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opencc-by-4.0Aug 2020View details →

Datasets associated with paper "Heterotrophic eukaryotes show a fast-slow continuum, not a gleaner-exploiter trade-off"

This contains 6 data files used in the analysis of the paper "Heterotrophic eukaryotes show a fast-slow continuum, not a gleaner-exploiter trade-off", and one file describing their contents in detail.  Kiorboe_and_Hirst_dataset_edited_2020_03_21.csv FoRAGE_dataset_edited_2020_03_21.csv FoRAGE_dataset_taxonomic_info_edited_2020_03_21 FoRAGE_dataset_with_outliers_raw.csv Growth_ingestion_dataset_raw.csv Litchman_2007_phytoplankton_Vmax_and_affinity_data.csv   The primary contents of these files are compiled parameter estimates of the clearance, ingestion and growth rates of heterotrophic organisms. These have largely been taken from two published data compilations: Kiørboe T, Hirst AG (2014) Shifts in mass scaling of respiration, feeding, and growth rates across life-form transitions in marine pelagic organisms. Am Nat 183(4):E118-30. <a href="https://doi.org/10.1086/675241">https://doi.org/10.1086/675241</a> Uiterwaal SF, Lagerstrom IT, Lyon SR, DeLong JP (2018) Data paper: FoRAGE (Functional Responses from Around the Globe in all Ecosystems) database: a compilation of functional responses for consumers and parasitoids. bioRxiv doi: <a href="https://doi.org/10.1101/503334">https://doi.org/10.1101/503334</a>    The data files are described in detail in 'Data description.txt'. Scripts to analyse this data can be found at <a href="https://doi.org/10.5281/zenodo.4002083">https://doi.org/10.5281/zenodo.4002083</a> . The paper associated with the data and scripts, will be linked to here when published.

opencc-zeroSep 2020View details →

Data from: Metabolically similar cohorts of bacteria exhibit strong co-occurrence patterns with diet items and eukaryotic microbes in lizard guts

Gut microbiomes perform essential services for their hosts, including helping them to digest food and manage pathogens and parasites. Performing these services requires a diverse and constantly changing set of metabolic functions from the bacteria in the microbiome. The metabolic repertoire of the microbiome is ultimately dependent on the outcomes of the ecological interactions of its member microbes, as these interactions in part determine the taxonomic composition of the microbiome. The ecological processes that underpin the microbiome's ability to handle a variety of metabolic challenges might involve rapid turnover of the gut microbiome in response to new metabolic challenges, or it might entail maintaining sufficient diversity in the microbiome that any new metabolic demands can be met from an existing set of bacteria. To differentiate between these scenarios, we examine the gut bacteria and resident eukaryotes of two generalist-insectivore lizards, while simultaneously identifying the arthropod prey each lizard was digesting at the time of sampling. We find that the cohorts of bacteria that occur significantly more or less often than expected with arthropod diet items or eukaryotes include bacteria species that are highly similar to each other metabolically. This pattern in the bacteria microbiome could represent an early step in the taxonomic shifts in bacteria microbiome that occur when host lineages change their in diet niche over evolutionary timescales.

opencc-zeroDec 2010View details →

Data from: The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?

The use of nucleotide and amino acid sequences allows improved understanding of the timing of evolutionary events of life on earth. Molecular estimates of divergence times are, however, controversial and are generally much more ancient than suggested by the fossil record. The limited number of genes and species explored and pervasive variations in evolutionary rates are the most likely sources of such discrepancies. Here we compared concatenated amino acid sequences of 129 proteins from 36 eukaryotes to determine the divergence times of several major clades, including animals, fungi, plants, and various protists. Due to significant variations in their evolutionary rates, and to handle the uncertainty of the fossil record, we used a Bayesian relaxed molecular clock simultaneously calibrated by six paleontological constraints. We show that, according to 95% credibility intervals, the eukaryotic kingdoms diversified 950–1,259 million years ago (Mya), animals diverged from choanoflagellates 761–957 Mya, and the debated age of the split between protostomes and deuterostomes occurred 642–761 Mya. The divergence times appeared to be robust with respect to prior assumptions and paleontological calibrations. Interestingly, these relaxed clock time estimates are much more recent than those obtained under the assumption of a global molecular clock, yet bilaterian diversification appears to be ≈100 million years more ancient than the Cambrian boundary.

