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167 results for “Multicellularity”
Data from: Macroscopic fossils from Chuanlinggou Formation of North China: Evidence for an earlier origin of multicellular algae in late Paleoproterozoic
<p><span>The multicellular algae are the core topic for understanding the early life evolution on Earth. The timing of origin and cellular differentiation of multicellular algae, however, remains poorly constrained. The Paleo- to early Mesoproterozoic is a critical period, during which multicellular algae began to occur and started to evolve in marine environments. This paper reports well-preserved multicellular fossils from shales of the Chuanlinggou Formation in North China, with emphasis on their holdfast structure and putative cellular structures. These macroalgae fossils are reasonably diversified in this formation, and include <em>Chuaria circularis</em>, <em>Tawuia sinensis</em>, <em>Tawuia robusta</em>, <em>Glossophyton ovalis</em>, <em>Glossophyton</em> sp., <em>Tuanshanzia</em> sp., <em>Changchengia</em> sp., which are mainly preserved as carbonaceous compressions, with some in sideritized forms. FESEM observation reveals multicellular structures in <em>Chuaria</em>, confirming its biological attribute of multicellular eukaryote and providing direct evidence that multicellular algae had already originated by the terminal Paleoproterozoic, earlier than previous speculation. The <em>Tuanshanzia</em> sp. and <em>Changchengia</em> sp. developed with bare rhizome holdfast, suggesting their benthic sessile lifestyle in the late Paleoproterozoic oceanic habitat.</span></p>
Data from: Loss-of-heterozygosity facilitates a fitness valley crossing in experimentally evolved multicellular yeast
<p>These data sets are generated to investigate a simple evolutionary landscape that arises from underdominance at a single locus where the fitness valley consists of only one less-fit genotype. We make use of an experimental system previous evolved in the laboratory, the S<em>accharomyces cerevisiae</em> snowflake system. This system was experimentally selected resulting in a significant evolutionary shift, the transition from uni-to-multicellularity in asexual diploid populations. We carried out the phenotypic and fitness characterization of the strains. Additionally, we observed a rapid loss of heterozygosity (LOH) events in the heterozygote strains. Experimental evolution starting with the heterozygote strains suggests that LOH is common both under selection and without selection. LOH event drive adaptation that may enable rapid evolution in diploid yeast. </p>
Fossil-calibrated inference of divergence times among the Volvocine algae enables reconstruction of the steps that led to differentiated multicellularity
<p>Throughout its nearly four-billion-year history, life has undergone evolutionary transitions in which simpler subunits have become integrated to form a more complex whole. Many of these transitions opened the door to innovations that resulted in increased biodiversity and/or organismal efficiency. The evolution of multicellularity from unicellular forms represents one such transition, one that paved the way for cellular differentiation, including differentiation of male and female gametes. A useful model for studying the evolution of multicellularity and cellular differentiation is the volvocine algae, a clade of freshwater green algae whose members range from unicellular to colonial, from undifferentiated to completely differentiated, and whose gamete types can be isogamous, anisogamous, or oogamous. To better understand how multicellularity, differentiation, and gametes evolved in this group, we used comparative genomics and fossil data to establish a geologically calibrated roadmap of when these innovations occurred. Our results, presented as ancestral-state reconstructions, show that multicellularity arose independently twice in this clade. Our chronograms indicate multicellularity evolved during the Carboniferous-Triassic periods in Goniaceae + Volvocaceae, and possibly as early as the Cretaceous in Tetrabaenaceae. Using divergence time estimates we inferred when, and in what order, specific developmental changes occurred that led to differentiated multicellularity and oogamy. We find that in the volvocine algae the temporal sequence of developmental changes leading to differentiated multicellularity is much as proposed by David Kirk, and that multicellularity is correlated with the acquisition of anisogamy and oogamy. Lastly, morphological, molecular, and divergence time data suggest the possibility of cryptic species in Tetrabaenaceae.</p>
Macroalgal deep genomics illuminate multiple paths to aquatic, photosynthetic multicellularity - Supplementary Data - ANNOTATIONS - Data S2
