evolutionary scenario
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2021 ◽  
Author(s):  
Carlos Santana-Molina ◽  
Valentina Henriques ◽  
Damaso Hornero-Méndez ◽  
Damien P. Devos ◽  
Elena Rivas-Marin

Squalene is mostly associated with the biosynthesis of polycyclic triterpenes. Although there have been suggestions that squalene could be involved in the biosynthesis of carotenoids, functionally and evolutionarily related to polycyclic triterpenes, evidence of this 'squalene route' in nature was lacking. We demonstrate that planctomycetes synthesize C30 carotenoids via squalene and that this 'squalene route' is widely distributed in Bacteria. We also investigated the functional roles of hopanoids and carotenoids in Planctomycetes and show that their protective functions under stress conditions are complementary. Our evolutionary analyses suggest that the C30 carotenoid biosynthetic pathway is the most ancestral, with a potential origin in Firmicutes or Planctomycetes . In addition, we propose an evolutionary scenario to explain the diversification of the different carotenoid and squalene pathways. Together, these results improve the evolutionary contextualization of these molecules. Likewise, the widespread occurrence of the squalene route in bacteria increases the functional repertoire of squalene.


2021 ◽  
Author(s):  
◽  
Anton Killin

<p>The philosophical and scientific explication of music is a cutting-edge field in contemporary academia. This thesis develops a naturalistic framework for theorising about music. The following novel philosophical positions are motivated and defended: a polysemy analysis of “sound”, conceptual pluralism about music, a pluralistic framework for approaching the science of music, and a fictionalist account of Western musical artworks. The adaptation/ by-product framework for couching discussion about the evolution of music is critiqued. A novel, co-evolutionary, niche construction model of the foundations of musicality and the origins, expansion and stabilisation of music is developed, couched in the general context of hominin evolution and prehistory. Conceptual and methodological reflection accompanies the evolutionary scenario developed.</p>


2021 ◽  
Author(s):  
◽  
Anton Killin

<p>The philosophical and scientific explication of music is a cutting-edge field in contemporary academia. This thesis develops a naturalistic framework for theorising about music. The following novel philosophical positions are motivated and defended: a polysemy analysis of “sound”, conceptual pluralism about music, a pluralistic framework for approaching the science of music, and a fictionalist account of Western musical artworks. The adaptation/ by-product framework for couching discussion about the evolution of music is critiqued. A novel, co-evolutionary, niche construction model of the foundations of musicality and the origins, expansion and stabilisation of music is developed, couched in the general context of hominin evolution and prehistory. Conceptual and methodological reflection accompanies the evolutionary scenario developed.</p>


2021 ◽  
Vol 288 (1961) ◽  
Author(s):  
M. R. Whitney ◽  
K. D. Angielczyk ◽  
B. R. Peecook ◽  
C. A. Sidor

The mammalian tusk is a unique and extreme morphotype among modern vertebrate dentitions. Tusks—defined here as ever-growing incisors or canines composed of dentine—evolved independently multiple times within mammals yet have not evolved in other extant vertebrates. This suggests that there is a feature specific to mammals that facilitates the evolution of this specialized dentition. To investigate what may underpin the evolution of tusks, we histologically sampled the tusks of dicynodont therapsids: the earliest iteration of tusk evolution and the only non-mammalian synapsid clade to have acquired such a dentition. We studied the tissue composition, attachment tissues, development and replacement in 10 dicynodont taxa and show multiple developmental pathways for the adult dentitions of dicynodont tusks and tusk-like caniniforms. In a phylogenetic context, these developmental pathways reveal an evolutionary scenario for the acquisition of an ever-growing tusk—an event that occurred convergently, but only in derived members of our sample. We propose that the evolution of an ever-growing dentition, such as a tusk, is predicated on the evolution of significantly reduced tooth replacement and a permanent soft-tissue attachment. Both of these features are fixed in the dentitions of crown-group mammals, which helps to explain why tusks are restricted to this clade among extant vertebrates.