opencc-zeroDec 2016View details →

Data from: Early photosynthetic eukaryotes inhabited low-salinity habitats

The early evolutionary history of the chloroplast lineage remains an open question. It is widely accepted that the endosymbiosis that established the chloroplast lineage in eukaryotes can be traced back to a single event, in which a cyanobacterium was incorporated into a protistan host. It is still unclear, however, which Cyanobacteria are most closely related to the chloroplast, when the plastid lineage first evolved, and in what habitats this endosymbiotic event occurred. We present phylogenomic and molecular clock analyses, including data from cyanobacterial and chloroplast genomes using a Bayesian approach, with the aim of estimating the age for the primary endosymbiotic event, the ages of crown groups for photosynthetic eukaryotes, and the independent incorporation of a cyanobacterial endosymbiont by Paulinella. Our analyses include both broad taxon sampling (119 taxa) and 18 fossil calibrations across all Cyanobacteria and photosynthetic eukaryotes. Phylogenomic analyses support the hypothesis that the chloroplast lineage diverged from its closet relative Gloeomargarita, a basal cyanobacterial lineage, ∼2.1 billion y ago (Bya). Our analyses suggest that the Archaeplastida, consisting of glaucophytes, red algae, green algae, and land plants, share a common ancestor that lived ∼1.9 Bya. Whereas crown group Rhodophyta evolved in the Mesoproterozoic Era (1,600–1,000 Mya), crown groups Chlorophyta and Streptophyta began to radiate early in the Neoproterozoic (1,000–542 Mya). Stochastic mapping analyses indicate that the first endosymbiotic event occurred in low-salinity environments. Both red and green algae colonized marine environments early in their histories, with prasinophyte green phytoplankton diversifying 850–650 Mya.

opencc-zeroDec 2016View details →

Data from: DNA metabarcoding reveals that 200-μm-size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes

Microeukaryotic plankton (0.2–200 μm) are critical components of aquatic ecosystems and key players in global ecological processes. High-throughput sequencing is currently revolutionizing their study on an unprecedented scale. However, it is currently unclear whether we can accurately, effectively and quantitatively depict the microeukaryotic plankton communities using traditional size-fractionated filtering combined with molecular methods. To address this, we analysed the eukaryotic plankton communities both with, and without, prefiltering with a 200 μm pore-size sieve –by using SSU rDNA-based high-throughput sequencing on 16 samples with three replicates in each sample from two subtropical reservoirs sampled from January to October in 2013. We found that ~25% reads were classified as metazoan in both size groups. The species richness, alpha and beta diversity of plankton community and relative abundance of reads in 99.2% eukaryotic OTUs showed no significant changes after prefiltering with a 200 μm pore-size sieve. We further found that both >0.2 μm and 0.2–200 μm eukaryotic plankton communities, especially the abundant plankton subcommunities, exhibited very similar, and synchronous, spatiotemporal patterns and processes associated with almost identical environmental drivers. The lack of an effect on community structure from prefiltering suggests that environmental DNA from larger metazoa is introduced into the smaller size class. Therefore, size-fractionated filtering with 200 μm is insufficient to discriminate between the eukaryotic plankton size groups in metabarcoding approaches. Our results also highlight the importance of sequencing depth, and strict quality filtering of reads, when designing studies to characterize microeukaryotic plankton communities.

opencc-zeroDec 2015View details →

Data from: Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system

Understanding if the members of an ecological community have co-diversified is a central concern of evolutionary biology, as co-diversification suggests prolonged association and possible coevolution. By sampling associated species from an ecosystem, researchers can better understand how abiotic and biotic factors influence diversification in a region. In particular, studies of co-distributed species that interact ecologically can allow us to disentangle the effect of how historical processes have helped shape community level structure and interactions. Here we investigate the Sarracenia alata pitcher plant system, an ecological community where many species from disparate taxonomic groups live inside the fluid-filled pitcher leaves. Direct sequencing of the eukaryotes present in the pitcher plant fluid enables us to better understand how a host plant can shape and contribute to the genetic structure of its associated inquilines, and to ask whether genetic variation in the taxa are structured in a similar manner to the host plant. We used 454 amplicon-based metagenomics to demonstrate that the pattern of genetic diversity in many, but not all, of the eukaryotic community is similar to that of S. alata, providing evidence that associated eukaryotes share an evolutionary history with the host pitcher plant. Our work provides further evidence that a host plant can influence the evolution of its associated commensals.