<p>Macroalgae are a polyphyletic group of multicellular aquatic organisms vital to global climate maintenance and have a wide variety of commercial applications. The lack of genomic datasets and poor physiological records preclude understanding their ecological roles and industrial potential. We <em>de novo</em> sequenced 121 macroalgal genomes from various climates spanning five major latitude parallels. The resultant genomic datasets illuminate the evolutionary mechanisms behind macroalgal diversification and specialization and reveal genetic bases for niche habitation facilitated by morphological complexity. Adhesome genes (e.g., cadherins, integrins, and lectins), extracellular matrix enzymes, and cytoskeletal organization regulating genes (e.g., spondins, Rho-type GTPases) predominantly distinguished macroalgal genomes from their microalgae correlates. Artificial neural networks could accurately classify an alga as micro- or macro- from set of significance-ranked genomic features (n = 251, entropy R<sup>2</sup> > 0.99) as well as adhesome gene sets (n = 110, entropy R<sup>2</sup> > 0.92). By deciphering the macroalgal adhesome, a clear picture of the genetic basis for the development and maintenance of complex algal tissues could be resolved in the three macroalgal phyla. Sequences from giant viruses were rampant in the macroalgal genomes and coded for zinc-finger transcription factors, ankyrins, Rieske proteins, and other exotic codomains. Lineage-specific retentions of transcription factors, cadherins, integrins, polysaccharide-acting enzymes, and receptor kinases, many with predicted viral origins, outline the divergent mechanisms facilitating multicellularity in these three macroalgal lineages. This work sheds new light on the evolution of multicellularity in three phyla (Rhodophyceae, Chlorophyceae, and Ochrophyceae v. Phaeophyceae) through the lens of large-scale genomics and paves the way for the genomic exploration of macroalgal biology.</p>
Macroalgal deep genomics illuminate multiple paths to aquatic, photosynthetic multicellularity - Supplementary Data - ANALYSES - Data S3
<p>Macroalgae are a polyphyletic group of multicellular aquatic organisms vital to global climate maintenance and have a wide variety of commercial applications. The lack of genomic datasets and poor physiological records preclude understanding their ecological roles and industrial potential. We <em>de novo</em> sequenced 121 macroalgal genomes from various climates spanning five major latitude parallels. The resultant genomic datasets reveal genetic bases for niche habitation facilitated by morphological complexity in diverse and extreme regions and illuminate the evolutionary mechanisms behind macroalgal diversification and specialization. Adhesome genes (e.g., cadherins, integrins, and lectins), extracellular matrix enzymes, and cytoskeletal organization regulating genes (e.g., spondins, Rho-type GTPases) predominantly distinguished macroalgal genomes from their microalgae correlates. Deep neural networks could accurately classify an alga as micro- or macro- from set of significance-ranked genomic features (n = 251, entropy R<sup>2</sup> > 0.99, RASE = 0.001) as well as adhesome gene sets (n = 110, entropy R<sup>2</sup> > 0.86). By deciphering the macroalgal adhesome, a clear picture of the genetic basis for the development and maintenance of complex algal tissues could be resolved. Sequences from giant viruses were rampant in the macroalgal genomes and coded for zinc-finger transcription factors, ankyrins, Rieske proteins, and other exotic codomains. Lineage-specific retentions of transcription factors, cadherins, integrins, polysaccharide-acting enzymes, and receptor kinases, many with predicted viral origins, outline the divergent mechanisms facilitating multicellularity in these three macroalgal lineages. This work sheds new light on the evolution of multicellularity in three phyla (Rhodophyceae, Chlorophyceae, and Ochrophyceae v. Phaeophyceae) through the lens of large-scale genomics and paves the way for the genomic exploration of macroalgal biology.</p> <p> </p> <p><strong>Data S3.</strong> <strong>Analysis data files.</strong> This dataset includes data files for the analyses presented in the manuscript, including</p> <p>(A) Decontamination analysis, including iterative BLEACH contamination calls, GFF coordinates for contaminants, and downsampling analyses of decontaminated genomes. Related to Fig. S1.</p> <p>(B) HMMsearch results for decontaminated assemblies for PFAMs. Related to Figs. 2-6.</p> <p>(C) Ternary analyses including dcGO enrichment for >80% purity sets for the three phyla. Related to Fig. 2.</p> <p>(D) Comparative genomics analyses of micro- and macroalgal genomes, including intersection, response screening, metabolic pathway, GO enrichment, and aNN modeling analyses. Related to Fig. 3.</p> <p>(E) Adhesome analysis including HMMsearch results for adhesome domains and codomains and response screening analyses between phyla, habitat, climate, and micro- vs. macroalgae. The neural network model using the 110 adhesome PFAMs is also included in this dataset. Related to Fig. 4.</p> <p>(F) Endogenous viral element analyses, including VFAM HMMsearch results, EVOPs, macroalgal sequences with EsV-1-7 codomains and comparative analyses including response screens and hierarchical clustering results. Related to Fig. 5.</p> <p>(G) All computational scripts used for analyses in this study. Scripts are either ‘.sh’ or ‘.sbatch’ files for execultion in a Linux environment with a SLURM (<a href="https://github.com/SchedMD/slurm">https://github.com/SchedMD/slurm</a>) high-performance computing (HPC) scheduler. Related to all analyses.</p>
The circadian clock of the bacterium B. subtilis evokes properties of complex, multicellular circadian systems
