Cytoskeletal architecture and its evolutionary significance in amoeboid eukaryotes and their mode of locomotion

The cytoskeleton is the hallmark of eukaryotic evolution. The molecular and architectural aspects of the cytoskeleton have been playing a prominent role in our understanding of the origin and evolution of eukaryotes. In this study, we seek to investigate the cytoskeleton architecture and its evolutionary significance in understudied amoeboid lineages belonging to Amoebozoa. These amoebae primarily use cytoplasmic extensions supported by the cytoskeleton to perform important cellular processes such as movement and feeding. Amoeboid structure has important taxonomic significance, but, owing to techniques used, its potential significance in understanding diversity of the group has been seriously compromised, leading to an under-appreciation of its value. Here, we used immunocytochemistry and confocal microscopy to study the architecture of microtubules (MTs) and F-actin in diverse groups of amoebae. Our results demonstrate that all Amoebozoa examined are characterized by a complex cytoskeletal array, unlike what has been previously thought to exist. Our results not only conclusively demonstrate that all amoebozoans possess complex cytoplasmic MTs, but also provide, for the first time, a potential synapomorphy for the molecularly defined Amoebozoa clade. Based on this evidence, the last common ancestor of amoebozoans is hypothesized to have had a complex interwoven MT architecture limited within the granular cell body. We also generate several cytoskeleton characters related to MT and F-actin, which are found to be robust for defining groups in deep and shallow nodes of Amoebozoa.

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Phylogenetic supertree reveals detailed evolution of SARS-CoV-2

10.21203/rs.3.rs-33194/v1 ◽

2020 ◽

Author(s):

Tingting Li ◽

Dongxia Liu ◽

Yadi Yang ◽

Jiali Guo ◽

Yujie Feng ◽

...

Keyword(s):

Phylogenetic Tree ◽

Common Ancestor ◽

Virus Disease ◽

Evolutionary Relationship ◽

Critical Issue ◽

Last Common Ancestor ◽

Genome Sequences ◽

Phylogenetic Tree Analysis ◽

Origin And Evolution ◽

Bat Coronavirus

Abstract Corona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-19 and its evolutionary relationship is still ambiguous. Several reports attempted to figure out this critical issue by genome-based phylogenetic analysis, with limited progress. Here we applied phylogenetic supertree analysis to study the origin and evolution of SARS-CoV-2. Phylogenetic supertree analysis firmly disputes the accuracy of bat coronavirus RaTG13 be the last common ancestor of SARS- CoV-2s reported in other phylogenetic tree analysis based on viral genome sequences, although RaTG13 shows 96.5% similarity with SARS-CoV-2 in the genome. Therefore, viewing RaTG13 as the last common ancestor of SARS-CoV-2 would seriously mislead phylogenetic inference of SARS-CoV-2. Importantly, the discovery of evolution and mutation in SARS-CoV-2s was achieved by phylogenetic supertree analysis. Taken together, the phylogenetic supertree showed extraordinary priority on the SARS-CoV-2 evolution inference relative to the normal phylogenetic tree based on full-length genomic sequences.

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CT-Informed Skull Osteology of Palaeolagus haydeni (Mammalia: Lagomorpha) and Its Bearing on the Reconstruction of the Early Lagomorph Body Plan

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.634757 ◽

2021 ◽

Vol 9 ◽

Author(s):

Andrzej S. Wolniewicz ◽

Łucja Fostowicz-Frelik

Keyword(s):

Common Ancestor ◽

Late Eocene ◽

Last Common Ancestor ◽

Western North America ◽

Micro Computed Tomography ◽

Early Oligocene ◽

Phylogenetic Status ◽

Herbivorous Mammals ◽

Latest Eocene ◽

First Time

Lagomorpha is a clade of herbivorous mammals nested within Euarchontoglires, one of the major placental groups represented today. It comprises two extant families with markedly different body plans: the long-eared and long-limbed Leporidae (hares and rabbits) and the short-eared and short-limbed Ochotonidae (pikas). These two lagomorph lineages diverged probably during the latest Eocene/early Oligocene, but it is unclear whether the last common ancestor of crown lagomorphs was more leporid- or more ochotonid-like in morphology. Palaeolagus, an early lagomorph dominant in western North America from the late Eocene to Oligocene is of particular importance for addressing this controversy. Here, we present new and comprehensive data on the cranial anatomy of Palaeolagus haydeni, the type species for the genus, based on micro-computed tomography (μCT). Our μCT data allow us to confirm, revise and score for the very first time the states of several leporid-like and ochotonid-like characters in the skull of Palaeolagus. This mixed cranial architecture differentiates Palaeolagus from the crown groups of Lagomorpha and supports its phylogenetic status as a stem taxon.

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Origin and Evolution of Water Oxidation before the Last Common Ancestor of the Cyanobacteria

Molecular Biology and Evolution ◽

10.1093/molbev/msv024 ◽

2015 ◽

Vol 32 (5) ◽

pp. 1310-1328 ◽

Cited By ~ 63

Author(s):

Tanai Cardona ◽

James W. Murray ◽

A. William Rutherford

Keyword(s):

Water Oxidation ◽

Common Ancestor ◽

Last Common Ancestor ◽

Origin And Evolution

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Do chimpanzees like alcohol?

