scholarly journals Evolution of a chordate-specific mechanism for myoblast fusion

2021 ◽  
Author(s):  
Haifeng Zhang ◽  
Renjie Shang ◽  
Kwantae Kim ◽  
Wei Zheng ◽  
Christopher J. Johnson ◽  
...  
Keyword(s):  
Evolutionary History ◽  
De Novo ◽  
Myoblast Fusion ◽  
Last Common Ancestor ◽  
Functional Tests ◽  
Evolutionary Origins ◽  
New Genes ◽  
History Of ◽  
Early Vertebrates ◽  
And Function

The size of an animal is determined by the size of its musculoskeletal system. Myoblast fusion is an innovative mechanism that allows for multinucleated muscle fibers to compound the size and strength of individual mononucleated cells. However, the evolutionary history of the control mechanism underlying this important process is currently unknown. The phylum Chordata hosts closely related groups that span distinct myoblast fusion states: no fusion in cephalochordates, restricted fusion and multinucleation in tunicates, and extensive, obligatory fusion in vertebrates. To elucidate how these differences may have evolved, we studied the evolutionary origins and function of membrane-coalescing agents Myomaker and Myomixer in various groups of chordates. Here we report that Myomaker likely arose through gene duplication in the last common ancestor of tunicates and vertebrates, while Myomixer appears to have evolved de novo in early vertebrates. Functional tests revealed an unexpectedly complex evolutionary history of myoblast fusion in chordates. A pre-vertebrate phase of muscle multinucleation driven by Myomaker was followed by the later emergence of Myomixer that enables the highly efficient fusion system of vertebrates. Thus, our findings reveal the evolutionary origins of chordate-specific fusogens and illustrate how new genes can shape the emergence of novel morphogenetic traits and mechanisms.

scholarly journals Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yoichiro Nakatani ◽  
Prashant Shingate ◽  
Vydianathan Ravi ◽  
Nisha E. Pillai ◽  
Aravind Prasad ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Gene Loss ◽  
De Novo ◽  
Genome Structure ◽  
Origin And Evolution ◽  
Long Read ◽  
History Of ◽  
And Function ◽  
Genome Assemblies ◽  
Key Questions

AbstractAncient polyploidization events have had a lasting impact on vertebrate genome structure, organization and function. Some key questions regarding the number of ancient polyploidization events and their timing in relation to the cyclostome-gnathostome divergence have remained contentious. Here we generate de novo long-read-based chromosome-scale genome assemblies for the Japanese lamprey and elephant shark. Using these and other representative genomes and developing algorithms for the probabilistic macrosynteny model, we reconstruct high-resolution proto-vertebrate, proto-cyclostome and proto-gnathostome genomes. Our reconstructions resolve key questions regarding the early evolutionary history of vertebrates. First, cyclostomes diverged from the lineage leading to gnathostomes after a shared tetraploidization (1R) but before a gnathostome-specific tetraploidization (2R). Second, the cyclostome lineage experienced an additional hexaploidization. Third, 2R in the gnathostome lineage was an allotetraploidization event, and biased gene loss from one of the subgenomes shaped the gnathostome genome by giving rise to remarkably conserved microchromosomes. Thus, our reconstructions reveal the major evolutionary events and offer new insights into the origin and evolution of vertebrate genomes.

scholarly journals Global Epidemiology and Evolutionary History of Staphylococcus aureus ST45

2020 ◽  
Vol 59 (1) ◽  
pp. e02198-20
Author(s):  
N. Effelsberg ◽  
M. Stegger ◽  
L. Peitzmann ◽  
O. Altinok ◽  
G. W. Coombs ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Evolutionary History ◽  
De Novo ◽  
Clinical Symptoms ◽  
Phylogenetic Analyses ◽  
Invasive Disease ◽  
Phylogenetic Groups ◽  
Content Type ◽  
Global Epidemiology ◽  
History Of

ABSTRACTStaphylococcus aureus ST45 is a major global MRSA lineage with huge strain diversity and a high clinical impact. It is one of the most prevalent carrier lineages but also frequently causes severe invasive disease, such as bacteremia. Little is known about its evolutionary history. In this study, we used whole-genome sequencing to analyze a large collection of 451 diverse ST45 isolates from 6 continents and 26 countries. De novo-assembled genomes were used to understand genomic plasticity and to perform coalescent analyses. The ST45 population contained two distinct sublineages, which correlated with the isolates’ geographical origins. One sublineage primarily consisted of European/North American isolates, while the second sublineage primarily consisted of African and Australian isolates. Bayesian analysis predicted ST45 originated in northwestern Europe about 500 years ago. Isolation time, host, and clinical symptoms did not correlate with phylogenetic groups. Our phylogenetic analyses suggest multiple acquisitions of the SCCmec element and key virulence factors throughout the evolution of the ST45 lineage.