<p>Circadian clocks are pervasive throughout nature, yet only recently has this adaptive regulatory program been described in non-photosynthetic bacteria. Here, we describe an inherent complexity in the <em>Bacillus</em> <em>subtilis</em> circadian clock. We find that <em>B. subtilis</em> entrains to blue and red light and that circadian entrainment is separable from masking through fluence titration and frequency demultiplication protocols. We identify circadian rhythmicity in constant light, consistent with Aschoff's Rule, and entrainment aftereffects, both of which are properties described for eukaryotic circadian clocks. We report that circadian rhythms occur in wild isolates of this prokaryote, thus establishing them as a general property of this species, and that its circadian system responds to the environment in a complex fashion that is consistent with multicellular eukaryotic circadian systems.</p>
Historical effects during experimental evolution of multicellularity in <em>Saccharomyces cerevisiae</em>
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Data from: Loss-of-heterozygosity facilitates a fitness valley crossing in experimentally evolved multicellular yeast
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Data from: Macroscopic fossils from Chuanlinggou Formation of North China: Evidence for an earlier origin of multicellular algae in late Paleoproterozoic
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Optimal mechanical interactions direct multicellular network formation on elastic substrates
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Fossil-calibrated inference of divergence times among the Volvocine algae enables reconstruction of the steps that led to differentiated multicellularity
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The circadian clock of the bacterium B. subtilis evokes properties of complex, multicellular circadian systems
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Data from: Evolution of altruistic cooperation among nascent multicellular organisms
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Wild Dictyostelium discoideum social amoebae show plastic responses to the presence of nonrelatives during multicellular development
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Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity
<h2>Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity</h2> <p>Repository accompanying "Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity" manuscript</p> <p> </p> <h3>microRNA curation</h3> <p>Potential miRNA clusters, generated using Shortstack (https://github.com/MikeAxtell/ShortStack), are analyzed with <strong>miRNA_curation.py</strong>. An example run of the miRNA curation can be performed by running the 'example_run/explore_all.sh' and 'example_run/refine_all.sh' scripts in order. A sample of the sRNA sequences from <em>D. discoideum</em> is included in the 'example/example_sizeselected_data' folder. A sample of miRNA candidates are included in 'example_run/pot-miRNAs_merged.fa' to facilitate the example run.</p> <p><em>Prerequisites: Python 3, Biopython, RNAlib, matplotlib, numpy</em></p> <p> </p> <h3>microRNA analysis</h3> <p>Following miRNA curation, high confidence miRNAs are identified and further analysed in <strong>amoeba_miRNAevo.Rmd</strong>. The data for the analysis is located in 'data_in' and are mostly derived from the miRNA_curation.py script and other scripts located in the 'helper_scripts' folder. The plots generated in the analysis is located in the 'plots' folder. Tables and other data generated from the analysis are located in the 'data_out' folder. In order to perform the <strong>miRNA conservation search</strong>, refer to the '<strong>helper_scripts/miRNA_conservation_search/</strong>' folder.</p> <p><em>Prerequisites: R, Blast, bash</em></p> <p> </p> <h3>Access genomes/annotations</h3> <p>For <em>Dictyostelium firmibasis</em>, the genome was de-novo sequenced and assembled and is located in '<strong>data_in/novel_assembly'</strong>. Assembly was done using Flye v2.9.1 in nano-hq mode, and two rounds of long-read polishing were done using Medaka v1.7.2. The filtered reads used for assembly can be accessed from NCBI BioProject PRJNA972620. The <em>Acanthamoeba castellanii</em> genome and annotation were accessed at https://www.doi.org/10.5281/zenodo.680005. The other genomes and annotations for this study were accessed from NCBI and can be downloaded using the 'get_references.sh' script located in the helper_scripts folder.</p>
Mutation of rpoB shifts the nutrient threshold triggering Myxococcus multicellular development
