineages

Fig. 2. Maximum likelihood phylogenetic tree as inferred from ITS2 sequences. The tree was computed using the GTR model with discrete gamma distribution in four categories. Numbers above branches indicate ML bootstrap support (1 000 replicates)/Bayesian posterior probabilities (PhyloBayes; see Methods for details)/MP bootstrap support (1 000 replicates). Sequences newly reported in this study are bold typed. The three basic clades of genus Trichuris are highlighted. Tree was rooted to Trichuris skrjabini Baskakov, 1924 (AJ489248).

opencc-by-4.0Dec 2019View details →

"The sound comes from a meadow in the Sierra Nevada Mountains in California. The meadow is at an elevation of 2400 meters near a mountain named Olancha Peak, which is 3700 meters in altitude. Ihave a group of friends with which Ibackpack (trek) into the mountains. Our goal was to spend some time in the mountains and hike to the top of Olancha Peak (…) By the time we reached the meadow, we were in a forest and there was still snow on the ground in some places. We took the trip in June of 2006. The Sierra Nevada Mountains are a large mountain range. Much of the range is protected by national parks or preserved areas we call 'wilderness areas' (…) Ihave been backpacking for nearly 40 years and Iwill hopefully continue with this challenging activity for 40 years more! Many of my friends are much younger than Iam and it gives me much satisfaction to be able to have as much or more stamina for this activity than they have! When we are on these trips, we hike up peaks, catch fish, drink some whiskey around campfires and enjoy our time in the beautiful solitude. My memories of this trip were of the steep, hot hike from the desert to the cool meadow; the overall beauty of the nature, the absolute solitude of our campsite near the meadow; the strenuous hike to the top of Olancha Peak; the camaraderie of my friends; and, of course the sound of the frogs in the meadow. The frog sounds were astounding to me and Iwould listen in awe of the creature's instinctual desire to reproduce and continue the existence of their kind. Surely there were different species in the meadow for some of the frog sounds were different than others. The sounds only occurred after the Sun went down for the evening. Istood next to the creek in the meadow and recorded the sounds using my digital camera." [Peter/plentz1960]16 in Collecting Sounds. Online Sharing of Field Recordings as Cultural Practice

"The sound comes from a meadow in the Sierra Nevada Mountains in California. The meadow is at an elevation of 2400 meters near a mountain named Olancha Peak, which is 3700 meters in altitude. Ihave a group of friends with which Ibackpack (trek) into the mountains. Our goal was to spend some time in the mountains and hike to the top of Olancha Peak (…) By the time we reached the meadow, we were in a forest and there was still snow on the ground in some places. We took the trip in June of 2006. The Sierra Nevada Mountains are a large mountain range. Much of the range is protected by national parks or preserved areas we call 'wilderness areas' (…) Ihave been backpacking for nearly 40 years and Iwill hopefully continue with this challenging activity for 40 years more! Many of my friends are much younger than Iam and it gives me much satisfaction to be able to have as much or more stamina for this activity than they have! When we are on these trips, we hike up peaks, catch fish, drink some whiskey around campfires and enjoy our time in the beautiful solitude. My memories of this trip were of the steep, hot hike from the desert to the cool meadow; the overall beauty of the nature, the absolute solitude of our campsite near the meadow; the strenuous hike to the top of Olancha Peak; the camaraderie of my friends; and, of course the sound of the frogs in the meadow. The frog sounds were astounding to me and Iwould listen in awe of the creature's instinctual desire to reproduce and continue the existence of their kind. Surely there were different species in the meadow for some of the frog sounds were different than others. The sounds only occurred after the Sun went down for the evening. Istood next to the creek in the meadow and recorded the sounds using my digital camera." [Peter/plentz1960]16

opencc-zeroNov 2019View details →

Data from: The Chord-Normalized Expected Species Shared (CNESS)-distance represents a superior measure of species turnover patterns

1. Measures of β-diversity characterizing the difference in species composition between samples are commonly used in ecological studies. Nonetheless, commonly used dissimilarity measures require high sample completeness, or at least similar sample sizes between samples. In contrast, the Chord-Normalized Expected Species Shared (CNESS) dissimilarity measure calculates the probability of collecting the same set of species in random samples of a standardized size, and hence is not sensitive to completeness or size of compared samples. To date, this index has enjoyed limited use due to difficulties in its calculation and scarcity of studies systematically comparing it with other measures. 2. Here, we developed a novel R function that enables users to calculate ESS (Expected Species Shared)-associated measures. We evaluate the performance of the CNESS index based on simulated datasets of known species distribution structure, and compared CNESS with more widespread dissimilarity measures (Bray-Curtis index, Chao-Sørensen index, and proportionality based Euclidean distances) for varying sample completeness and sample sizes. 3. Simulation results indicated that for small sample size (m) values, CNESS chiefly reflects similarities in dominant species, while selecting large m values emphasizes differences in the overall species assemblages. Permutation tests revealed that CNESS has a consistently low CV (coefficient of variation) even where sample completeness varies, while the Chao-Sørensen index has a high CV particularly for low sampling completeness. CNESS distances are also more robust than other indices with regards to undersampling, particularly when chiefly rare species are shared between two assemblages. 4. Our results emphasize the superiority of CNESS for comparisons of samples diverging in sample completeness and size, which is particularly important in studies of highly mobile and species-rich taxa where sample completeness is often low. Via changes in the sample size parameter m, CNESS furthermore cannot only provide insights into the similarity of the overall distribution structure of shared species, but also into the differences in dominant and rare species, hence allowing additional, valuable insights beyond the capability of more widespread measures.