International journal of psychological research ◽

10.21500/20112084.2299 ◽

2016 ◽

Vol 9 (2) ◽

pp. 70-75

Author(s):

Ruth Maria Thomsen ◽

Anja Zschoke

Keyword(s):

Common Ancestor ◽

Great Apes ◽

Genetic Mutation ◽

Last Common Ancestor ◽

Food Scarcity ◽

In The Wild ◽

First Time ◽

Apple Puree ◽

Feeding Behaviours ◽

Apple Purée

In the last common ancestor of modern humans and the three living African ape species a genetic mutation occurred that increased the rate that alcohol was metabolized. This fact initially supports the "drunken monkey hypothesis" which states that natural selection should have favoured individuals that routinely incorporated alcohol- and thus energy-rich fruits into their diet. However, random observations from apes living in the wild do not provide evidence for such kind of choosey feeding behaviours. To investigate whether or not the living great apes have evolved a preference of alcohol-rich fruits over normal ripe fruits we performed a bioassay with captive chimpanzees offering them apple puree with and without rum flavour. Initially, the chimpanzees were curious about the alcohol-flavoured apple puree and feed on it when it was presented to them for the very first time. Once tasted, however, they lost interest in it indicating that chimpanzees are able to perceive, but do not prefer alcohol-rich fruits more than non-alcoholic fruits. Thus, we think that for our hominoid ancestors from the late Miocene the possibility to consume alcohol-rich fruits was helpful to survive periods of food scarcity, but did not lead to a genetic predisposition for alcohol.

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What have the revelations about Neanderthal DNA revealed about Homo sapiens?

Anthropological Review ◽

10.2478/anre-2020-0008 ◽

2020 ◽

Vol 83 (1) ◽

pp. 93-107

Author(s):

Santiago Wolnei Ferreira Guimarães ◽

Hilton P. Silva

Keyword(s):

Gene Flow ◽

Morphological Traits ◽

Common Ancestor ◽

Homo Sapiens ◽

Explanatory Models ◽

The Other ◽

Last Common Ancestor ◽

Genetic Studies ◽

Origin And Evolution ◽

Out Of Africa

AbstractGenetic studies have presented increasing indications about the complexity of the interactions between Homo sapiens, Neanderthals and Denisovans, during Pleistocene. The results indicate potential replacement or admixture of the groups of hominins that lived in the same region at different times. Recently, the time of separation among these hominins in relation to the Last Common Ancestor – LCA has been reasonably well established. Events of mixing with emphasis on the Neanderthal gene flow into H. sapiens outside Africa, Denisovans into H. sapiens ancestors in Oceania and continental Asia, Neanderthals into Denisovans, as well as the origin of some phenotypic features in specific populations such as the color of the skin, eyes, hair and predisposition to develop certain kinds of diseases have also been found. The current information supports the existence of both replacement and interbreeding events, and indicates the need to revise the two main explanatory models, the Multiregional and the Out-of-Africa hypotheses, about the origin and evolution of H. sapiens and its co-relatives. There is definitely no longer the possibility of justifying only one model over the other. This paper aims to provide a brief review and update on the debate around this issue, considering the advances brought about by the recent genetic as well as morphological traits analyses.

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Evolution of protein kinase substrate recognition at the active site

10.1101/443945 ◽

2018 ◽

Author(s):

David Bradley ◽

Pedro Beltrao

Keyword(s):

Protein Kinase ◽

Sequence Variation ◽

Common Ancestor ◽

Last Common Ancestor ◽

Kinase Substrate ◽

Cellular Processes ◽

Eukaryotic Species ◽

Target Sites ◽

Kinase Specificity ◽

Substrate Motif

AbstractProtein kinases catalyse the phosphorylation of target proteins, controlling most cellular processes. The specificity of serine/threonine kinases is partly determined by interactions with a few residues near the phospho-acceptor residue, forming the so-called kinase substrate motif. Kinases have been extensively duplicated throughout evolution but little is known about when in time new target motifs have arisen. Here we show that sequence variation occurring early in the evolution of kinases is dominated by changes in specificity determining residues. We then analysed kinase specificity models, based on known target sites, observing that specificity has remained mostly unchanged for recent kinase duplications. Finally, analysis of phosphorylation data from a taxonomically broad set of 48 eukaryotic species indicates that most phosphorylation motifs are broadly distributed in eukaryotes but not present in prokaryotes. Overall, our results suggest that the set of eukaryotes kinase motifs present today was acquired soon after the eukaryotic last common ancestor and that early expansions of the protein kinase fold rapidly explored the space of possible target motifs.

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3D genomics across the tree of life reveals condensin II as a determinant of architecture type

Science ◽

10.1126/science.abe2218 ◽

2021 ◽

Vol 372 (6545) ◽

pp. 984-989

Author(s):

Claire Hoencamp ◽

Olga Dudchenko ◽

Ahmed M. O. Elbatsh ◽

Sumitabha Brahmachari ◽

Jonne A. Raaijmakers ◽

...