opencc-zeroDec 2016View details →

Data from: Asgard archaea illuminate the origin of eukaryotic cellular complexity

The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the 'Asgard' superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota. Asgard archaea affiliate with eukaryotes in phylogenomic analyses, and their genomes are enriched for proteins formerly considered specific to eukaryotes. Notably, thorarchaeal genomes encode several homologues of eukaryotic membrane-trafficking machinery components, including Sec23/24 and TRAPP domains. Furthermore, we identify thorarchaeal proteins with similar features to eukaryotic coat proteins involved in vesicle biogenesis. Our results expand the known repertoire of 'eukaryote-specific' proteins in Archaea, indicating that the archaeal host cell already contained many key components that govern eukaryotic cellular complexity.

opencc-zeroApr 2016View details →

Data used for ALife 2016 paper "Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-Length Genomes"

The results files in this directory contain the evolved critical mutation rates, exponential or quadratic curves produced by curve-fitting using the given data in R, and biological data used for comparison in the following paper: Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-Length Genomes, accepted for publication in ALife 2016: Proceedings of the 15th International Conference on the Synthesis and Simulation of Living Systems (ALIFE XV)

Data used for submission entitled "Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-length Genomes with Crossover"

Datasets generated and presented in the submission entitled "Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-length Genomes with Crossover".

Cloning, eukaryotic expression and purification of full-length huntingtin Q23 (2017/06/01)

Huntingtin structure function open lab notebook project

Data used for submission entitled "Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-length Genomes with Crossover".

Datasets generated and presented in the submission entitled "Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-length Genomes with Crossover". Includes the results of statistical analysis.

Data used for submission entitled "Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-length Genomes with Crossover".

opencc-by-4.0Feb 2024View details →

Dataset for the manuscript: Changes in isotope fractionation during nitrate assimilation by eukaryotic and prokaryotic algae under different pH and CO2 conditions

This is the dataset for the manuscript: Different effects of ocean acidification on isotope fractionation during nitrate assimilation by eukaryotic and prokaryotic algae

opencc-zeroMar 2024View details →

Eukaryotic gene trees with 150 leaves

Gene loss is an important process in gene and genome evolution. If a gene is present at the root of a rooted binary phylogenetic tree and can be lost in one descendant lineage, it can be lost in other descendant lineages as well, and potentially can be lost in all of them, leading to extinction of the gene on the tree. In that case, just before the gene goes extinct in the rooted phylogeny, there will be one lineage that still retains the gene for some period of time, representing a 'last-one-out' distribution. If there are many (hundreds) of leaves in one clade of a phylogenetic tree, yet only one leaf possesses the gene, it will look like the result of a recent gene acquisition, even though the distribution at the tips was generated by loss. Here we derive the probability of observing last-one-out distributions under a Markovian loss model and a given gene loss rate μ. We find that the probability of observing such cases can be calculated mathematically, and can be surprisingly high, depending upon the tree and the rate of gene loss. Examples from real data show that gene loss can readily account for the observed frequency of last-one-out gene distribution patterns that might otherwise be attributed to lateral gene transfer.

