scholarly journals Phylogenetic reconciliation reveals extensive ancestral recombination in Sarbecoviruses and the SARS-CoV-2 lineage

2021 ◽  
Author(s):  
Sumaira Zaman ◽  
Samuel Sledzieski ◽  
Bonnie Berger ◽  
Yi-Chieh Wu ◽  
Mukul S. Bansal
Keyword(s):  
Evolutionary History ◽  
Viral Evolution ◽  
Emerging Pathogens ◽  
Phylogenetic Methods ◽  
History Of ◽  
Tree Estimation ◽  
Phylogenetic Reconciliation ◽  
Horseshoe Bat ◽  
Insight Into ◽  
Family Trees

An accurate understanding of the evolutionary history of rapidly-evolving viruses like SARS-CoV-2, responsible for the COVID-19 pandemic, is crucial to tracking and preventing the spread of emerging pathogens. However, viruses undergo frequent recombination, which makes it difficult to trace their evolutionary history using traditional phylogenetic methods. Here, we present a phylogenetic workflow, virDTL, for analyzing viral evolution in the presence of recombination. Our approach leverages reconciliation methods developed for inferring horizontal gene transfer in prokaryotes, and, compared to existing tools, is uniquely able to identify ancestral recombinations while accounting for several sources of inference uncertainty, including in the construction of a strain tree, estimation and rooting of gene family trees, and reconciliation itself. We apply this workflow to the Sarbecovirus subgenus and demonstrate how a principled analysis of predicted recombination gives insight into the evolution of SARS-CoV-2. In addition to providing confirming evidence for the horseshoe bat as its zoonotic origin, we identify several ancestral recombination events that merit further study.

The amphibamiform Nanobamus macrorhinus from the early Permian of Texas

2019 ◽  
Vol 94 (2) ◽  
pp. 366-377 ◽  
Author(s):  
Bryan M. Gee ◽  
Robert R. Reisz
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary History ◽  
Phylogenetic Position ◽  
Early Permian ◽  
Larval Form ◽  
Terrestrial Environments ◽  
History Of ◽  
Insight Into

AbstractNanobamus macrorhinus Schoch and Milner, 2014 is a small amphibamiform temnospondyl from the early Permian Arroyo Formation of Texas. It is most readily characterized by an elongate and partially subdivided naris. This condition is superficially reminiscent of that seen in the coeval trematopids, the group to which N. macrorhinus was originally referred to under an interpretation of the holotype as a larval form. This was discounted by later workers, but the amphibamiform affinities of the specimen were not formalized until recently. The specimen has never been described in the context of its amphibamiform affinities and remains poorly characterized, never having been sampled in a phylogenetic analysis. Here we present a complete, updated osteological description of N. macrorhinus, including an improved characterization of its unique mosaic of plesiomorphic and apomorphic features and clarification of the taxon's autapomorphies. Our analysis of the taxon's phylogenetic position within Amphibamiformes shows that N. macrorhinus was recovered as diverging after basal amphibamiforms, e.g., the micropholids, and before derived amphibamiforms, e.g., the amphibamids. This is supported by the unique mixture of retained plesiomorphies, e.g., nonforeshortened postparietals and an oval choana, and apomorphies, e.g., a narrow interorbital region and slender palatal rami of the pterygoid. These results reflect the complexity of terrestrial amphibamiform diversity and provide further insight into the evolutionary history of the lissamphibian stem in terrestrial environments.

scholarly journals Ancient origins and multiple appearances of carotenoid-pigmented feathers in birds

2014 ◽  
Vol 281 (1788) ◽  
pp. 20140806 ◽  
Author(s):  
Daniel B. Thomas ◽  
Kevin J. McGraw ◽  
Michael W. Butler ◽  
Matthew T. Carrano ◽  
Odile Madden ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
High Performance ◽  
Evolutionary History ◽  
Carotenoid Pigments ◽  
Biological Functions ◽  
The Family ◽  
Family Level ◽  
History Of ◽  
Living Species ◽  
Insight Into

The broad palette of feather colours displayed by birds serves diverse biological functions, including communication and camouflage. Fossil feathers provide evidence that some avian colours, like black and brown melanins, have existed for at least 160 million years (Myr), but no traces of bright carotenoid pigments in ancient feathers have been reported. Insight into the evolutionary history of plumage carotenoids may instead be gained from living species. We visually surveyed modern birds for carotenoid-consistent plumage colours (present in 2956 of 9993 species). We then used high-performance liquid chromatography and Raman spectroscopy to chemically assess the family-level distribution of plumage carotenoids, confirming their presence in 95 of 236 extant bird families (only 36 family-level occurrences had been confirmed previously). Using our data for all modern birds, we modelled the evolutionary history of carotenoid-consistent plumage colours on recent supertrees. Results support multiple independent origins of carotenoid plumage pigmentation in 13 orders, including six orders without previous reports of plumage carotenoids. Based on time calibrations from the supertree, the number of avian families displaying plumage carotenoids increased throughout the Cenozoic, and most plumage carotenoid originations occurred after the Miocene Epoch (23 Myr). The earliest origination of plumage carotenoids was reconstructed within Passeriformes, during the Palaeocene Epoch (66–56 Myr), and not at the base of crown-lineage birds.

scholarly journals Bat-borne polyomaviruses in Europe reveal an evolutionary history of intrahost divergence with horseshoe bats distributed across the African and Eurasian continents