opencc-zeroMar 2020View details →

Disentangling the assembly mechanisms of ant cuticular bacterial communities of two Amazonian ant species sharing a common arboreal nest

Bacteria living on the cuticle of ants are generally studied for their protective role against pathogens, especially in the clade of fungus-growing ants. However, little is known of the diversity of cuticular bacteria in other ant host species, as well as of the mechanisms leading to the composition of these communities. Here, we used 16S rRNA gene amplicon sequencing to study the influence of host species, species interactions, and the pool of bacteria from the environment on the assembly of cuticular bacterial communities on two phylogenetically distant Amazonian ant species that frequently nest together inside the roots system of epiphytic plants, Camponotus femoratus and Crematogaster levior. Our results show that 1) the vast majority of the bacterial community on the cuticle is shared with the nest, suggesting that most bacteria on the cuticle are acquired through environmental acquisition, 2) 5.2% and 2.0% OTUs are respectively specific to Camponotus femoratus and Crematogaster levior, likely representing their respective core cuticular bacterial community, and 3) 3.6% of OTUs are shared between the two ant species. Additionally, mass spectrometry metabolomics analysis of metabolites on the cuticle of ants, which excludes the detection of cuticular hydrocarbons produced by the host, were conducted to evaluate correlations among bacterial OTUs and m/z ion mass. Although some positive and negative correlations are found, the cuticular chemical composition was weakly species specific which supports that cuticular bacterial communities are prominently environmentally acquired. Overall, our results suggest that the environment is the dominant source of bacteria found on the cuticle of ants.

opencc-zeroNov 2022View details →

Data from: Sharing detection heterogeneity information among species in community models of occupancy and abundance can strengthen inference

1. The estimation of abundance and distribution and factors governing patterns in these parameters is central to the field of ecology. The continued development of hierarchical models that best utilize available information to inform these processes is a key goal of quantitative ecologists. However, much remains to be learned about simultaneously modeling true abundance, presence, and trajectories of ecological communities. 2. Simultaneous modeling of the population dynamics of multiple species provides an interesting mechanism to examine patterns in community processes and, as we emphasize herein, to improve species-specific estimates by leveraging detection information among species. Here we demonstrate a simple but effective approach to share information about observation parameters among species in hierarchical community abundance and occupancy models, where we use shared random effects among species to account for spatiotemporal heterogeneity in detection probability. 3. We demonstrate the efficacy of our modeling approach using simulated abundance data, where we recover well our simulated parameters using N-mixture models. Our approach substantially increases precision in estimates of abundance compared to models that do not share detection information among species. We then expand this model, and apply it to repeated detection/non-detection data collected on six species of tits (Paridae) breeding at 119 1 km2 sampling sites across a P. montanus hybrid zone in northern Switzerland (2004-2020). We find strong impacts of forest cover and elevation on population persistence and colonisation in all species. We also demonstrate evidence for interspecific competition on population persistence and colonization probabilities, where the presence of marsh tits reduces population persistence and colonisation probability of sympatric willow tits, potentially decreasing gene flow among willow tit subspecies. 4. While conceptually simple, our results have important implications for the future modeling of population abundance, colonization, persistence, and trajectories in community frameworks. We suggest potential extensions of our modeling in this paper, and discuss how leveraging data from multiple species can improve model performance and sharpen ecological inference.

zenodo36/100

A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with C. elegans dauer larva

Some organisms in nature have developed the ability to enter a state of suspended metabolism called cryptobiosis1 when environmental conditions are unfavorable. This state-transition requires the execution of complex genetic and biochemical programs1,2,3, that enables the organism to survive for prolonged periods. Recently, nematode individuals have been reanimated from Siberian permafrost after remaining in cryptobiosis. Preliminary analysis indicates that these nematodes belong to the genera Panagrolaimus and Plectus4. Here, we present precise radiocarbon dating indicating that the Panagrolaimus individuals have remained in cryptobiosis since the late Pleistocene (~46,000 years). Phylogenetic inference based on our genome assembly and a detailed morphological analysis demonstrate that they belong to an undescribed species, which we named Panagrolaimus n. sp. Comparative genome analysis revealed that the molecular toolkit for cryptobiosis in Panagrolaimus n. sp. and in C. elegans is partly orthologous. We show that biochemical mechanisms employed by these two species to survive desiccation and freezing under laboratory conditions are similar. Our experimental evidence also reveals that C. elegans dauer larvae can remain viable for longer periods in suspended animation than previously reported. Altogether, our findings demonstrate that nematodes evolved mechanisms potentially allowing them to suspend life over geological time scales.

opencc-by-4.0May 2022View details →

zenodo36/100

FIG. 1 in Mallomonas vietnamica Gusev, Kezlya & Tran, sp. nov. (Synurales, Chrysophyceae), a new species, that shares some features with fossil taxa

FIG. 1. — Map of the study area (stars indicates sampling site).

opencc-zeroMar 2021View details →