scholarly journals Fossils with Feathers and Philosophy of Science

2019 ◽  
Vol 68 (5) ◽  
pp. 840-851 ◽  
Author(s):  
Joyce C Havstad ◽  
N Adam Smith
Keyword(s):  
Philosophy Of Science ◽  
Evolutionary History ◽  
Scientific Practice ◽  
Scientific Evidence ◽  
Thomas Kuhn ◽  
Karl Popper ◽  
Scientific Debate ◽  
Evolutionary Origins ◽  
Research Programmes ◽  
History Of

AbstractThe last half century of paleornithological research has transformed the way that biologists perceive the evolutionary history of birds. This transformation has been driven, since 1969, by a series of exciting fossil discoveries combined with intense scientific debate over how best to interpret these discoveries. Ideally, as evidence accrues and results accumulate, interpretive scientific agreement forms. But this has not entirely happened in the debate over avian origins: the accumulation of scientific evidence and analyses has had some effect, but not a conclusive one, in terms of resolving the question of avian origins. Although the majority of biologists have come to accept that birds are dinosaurs, there is lingering and, in some quarters, strident opposition to this view. In order to both understand the ongoing disagreement about avian origins and generate a prediction about the future of the debate, here we use a revised model of scientific practice to assess the current and historical state of play surrounding the topic of bird evolutionary origins. Many scientists are familiar with the metascientific scholars Sir Karl Popper and Thomas Kuhn, and these are the primary figures that have been appealed to so far, in prior attempts to assess the dispute. But we demonstrate that a variation of Imre Lakatos’s model of progressive versus degenerative research programmes provides a novel and productive assessment of the debate. We establish that a refurbished Lakatosian account both explains the intractability of the dispute and predicts a likely outcome for the debate about avian origins. In short, here, we offer a metascientific tool for rationally assessing competing theories—one that allows researchers involved in seemingly intractable scientific disputes to advance their debates.

scholarly journals Lineage-independent retrotransposition of UTP14 associated with male fertility has occurred multiple times throughout mammalian evolution

2017 ◽  
Vol 4 (12) ◽  
pp. 171049 ◽  
Author(s):  
Jan Rohozinski
Keyword(s):  
Evolutionary History ◽  
Male Gamete ◽  
Housekeeping Genes ◽  
Evolutionary Trees ◽  
South American ◽  
Mammalian Evolution ◽  
Interesting Aspect ◽  
New Genes ◽  
History Of ◽  
Gamete Production

In mammals, gamete production is essential for reproductive success. This is particularly true for males where large quantities of sperm are produced to fertilize a limited number of eggs released by the female. Because of this, new genes associated with increased spermatogenic efficiency have been accumulating throughout the evolution of therian mammals. Many of these new genes are testis-specific retrotransposed copies of housekeeping genes located on the X chromosome. Of particular interest are retrotransposed copies of UTP14 that are present in many distantly related eutherian mammals. Analysis of genomic data available in ENSEMBL indicates that these UTP14 retrogenes have arisen independently in the various eutherian clades. They represent an interesting aspect of evolution whereby new homologues of UTP14 have become independently fixed in multiple mammalian lineages due to the reproductive advantage that may be conferred to males. Surprisingly, these genes may also be lost, even after being present within a lineage for millions of years. This phenomenon may potentially be used to delineate evolutionary trees in closely related groups of mammals, particularly in the case of South American primates. Studying these retrogenes will yield new insights into the evolutionary history of male gamete production and the phylogeny of eutherian mammals.

scholarly journals How global extinctions impact regional biodiversity in mammals

2011 ◽  
Vol 8 (2) ◽  
pp. 222-225 ◽  
Author(s):  
Shan Huang ◽  
T. Jonathan Davies ◽  
John L. Gittleman
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Diversity ◽  
Spatial Scales ◽  
Spatial Location ◽  
Ecosystem Processes ◽  
Biodiversity Hotspots ◽  
Species Assemblage ◽  
Species Extinction ◽  
History Of ◽  
And Function

