scholarly journals Dating placentalia: Morphological clocks fail to close the molecular fossil gap

Evolution ◽  
2016 ◽  
Vol 70 (4) ◽  
pp. 873-886 ◽  
Author(s):  
Mark N. Puttick ◽  
Gavin H. Thomas ◽  
Michael J. Benton
Keyword(s):  
Molecular Fossil

scholarly journals Sterol and genomic analyses validate the sponge biomarker hypothesis

2016 ◽  
Vol 113 (10) ◽  
pp. 2684-2689 ◽  
Author(s):  
David A. Gold ◽  
Jonathan Grabenstatter ◽  
Alex de Mendoza ◽  
Ana Riesgo ◽  
Iñaki Ruiz-Trillo ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Duplication Event ◽  
Cambrian Explosion ◽  
Living Animal ◽  
Molecular Fossil ◽  
Molecular Fossils ◽  
Genomic Analyses ◽  
History Of ◽  
Salpingoeca Rosetta ◽  
Close Relatives

Molecular fossils (or biomarkers) are key to unraveling the deep history of eukaryotes, especially in the absence of traditional fossils. In this regard, the sterane 24-isopropylcholestane has been proposed as a molecular fossil for sponges, and could represent the oldest evidence for animal life. The sterane is found in rocks ∼650–540 million y old, and its sterol precursor (24-isopropylcholesterol, or 24-ipc) is synthesized today by certain sea sponges. However, 24-ipc is also produced in trace amounts by distantly related pelagophyte algae, whereas only a few close relatives of sponges have been assayed for sterols. In this study, we analyzed the sterol and gene repertoires of four taxa (Salpingoeca rosetta,Capsaspora owczarzaki,Sphaeroforma arctica, andCreolimax fragrantissima), which collectively represent the major living animal outgroups. We discovered that all four taxa lack C30sterols, including 24-ipc. By building phylogenetic trees for key enzymes in 24-ipc biosynthesis, we identified a candidate gene (carbon-24/28 sterol methyltransferase, orSMT) responsible for 24-ipc production. Our results suggest that pelagophytes and sponges independently evolved C30sterol biosynthesis through clade-specificSMTduplications. Using a molecular clock approach, we demonstrate that the relevant spongeSMTduplication event overlapped with the appearance of 24-isopropylcholestanes in the Neoproterozoic, but that the algalSMTduplication event occurred later in the Phanerozoic. Subsequently, pelagophyte algae and their relatives are an unlikely alternative to sponges as a source of Neoproterozoic 24-isopropylcholestanes, consistent with growing evidence that sponges evolved long before the Cambrian explosion ∼542 million y ago.

scholarly journals Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Daniel Blanco-Melo ◽  
Robert J Gifford ◽  
Paul D Bieniasz
Keyword(s):  
Host Defense ◽  
Envelope Protein ◽  
Endogenous Retrovirus ◽  
Monocarboxylate Transporter ◽  
Close Relative ◽  
Cell Surfaces ◽  
Molecular Fossil ◽  
Monocarboxylate Transporter 1 ◽  
The Past ◽  
Functional Envelope

Endogenous retroviral sequences provide a molecular fossil record of ancient infections whose analysis might illuminate mechanisms of viral extinction. A close relative of gammaretroviruses, HERV-T, circulated in primates for ~25 million years (MY) before apparent extinction within the past ~8 MY. Construction of a near-complete catalog of HERV-T fossils in primate genomes allowed us to estimate a ~32 MY old ancestral sequence and reconstruct a functional envelope protein (ancHTenv) that could support infection of a pseudotyped modern gammaretrovirus. Using ancHTenv, we identify monocarboxylate transporter-1 (MCT-1) as a receptor used by HERV-T for attachment and infection. A single HERV-T provirus in hominid genomes includes an env gene (hsaHTenv) that has been uniquely preserved. This apparently exapted HERV-T env could not support virion infection but could block ancHTenv mediated infection, by causing MCT-1 depletion from cell surfaces. Thus, hsaHTenv may have contributed to HERV-T extinction, and could also potentially regulate cellular metabolism.

scholarly journals Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics

2016 ◽  
Vol 114 (2) ◽  
pp. E171-E180 ◽  
Author(s):  
Jan Janouškovec ◽  
Gregory S. Gavelis ◽  
Fabien Burki ◽  
Donna Dinh ◽  
Tsvetan R. Bachvaroff ◽  
...  
Keyword(s):  
Cell Division ◽  
Dna Binding Proteins ◽  
Tetrapyrrole Biosynthesis ◽  
Molecular Fossil ◽  
Free Living ◽  
Major Transitions ◽  
Single Origin ◽  
Key Species ◽  
Phylogenetic Framework ◽  
Group Relationships

Dinoflagellates are key species in marine environments, but they remain poorly understood in part because of their large, complex genomes, unique molecular biology, and unresolved in-group relationships. We created a taxonomically representative dataset of dinoflagellate transcriptomes and used this to infer a strongly supported phylogeny to map major morphological and molecular transitions in dinoflagellate evolution. Our results show an early-branching position of Noctiluca, monophyly of thecate (plate-bearing) dinoflagellates, and paraphyly of athecate ones. This represents unambiguous phylogenetic evidence for a single origin of the group’s cellulosic theca, which we show coincided with a radiation of cellulases implicated in cell division. By integrating dinoflagellate molecular, fossil, and biogeochemical evidence, we propose a revised model for the evolution of thecal tabulations and suggest that the late acquisition of dinosterol in the group is inconsistent with dinoflagellates being the source of this biomarker in pre-Mesozoic strata. Three distantly related, fundamentally nonphotosynthetic dinoflagellates, Noctiluca, Oxyrrhis, and Dinophysis, contain cryptic plastidial metabolisms and lack alternative cytosolic pathways, suggesting that all free-living dinoflagellates are metabolically dependent on plastids. This finding led us to propose general mechanisms of dependency on plastid organelles in eukaryotes that have lost photosynthesis; it also suggests that the evolutionary origin of bioluminescence in nonphotosynthetic dinoflagellates may be linked to plastidic tetrapyrrole biosynthesis. Finally, we use our phylogenetic framework to show that dinoflagellate nuclei have recruited DNA-binding proteins in three distinct evolutionary waves, which included two independent acquisitions of bacterial histone-like proteins.