2020 ◽  
Vol 101 (10) ◽  
pp. 1119-1130
Author(s):  
Márton Z. Vidovszky ◽  
Zhizhou Tan ◽  
Michael J. Carr ◽  
Sándor Boldogh ◽  
Balázs Harrach ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Genetic Relatedness ◽  
Relationship Analysis ◽  
Geographical Distances ◽  
Pathogenic Viruses ◽  
History Of ◽  
Capsid Protein Vp1 ◽  
Horseshoe Bat ◽  
Dsdna Viruses ◽  
Horseshoe Bats

Polyomaviruses (PyVs) are small, circular dsDNA viruses carried by diverse vertebrates, including bats. Although previous studies have reported several horseshoe bat PyVs collected in Zambia and China, it is still unclear how PyVs evolved in this group of widely dispersed mammals. Horseshoe bats (genus Rhinolophus) are distributed across the Old World and are natural reservoirs of numerous pathogenic viruses. Herein, non-invasive bat samples from European horseshoe bat species were collected in Hungary for PyV identification and novel PyVs with complete genomes were successfully recovered from two different European horseshoe bat species. Genomic and phylogenetic analysis of the Hungarian horseshoe bat PyVs supported their classification into the genera Alphapolyomavirus and Betapolyomavirus. Notably, despite the significant geographical distances between the corresponding sampling locations, Hungarian PyVs exhibited high genetic relatedness with previously described Zambian and Chinese horseshoe bat PyVs, and phylogenetically clustered with these viruses in each PyV genus. Correlation and virus–host relationship analysis suggested that these PyVs co-diverged with their European, African and Asian horseshoe bat hosts distributed on different continents during their evolutionary history. Additionally, assessment of selective pressures over the major capsid protein (VP1) of horseshoe bat PyVs showed sites under positive selection located in motifs exposed to the exterior of the capsid. In summary, our findings revealed a pattern of stable intrahost divergence of horseshoe bat PyVs with their mammalian hosts on the African and Eurasian continents over evolutionary time.

scholarly journals Approximating the coalescent under facultative sex

2019 ◽  
Author(s):  
Matthew Hartfield
Keyword(s):  
Population Size ◽  
Evolutionary History ◽  
Sampling Strategies ◽  
Effective Population ◽  
Sexual Species ◽  
History Of ◽  
Mitotic Gene Conversion ◽  
Evolutionary Consequences ◽  
Insight Into ◽  
Coalescent Time

AbstractGenome studies of facultative sexual species, which can either reproduce sexually or asexually, are providing insight into the evolutionary consequences of mixed reproductive modes. It is currently unclear to what extent the evolutionary history of facultative sexuals’ genomes can be approximated by the standard coalescent, and if a coalescent effective population size Ne exists. Here, I determine if and when these approximations can be made. When sex is frequent (occurring at a frequency much greater than 1/N per reproduction per generation, for N the actual population size), the underlying genealogy can be approximated by the standard coalescent, with a coalescent Ne ≈ N. When sex is very rare (at frequency much lower than 1/N), approximations for the pairwise coalescent time can be obtained, which is strongly influenced by the frequencies of sex and mitotic gene conversion, rather than N. However, these terms do not translate into a coalescent Ne. These results are used to discuss the best sampling strategies for investigating the evolutionary history of facultative sexual species.

Biological evolution

2018 ◽  
Author(s):  
Andrew Briggs ◽  
Hans Halvorson ◽  
Andrew Steane
Keyword(s):  
Design Education ◽  
Evolutionary Biology ◽  
Evolutionary History ◽  
Biological Evolution ◽  
Sequence Of Events ◽  
Living Things ◽  
History Of ◽  
Informed Opinion ◽  
Life On Earth ◽  
Insight Into

The chapter discusses the history of life on Earth, and the lessons to be learned from the neo-Darwinian synthesis of evolutionary biology. The long and complex sequence of events in the evolutionary history of life on Earth requires considered interpretation. The neo-Darwinian synthesis is well-supported by evidence and gives rich insight into this process, but does not itself furnish a complete explanation or understanding of living things. This is because a process of exploration can only explore; it cannot fully dictate and can only partially constrain what type of thing will be found. What is found is constrained by other considerations, such as what is possible, and what can make sense. A brief critique of some of Richard Dawkins’ work is given, and also of the movement known as ‘Intelligent Design’. Education policy is well served by a fair appraisal of informed opinion in this area.

Molecular phylogeography of Thymus herba-barona (Lamiaceae): Insight into the evolutionary history of the flora of the western Mediterranean islands

Taxon ◽  
2011 ◽  
Vol 60 (5) ◽  
pp. 1295-1305 ◽  
Author(s):  
Arántzazu Molins ◽  
Gianluigi Bacchetta ◽  
Marcela Rosato ◽  
Josep A. Rosselló ◽  
Maria Mayol
Keyword(s):  
Evolutionary History ◽  
Western Mediterranean ◽  
Mediterranean Islands ◽  
Molecular Phylogeography ◽  
History Of ◽  
Insight Into

scholarly journals Expression and genomic organization of zonadhesin-like genes in three species of fish give insight into the evolutionary history of a mosaic protein

BMC Genomics ◽  
2005 ◽  
Vol 6 (1) ◽  
Author(s):  
Peter ND Hunt ◽  
Michael D Wilson ◽  
Kristian R von Schalburg ◽  
William S Davidson ◽  
Ben F Koop
Keyword(s):  
Evolutionary History ◽  
Genomic Organization ◽  
History Of ◽  
Mosaic Protein ◽  
Insight Into
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