Phylogenetic diversity (PD) represents the evolutionary history of a species assemblage and is a valuable measure of biodiversity because it captures not only species richness but potentially also genetic and functional diversity. Preserving PD could be critical for maintaining the functional integrity of the world's ecosystems, and species extinction will have a large impact on ecosystems in areas where the ecosystem cost per species extinction is high. Here, we show that impacts from global extinctions are linked to spatial location. Using a phylogeny of all mammals, we compare regional losses of PD against a model of random extinction. At regional scales, losses differ dramatically: several biodiversity hotspots in southern Asia and Amazonia will lose an unexpectedly large proportion of PD. Global analyses may therefore underestimate the impacts of extinction on ecosystem processes and function because they occur at finer spatial scales within the context of natural biogeography.

scholarly journals Tissue-specific geometry and chemistry of modern and fossilized melanosomes reveal internal anatomy of extinct vertebrates

2019 ◽  
Vol 116 (36) ◽  
pp. 17880-17889 ◽  
Author(s):  
Valentina Rossi ◽  
Maria E. McNamara ◽  
Sam M. Webb ◽  
Shosuke Ito ◽  
Kazumasa Wakamatsu
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Distribution ◽  
Internal Anatomy ◽  
Anatomical Distribution ◽  
Tissue Specific ◽  
Anatomical Features ◽  
Evolutionary Origins ◽  
History Of ◽  
Specific Geometry ◽  
Holistic Method

Recent discoveries of nonintegumentary melanosomes in extant and fossil amphibians offer potential insights into the physiological functions of melanin not directly related to color production, but the phylogenetic distribution and evolutionary history of these internal melanosomes has not been characterized systematically. Here, we present a holistic method to discriminate among melanized tissues by analyzing the anatomical distribution, morphology, and chemistry of melanosomes in various tissues in a phylogenetically broad sample of extant and fossil vertebrates. Our results show that internal melanosomes in all extant vertebrates analyzed have tissue-specific geometries and elemental signatures. Similar distinct populations of preserved melanosomes in phylogenetically diverse vertebrate fossils often map onto specific anatomical features. This approach also reveals the presence of various melanosome-rich internal tissues in fossils, providing a mechanism for the interpretation of the internal anatomy of ancient vertebrates. Collectively, these data indicate that vertebrate melanins share fundamental physiological roles in homeostasis via the scavenging and sequestering of metals and suggest that intimate links between melanin and metal metabolism in vertebrates have deep evolutionary origins.

scholarly journals Evolutionary history and metabolic insights of ancient mammalian uricases

2014 ◽  
Vol 111 (10) ◽  
pp. 3763-3768 ◽  
Author(s):  
James T. Kratzer ◽  
Miguel A. Lanaspa ◽  
Michael N. Murphy ◽  
Christina Cicerchi ◽  
Christina L. Graves ◽  
...  
Keyword(s):  
Uric Acid ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Tumor Lysis Syndrome ◽  
Integrated Approach ◽  
Last Common Ancestor ◽  
Evolutionary Models ◽  
Monosodium Urate ◽  
Domains Of Life ◽  
History Of

Uricase is an enzyme involved in purine catabolism and is found in all three domains of life. Curiously, uricase is not functional in some organisms despite its role in converting highly insoluble uric acid into 5-hydroxyisourate. Of particular interest is the observation that apes, including humans, cannot oxidize uric acid, and it appears that multiple, independent evolutionary events led to the silencing or pseudogenization of the uricase gene in ancestral apes. Various arguments have been made to suggest why natural selection would allow the accumulation of uric acid despite the physiological consequences of crystallized monosodium urate acutely causing liver/kidney damage or chronically causing gout. We have applied evolutionary models to understand the history of primate uricases by resurrecting ancestral mammalian intermediates before the pseudogenization events of this gene family. Resurrected proteins reveal that ancestral uricases have steadily decreased in activity since the last common ancestor of mammals gave rise to descendent primate lineages. We were also able to determine the 3D distribution of amino acid replacements as they accumulated during evolutionary history by crystallizing a mammalian uricase protein. Further, ancient and modern uricases were stably transfected into HepG2 liver cells to test one hypothesis that uricase pseudogenization allowed ancient frugivorous apes to rapidly convert fructose into fat. Finally, pharmacokinetics of an ancient uricase injected in rodents suggest that our integrated approach provides the foundation for an evolutionarily-engineered enzyme capable of treating gout and preventing tumor lysis syndrome in human patients.