<p><span>The ability to perceive and respond to environmental change is essential to all organisms. In response to nutrient depletion, cells of the soil-dwelling δ-proteobacterium<em> Myxococcus xanthus</em> undergo collective morphogenesis into multicellular fruiting bodies and transform into stress-resistant spores. This process is strictly regulated by gene networks that incorporate both inter- and intracellular signals. While commonly studied <em>M. xanthus </em>reference strains and some natural isolates undergo development only in nutrient-poor conditions, some lab mutants and other natural isolates commit to development at much higher nutrient levels, but mechanisms enabling such rich-medium development remain elusive. Here we investigate the genetic basis of rich-medium development in one mutant and find that a single amino-acid change (S534L) in RpoB, the β-subunit of RNA polymerase, is responsible for the phenotype. Ectopic expression of the mutant <em>rpoB</em> allele was sufficient to induce nutrient-rich development. These results suggest that the universal bacterial transcription machinery bearing the altered β-subunit can relax regulation of developmental genes that are normally strictly controlled by the bacterial stringent response. Moreover, the mutation also pleiotropically mediates a tradeoff in fitness during vegetative growth between high vs low nutrient conditions and generates resistance to exploitation by a developmental cheater. Our findings reveal a previously unknown connection between the universal transcription machinery and one of the most behaviorally complex responses to environmental stress found among bacteria.</span></p>
A dynamic multicellularity emerges for collective invasion within opisthokonta
<p>Raw data used for the quantification of the Fonticula Collective behaviours : https://github.com/apicco/Fonticula_collective_invasion</p>
FIGURE 2. Stylotrichium hortensiae. A. Floriferous branch. B. Abaxial surface showing the venation reticulodromous. C. Leaf transverse section. D. Uniseriate tector trichome. E. Uniseriate glandular trichome with multicellular head. F. Biseriate glandular trichome with unicellular head. G. Capitulum. H. Receptacles convex pilose. I. Corolla. J. Stamen. K. Style. L in Stylotrichium hortensiae (Asteraceae-Eupatorieae): A new species from Chapada Diamantina, Bahia, Brazil
FIGURE 2. Stylotrichium hortensiae. A. Floriferous branch. B. Abaxial surface showing the venation reticulodromous. C. Leaf transverse section. D. Uniseriate tector trichome. E. Uniseriate glandular trichome with multicellular head. F. Biseriate glandular trichome with unicellular head. G. Capitulum. H. Receptacles convex pilose. I. Corolla. J. Stamen. K. Style. L. Cypselae with subpaleaceous pappus. Illustrations by N. Nascimento.
Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae
<p class="western">The volvocine algae, which include the single-celled species <i>Chlamydomonas reinhardtii</i> and the colonial species <i>Volvox carteri</i>, serve as a model in which to study the evolution of multicellularity and cellular differentiation. Studies reconstructing the history of this group have by and large relied on datasets of one to a few genes for phylogenetic inference and ancestral character state reconstruction. As a result, volvocine phylogenies lack concordance depending on the number and/or type of genes (i.e., chloroplast vs nuclear) chosen for phylogenetic inference. While multiple studies suggest that multicellularity evolved only once in the volvocine algae, that each of its three colonial families is monophyletic, and that there have been at least three independent origins of cellular differentiation in the group, other studies call into question one or more of these conclusions. An accurate assessment of the evolutionary history of the volvocine algae requires inference of a more robust phylogeny. We performed RNA sequencing (RNA-seq) on 55 strains representing 47 volvocine algal species and obtained similar data from curated databases on 13 additional strains. We then compiled a dataset consisting of transcripts for 40 single-copy, protein-coding, nuclear genes, and subjected the predicted amino acid sequences of these genes to maximum likelihood, Bayesian inference, and coalescent-based analyses. These analyses show that multicellularity independently evolved at least twice in the volvocine algae and that the colonial family Goniaceae is not monophyletic. Our data further indicate that cellular differentiation arose independently at least four, and possibly as many as six times, within the volvocine algae. Altogether, our results demonstrate that multicellularity and cellular differentiation are evolutionarily labile in the volvocine algae, affirming the importance of this group as a model system for the study of major transitions in the history of life.</p>
Multicellularity and sex helped shape the Tree of Life
<p>Across the Tree of Life, there are dramatic differences in species numbers among groups. However, the factors that explain the differences among the deepest branches have remained unknown. We tested whether multicellularity and sexual reproduction might explain these patterns, since the most species-rich groups share these traits. We found that groups with multicellularity and sexual reproduction have accelerated rates of species proliferation (diversification), and that multicellularity has a stronger effect than sexual reproduction. Patterns of species richness among clades are then strongly related to these differences in diversification rates. Taken together, these results help explain patterns of biodiversity among groups of organisms at the very broadest scales. They may also help explain the mysterious preponderance of sexual reproduction among species (the "paradox of sex") by showing that organisms with sexual reproduction proliferate more rapidly. </p>
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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