scholarly journals Paleogenomics illuminates the evolutionary history of the extinct Holocene “horned” crocodile of Madagascar, Voay robustus

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
E. Hekkala ◽  
J. Gatesy ◽  
A. Narechania ◽  
R. Meredith ◽  
M. Russello ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Molecular Data ◽  
Sister Group Relationship ◽  
Molecular Fossil ◽  
Close Relationship ◽  
History Of ◽  
Competing Hypotheses

AbstractAncient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300–1400 year old specimens (n = 2) of the extinct “horned” crocodile, Voay robustus, collected from Holocene deposits in southwestern Madagascar. Phylogenetic analyses of partial mt genomes and tip-dated timetrees based on molecular, fossil, and stratigraphic data favor a sister group relationship between Voay and Crocodylus (true crocodiles). These well supported trees conflict with recent morphological systematic work that has consistently placed Voay within Osteolaeminae (dwarf crocodiles and kin) and provide evidence for likely homoplasy in crocodylian cranial anatomy and snout shape. The close relationship between Voay and Crocodylus lends additional context for understanding the biogeographic origins of these genera and refines competing hypotheses for the recent extinction of Voay from Madagascar.

scholarly journals Urm1: A Non-Canonical UBL

Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 139
Author(s):  
Martin Termathe ◽  
Sebastian A. Leidel
Keyword(s):  
Stress Sensitivity ◽  
Protein Homeostasis ◽  
Main Function ◽  
Carrier Proteins ◽  
Molecular Fossil ◽  
Wobble Position ◽  
Nucleotide Modification ◽  
Domains Of Life ◽  
Carrier Systems ◽  
Sulfur Donor

Urm1 (ubiquitin related modifier 1) is a molecular fossil in the class of ubiquitin-like proteins (UBLs). It encompasses characteristics of classical UBLs, such as ubiquitin or SUMO (small ubiquitin-related modifier), but also of bacterial sulfur-carrier proteins (SCP). Since its main function is to modify tRNA, Urm1 acts in a non-canonical manner. Uba4, the activating enzyme of Urm1, contains two domains: a classical E1-like domain (AD), which activates Urm1, and a rhodanese homology domain (RHD). This sulfurtransferase domain catalyzes the formation of a C-terminal thiocarboxylate on Urm1. Thiocarboxylated Urm1 is the sulfur donor for 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U), a chemical nucleotide modification at the wobble position in tRNA. This thio-modification is conserved in all domains of life and optimizes translation. The absence of Urm1 increases stress sensitivity in yeast triggered by defects in protein homeostasis, a hallmark of neurological defects in higher organisms. In contrast, elevated levels of tRNA modifying enzymes promote the appearance of certain types of cancer and the formation of metastasis. Here, we summarize recent findings on the unique features that place Urm1 at the intersection of UBL and SCP and make Urm1 an excellent model for studying the evolution of protein conjugation and sulfur-carrier systems.

scholarly journals 100-My history of bornavirus infections hidden in vertebrate genomes

2021 ◽  
Vol 118 (20) ◽  
pp. e2026235118
Author(s):  
Junna Kawasaki ◽  
Shohei Kojima ◽  
Yahiro Mukai ◽  
Keizo Tomonaga ◽  
Masayuki Horie
Keyword(s):  
Phylogenetic Analyses ◽  
Migration Route ◽  
Messenger Rnas ◽  
Molecular Fossil ◽  
History Of ◽  
Geographic Distributions ◽  
Fossil Records ◽  
Insight Into ◽  
Animal Genomes

Although viruses have threatened our ancestors for millions of years, prehistoric epidemics of viruses are largely unknown. Endogenous bornavirus-like elements (EBLs) are ancient bornavirus sequences derived from the viral messenger RNAs that were reverse transcribed and inserted into animal genomes, most likely by retrotransposons. These elements can be used as molecular fossil records to trace past bornaviral infections. In this study, we systematically identified EBLs in vertebrate genomes and revealed the history of bornavirus infections over nearly 100 My. We confirmed that ancient bornaviral infections have occurred in diverse vertebrate lineages, especially in primate ancestors. Phylogenetic analyses indicated that primate ancestors were infected with various bornaviral lineages during evolution. EBLs in primate genomes formed clades according to their integration ages, suggesting that bornavirus lineages infected with primate ancestors had changed chronologically. However, some bornaviral lineages may have coexisted with primate ancestors and underwent repeated endogenizations for tens of millions of years. Moreover, a bornaviral lineage that coexisted with primate ancestors also endogenized in the genomes of some ancestral bats. The habitats of these bat ancestors have been reported to overlap with the migration route of primate ancestors. These results suggest that long-term virus–host coexistence expanded the geographic distributions of the bornaviral lineage along with primate migration and may have spread their infections to these bat ancestors. Our findings provide insight into the history of bornavirus infections over geological timescales that cannot be deduced from research using extant viruses alone, thus broadening our perspective on virus–host coevolution.

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