scholarly journals Mycenagenomes resolve the evolution of fungal bioluminescence

2020 ◽  
Vol 117 (49) ◽  
pp. 31267-31277
Author(s):  
Huei-Mien Ke ◽  
Hsin-Han Lee ◽  
Chan-Yi Ivy Lin ◽  
Yu-Ching Liu ◽  
Min R. Lu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Developmental Stages ◽  
De Novo ◽  
Fungal Species ◽  
Last Common Ancestor ◽  
Diverse Group ◽  
Mushroom Species ◽  
Genome Assemblies

Mushroom-forming fungi in the order Agaricales represent an independent origin of bioluminescence in the tree of life; yet the diversity, evolutionary history, and timing of the origin of fungal luciferases remain elusive. We sequenced the genomes and transcriptomes of five bonnet mushroom species (Mycenaspp.), a diverse lineage comprising the majority of bioluminescent fungi. Two species with haploid genome assemblies ∼150 Mb are among the largest in Agaricales, and we found that a variety of repeats betweenMycenaspecies were differentially mediated by DNA methylation. We show that bioluminescence evolved in the last common ancestor of mycenoid and the marasmioid clade of Agaricales and was maintained through at least 160 million years of evolution. Analyses of synteny across genomes of bioluminescent species resolved how the luciferase cluster was derived by duplication and translocation, frequently rearranged and lost in mostMycenaspecies, but conserved in theArmillarialineage. Luciferase cluster members were coexpressed across developmental stages, with the highest expression in fruiting body caps and stipes, suggesting fruiting-related adaptive functions. Our results contribute to understanding a de novo origin of bioluminescence and the corresponding gene cluster in a diverse group of enigmatic fungal species.

scholarly journals The evolutionary history of a gammaretrovirus currently colonizing the mule deer genome is marked by extensive recombination

2021 ◽  
Author(s):  
Lei Yang ◽  
Raunaq Malhotra ◽  
Rayan Chikhi ◽  
Daniel Elleder ◽  
Theodora Kaiser ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Mule Deer ◽  
Endogenous Retrovirus ◽  
Host Population ◽  
Endogenous Retroviruses ◽  
Genomic Diversity ◽  
Evolutionary Trajectory ◽  
History Of

AbstractBackgroundAll vertebrate genomes have been colonized by retroviruses along their evolutionary trajectory. Although it is clear that endogenous retroviruses (ERVs) can contribute important physiological functions to contemporary hosts, such benefits are attributed to long-term co-evolution of ERV and host. Newly colonized ERVs are thought unlikely to contribute to host genome evolution because germline infections are rare and because the host effectively silences them. The genomes of several outbred species including mule deer (Odocoileus hemionus) are currently being colonized by ERVs, which provides an opportunity to study ERV dynamics at a time when few are fixed.Here we investigate the history of cervid endogenous retrovirus (CrERV) acquisition and expansion in the mule deer genome to determine the potential impact of endogenizing retroviruses on host genomic diversity.MethodsA mule deer genome was de novo assembled from short and long insert mate pair reads. Scaffolds were further assembled using reference assisted chromosome assembly (RACA) to provide spatial orientation of CrERV insertion sites and to facilitate assembly of CrERV sequences. We applied phylogenetic and coalescent approaches to non-recombinant genomes to determine CrERV evolutionary history, augmenting ancestral divergence estimates with the prevalence of each CrERV locus in a population of mule deer. Recombination history was investigated on partial genome alignments.ResultsThe CrERV composition and diversity in the mule deer genome has recently measurably increased by horizontal acquisition of a new retroviruses lineage and because of recombination with existing CrERV. Resulting interlineage recombinants also endogenized and subsequently retrotransposed. CrERV loci are significantly closer to genes than expected if integration were random and gene proximity might explain the recent expansion by retrotransposition of one recombinant CrERV lineage.ConclusionsThere has been a burst of CrERV integrations during a recent retrovirus epizootic that increased genomic CrERV burden and has resulted in extensive insertional polymorphism in contemporary mule deer genomes. Recombination is a defining feature of CrERV evolutionary dynamics driven by this colonization, increasing CrERV burden and CrERV genetic diversity. These data support that retroviral colonization during an epizootic provides a burst of genomic diversity to the host population.

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