opencc-zeroApr 2024View details →

Data from: The evolution of protein-coding gene structure in eukaryotes

Introns are highly prevalent in most eukaryotic genomes. Despite the accumulating evidence for benefits conferred by the possession of introns, their specific roles and functions, as well as the processes shaping their evolution, are still only partially understood. Here we explore the evolution of the eukaryotic gene intron-exon structure by focusing on several key features such as the intron length, the number of introns, and the intron-to-exon ratio of protein-coding genes. We utilize whole genome data from 590 species covering the main eukaryotic taxonomic groups and analyze them within a statistical phylogenetic framework. We found that the basic gene structure differs markedly among the main eukaryotic phyla, with animals, and particularly chordates, displaying intron-rich genes, compared to plants and fungi. Reconstruction of gene structure evolution suggests that these differences had evolved prior to the divergence of the phyla, and have remained mostly conserved within groups. We revisit the previously reported association between the genome size and the mean intron length, and report that the correlation patterns differ considerably among phyla. Our findings suggest that the evolution of introns may be affected by different processes across the eukaryotic tree. The substantial diversity in gene structures may indicate that introns play different molecular and evolutionary roles in different organisms.

opencc-by-4.0Feb 2024View details →

TIdeS: a comprehensive framework for accurate open reading frame identification and classification in eukaryotic transcriptomes

Includes: <ul> <li>ORF predictions for 28 diverse eukaryotic taxa, employing common tools/approaches</li> <li>Raw transcriptome assemblies used for ORF predictions</li> <li>Phylogenetic trees used as the basis for contamination identification, as well as validating TIdeS's efficacy</li> <li>Various TIdeS outputs (ORF prediction/classification)</li> <li>Copy of current TIdeS source code</li> </ul>

opencc-by-4.0Apr 2024View details →

Chimeric Origin of Eukaryotes from Asgard archaea and Giant viruses

This repository contains supplementary data for the study "Chimeric Origin of Eukaryotes from Asgard archaea and Giant viruses"

opencc-zeroDec 2021View details →

Data from: Systematic evaluation of horizontal gene transfer between eukaryotes and viruses

Gene exchange between viruses and their hosts acts as a key facilitator of horizontal gene transfer and is hypothesized to be a major driver of evolutionary change. Our understanding of this process comes primarily from bacteria and phage co-evolution, but the mode and functional importance of gene transfers between eukaryotes and their viruses remains anecdotal. Here we systematically characterized viral-eukaryotic gene exchange across eukaryotic and viral diversity, identifying thousands of transfers, and revealing their frequency, taxonomic distribution, and projected functions. Eukaryote-derived viral genes, abundant in the Nucleocytoviricota, highlighted common strategies for viral host-manipulation, including metabolic reprogramming, proteolytic degradation, and extracellular modification. Furthermore, viral-derived eukaryotic genes implicate genetic exchange in the early evolution and diversification of eukaryotes, particularly through viral-derived glycosyltransferases, which have impacted structures as diverse as algal cell walls, trypanosome mitochondria, and animal tissues. These findings illuminate the nature of viral-eukaryotic gene exchange and its impact on the evolution of viruses and their eukaryotic hosts.

opencc-by-4.0Jul 2024View details →

In silico mock communities for evaluation of taxonomic profilers across eukaryotes in the human microbiome

In silico mock communities generated with CAMISIM for benchmarking the performance of taxonomic profilers across prokaryotic (50 communities), eukaryotic (30 communities), and viral communities (10 communities) of the human microbiome. Metagenomes were generated using CAMISIM (Fritz et al., 2019), which simulates 2.1 Gb of Illumina 2 ×150 bp paired end reads with the default HiSeq 2500 error profile and a mean insert size of 200 bp. Eukaryotic communities 30 eukaryotic in silico metagenomes comprising up to 200 randomly sampled genomes from a set of 113 eukaryotic species (See Supplementary Table 2 from the paper) corresponding to the eukaryotic species within both CHAMP and MetaPhlAn 4 (Blanco-Míguez et al., 2023) databasess. Prokaryotic and viral communities In silico data for prokaryotic and viral communities from the human microbiome can be found here: <a href="https://doi.org/10.5281/zenodo.10777404">doi: 10.5281/zenodo.10777404</a> References Blanco-Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., et al. (2023). Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nature Biotechnology 2023 41:11 41, 1633–1644. doi: 10.1038/s41587-023-01688-w Fritz, A., Hofmann, P., Majda, S., Dahms, E., Dröge, J., Fiedler, J., et al. (2019). CAMISIM: Simulating metagenomes and microbial communities. Microbiome 7, 1–12. doi: 10.1186/S40168-019-0633-6/FIGURES/5