Keyword(s):

Human Genome ◽

Physical Model ◽

Common Ancestor ◽

Three Dimensional ◽

Tree Of Life ◽

Genome Architecture ◽

Last Common Ancestor ◽

Eukaryotic Evolution ◽

3D Genome ◽

3D Genomics

We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.

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Experimental evidence for yawn contagion in orangutans (Pongo pygmaeus)

Scientific Reports ◽

10.1038/s41598-020-79160-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Evy van Berlo ◽

Alejandra P. Díaz-Loyo ◽

Oscar E. Juárez-Mora ◽

Mariska E. Kret ◽

Jorg J. M. Massen

Keyword(s):

Experimental Evidence ◽

Common Ancestor ◽

Great Apes ◽

Pongo Pygmaeus ◽

Last Common Ancestor ◽

Contagious Yawning ◽

Proximate Mechanism ◽

Social Species ◽

Ultimate Causation

AbstractYawning is highly contagious, yet both its proximate mechanism(s) and its ultimate causation remain poorly understood. Scholars have suggested a link between contagious yawning (CY) and sociality due to its appearance in mostly social species. Nevertheless, as findings are inconsistent, CY’s function and evolution remains heavily debated. One way to understand the evolution of CY is by studying it in hominids. Although CY has been found in chimpanzees and bonobos, but is absent in gorillas, data on orangutans are missing despite them being the least social hominid. Orangutans are thus interesting for understanding CY’s phylogeny. Here, we experimentally tested whether orangutans yawn contagiously in response to videos of conspecifics yawning. Furthermore, we investigated whether CY was affected by familiarity with the yawning individual (i.e. a familiar or unfamiliar conspecific and a 3D orangutan avatar). In 700 trials across 8 individuals, we found that orangutans are more likely to yawn in response to yawn videos compared to control videos of conspecifics, but not to yawn videos of the avatar. Interestingly, CY occurred regardless of whether a conspecific was familiar or unfamiliar. We conclude that CY was likely already present in the last common ancestor of humans and great apes, though more converging evidence is needed.

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Clinical and Environmental Isolates of Cryptococcus gattii from Australia That Retain Sexual Fecundity

Eukaryotic Cell ◽

10.1128/ec.4.8.1410-1419.2005 ◽

2005 ◽

Vol 4 (8) ◽

pp. 1410-1419 ◽

Cited By ~ 59

Author(s):

Leona T. Campbell ◽

James A. Fraser ◽

Connie B. Nichols ◽

Fred S. Dietrich ◽

Dee Carter ◽

...

Keyword(s):

Common Ancestor ◽

Dominant Mode ◽

Cryptococcus Gattii ◽

Sexual Cycle ◽

Environmental Isolates ◽

Molecular Type ◽

Pathogenic Yeast ◽

Cycle Dependent ◽

Mat Locus ◽

First Time

ABSTRACTCryptococcus gattiiis a primary pathogenic yeast that causes disease in both animals and humans. It is closely related toCryptococcus neoformansand diverged from a common ancestor ∼40 million years ago. WhileC. gattiihas a characterized sexual cycle dependent upon a dimorphic region of the genome known as the MAT locus, mating has rarely been observed in this species. In this study, we identify for the first time clinical (both human and veterinary) and environmental isolates from Australia that retain sexual fecundity. A collection of 120 isolates from a variety of geographic locations was analyzed for molecular type, mating type, and the ability to develop mating structures when cocultured with fertile tester strains. Nine isolates produced dikaryotic filaments with paired nuclei, fused clamp connections, and basidiospores. DNA sequence analysis of three genes (URA5, the MATα-specificSXI1α gene, and the MATa-specificSXI2agene) revealed little or no variability inURA5andSXI2a, respectively. However across the 108 MATα strains sequenced, theSXI1α gene was found to exist as 11 different alleles. Phylogenetic analysis found most variation to occur in the more fertile genotypes. Although some lineages of AustralianC. gattiihave retained the ability to mate, the majority of isolates were sterile, suggesting that asexuality is the dominant mode of propagation in these populations.

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Recombinant transfer in the basic genome ofEscherichia coli

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1510839112 ◽

2015 ◽

Vol 112 (29) ◽

pp. 9070-9075 ◽

Cited By ~ 59

Author(s):

Purushottam D. Dixit ◽

Tin Yau Pang ◽

F. William Studier ◽

Sergei Maslov

Keyword(s):

Common Ancestor ◽

Recipient Cell ◽

Gene Clusters ◽

Selective Advantage ◽

Last Common Ancestor ◽

Genome Sequences ◽

Bacterial Genomes ◽

Basic Genome ◽

Single Base Pair ◽

Generalized Transduction

An approximation to the ∼4-Mbp basic genome shared by 32 strains ofEscherichia colirepresenting six evolutionary groups has been derived and analyzed computationally. A multiple alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ∼90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single base-pair mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly between genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome pairs have one or two recombinant transfers of length ∼40–115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4–1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kilobase pairs. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. Most recombinant transfers seem likely to be due to generalized transduction by coevolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.

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