2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Seiya Watanabe ◽  
Yohsuke Murase ◽  
Yasunori Watanabe ◽  
Yasuhiro Sakurai ◽  
Kunihiko Tajima

AbstractAconitase superfamily members catalyze the homologous isomerization of specific substrates by sequential dehydration and hydration and contain a [4Fe-4S] cluster. However, monomeric and heterodimeric types of function unknown aconitase X (AcnX) have recently been characterized as a cis-3-hydroxy-L-proline dehydratase (AcnXType-I) and mevalonate 5-phosphate dehydratase (AcnXType-II), respectively. We herein elucidated the crystal structures of AcnXType-I from Agrobacterium tumefaciens (AtAcnX) and AcnXType-II from Thermococcus kodakarensis (TkAcnX) without a ligand and in complex with substrates. AtAcnX and TkAcnX contained the [2Fe-2S] and [3Fe-4S] clusters, respectively, conforming to UV and EPR spectroscopy analyses. The binding sites of the [Fe-S] cluster and substrate were clearlydifferent from those that were completely conserved in other aconitase enzymes; however, theoverall structural frameworks and locations of active sites were partially similar to each other.These results provide novel insights into the evolutionary scenario of the aconitase superfamilybased on the recruitment hypothesis.


Author(s):  
Arsham Nejad Kourki

Molecular methods have revolutionised virtually every area of biology, and metazoan phylogenetics is no exception: molecular phylogenies, molecular clocks, comparative phylogenomics, and developmental genetics have collectively transformed our understanding of the evolutionary history of animals. Moreover, the diversity of methods and models within molecular phylogenetics has resulted in significant disagreement among molecular phylogenies as well as between these and traditional phylogenies. Here, I argue that tackling this multifaceted problem lies in integrating evidence to infer the best evolutionary scenario. I begin with an overview of recent developments in early metazoan phylogenetics, followed by a discussion of key conceptual issues in phylogenetics revolving around phylogenetic evidence and theory. I then argue that integration of different kinds of evidence is necessary for arriving at the best evolutionary scenario rather than the best-fitting cladogram. Finally, I discuss the prospects of this view in stimulating interdisciplinary cross-talk in early metazoan research and beyond.


2021 ◽  
Author(s):  
Iraes Rabbers ◽  
Willi Gottstein ◽  
Adam Feist ◽  
Bas Teusink ◽  
Frank Bruggeman ◽  
...  

Overflow metabolism is ubiquitous in nature, and it is often considered inefficient because it leads to a relatively low biomass yield per consumed carbon. This metabolic strategy has been described as advantageous because it supports high growth rates during nutrient competition. Here we experimentally evolved bacteria without nutrient competition by repeatedly growing and mixing millions of parallel batch cultures of E. coli. Each culture originated from a water-in-oil emulsion droplet seeded with a single cell. Unexpectedly we found that overflow metabolism (acetate production) did not change. Instead the numerical cell yield during the consumption of the accumulated acetate increased as a consequence of a reduction in cell size. Our experiments and a mathematical model show that fast growth and overflow metabolism followed by the consumption of the overflow metabolite, leads to a higher numerical cell yield and therefore a higher fitness compared to full respiration of the substrate. This provides an evolutionary scenario where overflow metabolism can be favourable even in the absence of nutrient competition.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Polina Drozdova ◽  
Alena Kizenko ◽  
Alexandra Saranchina ◽  
Anton Gurkov ◽  
Maria Firulyova ◽  
...  

Abstract Background Vision is a crucial sense for the evolutionary success of many animal groups. Here we explore the diversity of visual pigments (opsins) in the transcriptomes of amphipods (Crustacea: Amphipoda) and conclude that it is restricted to middle (MWS) and long wavelength-sensitive (LWS) opsins in the overwhelming majority of examined species. Results We evidenced (i) parallel loss of MWS opsin expression in multiple species (including two independently evolved lineages from the deep and ancient Lake Baikal) and (ii) LWS opsin amplification (up to five transcripts) in both Baikal lineages. The number of LWS opsins negatively correlated with habitat depth in Baikal amphipods. Some LWS opsins in Baikal amphipods contained MWS-like substitutions, suggesting that they might have undergone spectral tuning. Conclusions This repeating two-step evolutionary scenario suggests common triggers, possibly the lack of light during the periods when Baikal was permanently covered with thick ice and its subsequent melting. Overall, this observation demonstrates the possibility of revealing climate history by following the evolutionary changes in protein families.


