evolution Archives

The coincident relationships of predictable genes and their predictors. The nodes are gene families, or groups of gene families with the same PAP, and the edges are coincidence relationships with the arrow pointing at the node whose presence is predicted by the other. Edge thickness is proportional to the GINI importance value scaling linearly from the thinnest at 0.01 to the thickest at 0.062, while node size is proportional to the PageRank (56) value for that node. The PageRank algorithm has been applied here to evaluate the relative importance of each node within the network. A larger node size indicates a higher PageRank score, suggesting that the node has more influence or is more central in the network. Node size scales linearly from the smallest with a PageRank of 0.000043 to the largest with 0.002945. This visualisation aids in quickly identifying key nodes that play pivotal roles in the connectivity and flow of the network. Node colour indicates community as identified by the Louvain algorithm (57). This figure can be thought of as a high-level summary of the results of this analysis, and attention should be paid to the number of nodes in a community, the discrepancy in the size of nodes, and the number of edges emerging from nodes, in this figure, source nodes can have a D score < 0. For a version of this figure with these nodes removed, see SI Appendix, Fig. S8. -- University of Nottingham

Evolution Is Not As Random As Previously Thought

by Keith CowingJanuary 9, 2024January 9, 2024

A groundbreaking study has found that evolution is not as unpredictable as previously thought, which could allow scientists to explore which genes could be useful to tackle real-world issues such […]

A screenshot of the interactive tool. A scatterplot showing the relationships between a collection of trees can be shown alongside a selected individual gene tree (or collection of individual gene trees) . Additional gene-level variables such as functional annotation can also be visualized. -- biorxiv.org

Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Origin & Evolution of Life, Status Report

Analyzing Microbial Evolution Through Gene And Genome Phylogenies

by Keith CowingJanuary 9, 2024January 9, 2024

Microbiome scientists critically need modern tools to explore and analyze microbial evolution. Often this involves studying the evolution of microbial genomes as a whole.

Topology weighting reveals genomic regions associated with reproductive mode. (A) For each genomic window, we inferred a tree for all haplotypes and then classified 10,000 “subtrees” by randomly picking one haplotype per group. Topology weights are the proportions of each topology among all subtrees. Windows were plotted in a ternary plot based on the weights. (B) Simulated distributions of weights. A greater opportunity for lineage sorting (i to iii) biases the distribution toward the topology that matches the demographic history. Incomplete lineage sorting yields genealogies that are a better fit to one of the discordant trees, but the distribution is always symmetrical between the left and right half-triangles. Additional factors, including gene flow, create a bias toward one discordant genealogy (iv to vi). (C) Possible topologies and the empirical distribution of weights for the 154,971 100-SNP windows (“C,” compressa; “A,” arcana; “I” Iberian saxatilis; “N,” northern saxatilis). Hexagonal bins are colored by window count. (D) Counts of windows in the left and right half-triangles, with asymmetry quantified using DLR. Further division into subtriangles reveals left-right asymmetry throughout the distribution. Asterisks indicate significant asymmetry between corresponding left- and right-sided subtriangles. (E) Distributions of weights >0.7. -- Science

Origin & Evolution of Life, Press Release

Biologists Uncover The Secrets Of Evolutionary Change

by Keith CowingJanuary 5, 2024January 5, 2024

Significant evolutionary changes happen gradually as opposed to in dramatic ‘monster’ steps, biologists have discovered, answering the long-debated question as to how game-changing innovations like flight, vision, and the bearing […]

An illustration of a protocell inside an aqueous medium buffered with monomeric food molecules, 𝐴(1)𝑒𝑥𝑡 . The protocell membrane is composed of dimer molecules 𝐴(2) -- Life

Biochemistry & Organic Chemistry, Biophysics, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Origin & Evolution of Life, Status Report

Multistable Protocells Can Aid the Evolution of Prebiotic Autocatalytic Sets

by Keith CowingDecember 27, 2023December 27, 2023

We present a simple mathematical model that captures the evolutionary capabilities of a prebiotic compartment or protocell.

Number of generic extinctions per century among in different classes of vertebrates. The low number of reptiles and amphibia, which underestimate the magnitude of extinction pattern, is probably the result of the lack of information in earlier centuries, where very few species had been described. The dotted line represent the background extinction rate. PNAS

Extinction events, Gaia - Planetary Perspectives, Press Release

Human-driven Mass Extinction Is Eliminating Entire Branches Of The Tree Of Life

by Keith CowingDecember 11, 2023

The passenger pigeon. The Tasmanian tiger. The Baiji, or Yangtze river dolphin. These rank among the best-known recent victims of what many scientists have declared the sixth mass extinction, as […]

Snowball Earth - Artist's concept - NASA.gov

Biophysics, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

Physical Constraints During Snowball Earth Drive The Evolution Of Multicellularity

by Keith CowingDecember 9, 2023December 9, 2023

Molecular and fossil evidence suggest that complex eukaryotic multicellularity evolved during the late Neoproterozoic era, coincident with Snowball Earth glaciations, where ice sheets covered most of the globe.

A central insight was to model the gene history using information from related species. The modelling demonstrated that the palindromes of microRNA genes are generated by single mutation events. CREDIT Ari Löytynoja

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Press Release

New Genes Can Arise From Nothing

by Keith CowingDecember 8, 2023December 8, 2023

The complexity of living organisms is encoded within their genes, but where do these genes come from? Researchers at the University of Helsinki resolved outstanding questions around the origin of […]

ΨThe orientation of all the genes in the entire cluster flipped for aligning with the other genomes. Each arrow represents a different location on a single complete scaffold; adjacent arrows do not indicate their order on the genome; genes within an arrow are contiguous. ¶Pseudogene; red diamond and red rectangle represent gene(s) absent in the corresponding genome/location; arrows within dashed red boxes are contiguous; HP: hypothetical protein; RNP1: ribonuclease P protein component 1; ORF: open reading frame/gene; #ORF(s) annotated as HP(s); Hsp20: heat shock protein 20; ßpartial gene. -- Archaea

Extremeophiles and Extreme Environments, Fossils & Paleontology, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Press Release

Connections Between Archaea And Eukarya

by Keith CowingDecember 6, 2023December 6, 2023

NASA-supported researchers have examined the order and organization of genes that code for ribosomal protein in a group of archaea known as Asgard. The study is helping scientists better understand […]

Chain length distributions created by foldcats’ cooperativity. (Left, black) Typical polymerizations produce mostly short chains (shown as bin filling), following a Flory distribution [62, 90]. (Right, red) Foldcats produce more long chains for 2 reasons: (i) Foldcats catalyze elongation of other chains (k1 and k2), and (ii) Folded chains degrade more slowly because their folded cores are protected from solvent (k3). For analytical forms, see Appendix A. -- physics.bio-ph

Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

The Prebiotic Emergence Of Biological Evolution

by Keith CowingDecember 4, 2023December 4, 2023

The origin of life must have been preceded by Darwin-like evolutionary dynamics that could propagate it. How did that adaptive dynamics arise?

ROP signaling -- Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences

Biochemistry & Organic Chemistry, Biophysics, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Plant Biology, Press Release

ROP Signaling: Origin At Dawn Of Multicellular Plant Life

by Keith CowingDecember 2, 2023December 2, 2023

Plants regulate their development with a distinct group of molecular players. ROP proteins, a group of plant-specific proteins, are known to control plant tissue formation. Now, Hugh Mulvey and Liam […]