2021 ◽  
Author(s):  
Keiya Uriu ◽  
Yusuke Kosugi ◽  
Narumi Suzuki ◽  
Jumpei Ito ◽  
Kei Sato

APOBEC3 proteins play pivotal roles in defenses against retroviruses, including HIV-1, as well as retrotransposons. Presumably due to the evolutionary arms race between the hosts and retroelements, APOBEC3 genes have rapidly evolved in primate lineages through sequence diversification, gene amplification and loss, and gene fusion. Consequently, modern primates possess a unique set or “repertoire” of APOBEC3 genes. The APOBEC3 gene repertoire of humans has been well investigated. There are three types of catalytic domains (Z domain; A3Z1, A3Z2, and A3Z3), 11 Z domains, and 7 independent genes, including 4 genes encoding double Z domains. However, the APOBEC3 gene repertoires of nonhuman primates remain largely unclear. Here, we characterize APOBEC3 gene repertoires among primates and investigated the evolutionary scenario of primate APOBEC3 genes using phylogenetic and comparative genomics approaches. In the 21 primate species investigated, we identified 145 APOBEC3 genes, including 69 double-domain type APOBEC3 genes. We further estimated the ages of the respective APOBEC3 genes and revealed that APOBEC3B, APOBEC3D, and APOBEC3F are the youngest in humans and were generated in the common ancestor of Catarrhini. Notably, invasion of the LINE1 retrotransposon peaked during the same period as the generation of these youngest APOBEC3 genes, implying that LINE1 invasion was one of the driving forces of the generation of these genes. Moreover, we found evidence suggesting that sequence diversification by gene conversions among APOBEC3 paralogs occurred in multiple primate lineages. Together, our analyses reveal the hidden diversity and the complicated evolutionary scenario of APOBEC3 genes in primates. Importance In terms of virus-host interactions and coevolution, the APOBEC3 gene family is one of the most important subjects in the field of retrovirology. APOBEC3 genes are composed of a repertoire of subclasses based on sequence similarity, and a paper by LaRue et al. provides the standard guideline for the nomenclature and genomic architecture of APOBEC3 genes. However, it has been over 10 years since this publication, and new information, including RefSeq, which we used in this study, is accumulating. Based on accumulating knowledge, APOBEC3 genes, particularly those of primates, should be refined and reannotated. This study updates knowledge of primate APOBEC3 genes and their genomic architectures. We further inferred the evolutionary scenario of primate APOBEC3 genes and the potential driving forces of APOBEC3 gene evolution. This study will be a landmark for the elucidation of the multiple aspects of APOBEC3 family genes in the future.


2021 ◽  
Vol 12 ◽  
Author(s):  
Nicolas Leurs ◽  
Camille Martinand-Mari ◽  
Stéphanie Ventéo ◽  
Tatjana Haitina ◽  
Mélanie Debiais-Thibaud

Matrix Gla protein (Mgp) and bone Gla protein (Bgp) are vitamin-K dependent proteins that bind calcium in their γ-carboxylated versions in mammals. They are recognized as positive (Bgp) or negative (Mgp and Bgp) regulators of biomineralization in a number of tissues, including skeletal tissues of bony vertebrates. The Mgp/Bgp gene family is poorly known in cartilaginous fishes, which precludes the understanding of the evolution of the biomineralization toolkit at the emergence of jawed vertebrates. Here we took advantage of recently released genomic and transcriptomic data in cartilaginous fishes and described the genomic loci and gene expression patterns of the Mgp/Bgp gene family. We identified three genes, Mgp1, Mgp2, and Bgp, in cartilaginous fishes instead of the single previously reported Mgp gene. We describe their genomic loci, resulting in a dynamic evolutionary scenario for this gene family including several events of local (tandem) duplications, but also of translocation events, along jawed vertebrate evolution. We describe the expression patterns of Mgp1, Mgp2, and Bgp in embryonic stages covering organogenesis in the small-spotted catshark Scyliorhinus canicula and present a comparative analysis with Mgp/Bgp family members previously described in bony vertebrates, highlighting ancestral features such as early embryonic, soft tissues, and neuronal expressions, but also derived features of cartilaginous fishes such as expression in fin supporting fibers. Our results support an ancestral function of Mgp in skeletal mineralization and a later derived function of Bgp in skeletal development that may be related to the divergence of bony vertebrates.


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