scholarly journals Intrahost speciations and host switches shaped the evolution of herpesviruses

2018 ◽  
Author(s):  
Anderson F. Brito ◽  
John W. Pinney
Keyword(s):  
Early Cretaceous ◽  
Late Cretaceous ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Continental Drift ◽  
Divergence Times ◽  
Crucial Information ◽  
Host Evolution ◽  
Over Time

ABSTRACTCospeciation has been suggested to be the main force driving the evolution of herpesviruses, with viral species co-diverging with their hosts along more than 400 million years of evolutionary history. Recent studies, however, have been challenging this assumption, showing that other co-phylogenetic events, such as intrahost speciations and host switches play a central role on their evolution. Most of these studies, however, were performed with undated phylogenies, which may underestimate or overestimate the frequency of certain events. In this study we performed co-phylogenetic analyses using time-calibrated trees of herpesviruses and their hosts. This approach allowed us to (i) infer co-phylogenetic events over time, and (ii) integrate crucial information about continental drift and host biogeography to better understand virus-host evolution. We observed that cospeciations were in fact relatively rare events, taking place mostly after the Late Cretaceous (~100 Millions of years ago). Host switches were particularly common among alphaherpesviruses, where at least 10 transfers were detected. Among beta- and gammaherpesviruses, transfers were less frequent, with intrahost speciations followed by losses playing more prominent roles, especially from the Early Jurassic to the Early Cretaceous, when those viral lineages underwent several intrahost speciations. Our study reinforces the understanding that cospeciations are uncommon events in herpesvirus evolution. More than topological incongruences, mismatches in divergence times were the main disagreements between host and viral phylogenies. In most cases, host switches could not explain such disparities, highlighting the important role of losses and intrahost speciations in the evolution of herpesviruses.

scholarly journals Diversification patterns based on the largest morphological phylogenetic analysis of Pleurodira

2015 ◽  
Author(s):  
Gabriel S Ferreira ◽  
Juliana Sterli ◽  
Mario Bronzati Filho ◽  
Max C Langer
Keyword(s):  
Early Cretaceous ◽  
Late Cretaceous ◽  
Evolutionary History ◽  
Feeding Habits ◽  
Phylogenetic Analyses ◽  
Morphological Data ◽  
Phylogenetic Hypothesis ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
History Of

Background. Most studies on pleurodiran turtles are about the behavior and/or feeding habits analyzes, description of new taxa or specimens (both extinct and extant), or phylogenetic analyzes of one of its subclades with extant taxa: Chelidae, Pelomedusidae or Podocnemididae. With the exception of some molecular phylogenies, there are no phylogenetic analyses of extant and extinct representatives of Pleurodira including all of its lineages. A broader understanding of the evolutionary history of Pleurodira requires a phylogenetic hypothesis based on more extensive taxonomic and character samplings.Methods. We constructed a taxon-character matrix including 227 morphological characters and 87 taxa from all the Pleurodira lineages, plus one stem Pan-Pleurodira, Notoemys laticentralis, and one stem-Testudinata, Proganochelys quenstedti, as outgroups. The resulting matrix was analyzed using parsimony, Tree Bisection and Reconnection (TBR) algorithms, with 5000 replicates, and a hold of 20. The obtained strict consensus tree was used as the basis of a diversification analysis using topology-based methods. A nestedgrowing tree approach was employed to create a corresponding tree for different intervals of the geological history of the group. Six distinct time bins were created for periods in which members of Pleurodira occur: Early Cretaceous, Late Cretaceous, Paleocene, Eocene, Miocene, and Recent. Results. All main pleurodiran clades were recovered in the strict consensus tree, but with some changes in their relationship compared to previous analyses, e.g. the inclusiveness of both Pelomedusoides and Bothremydidae. The diversification analysis shows that, after the establishment of the two major lineages (i.e. Chelidae and Pelomedusoides) in the Early Cretaceous, these subgroups diversified in distinct rates along their evolutionary history. Two main diversification shifts were identified: one at the early evolution of Podocnemoidea, during the Late Cretaceous, and another during the Miocene, deep nested in the Podocnemididae clade. Discussion. The resulting strict consensus tree is the largest exclusive phylogenetic hypothesis for Pleurodira, including both extant and extinct taxa. Based on morphological data, it allows more inclusive inferences on the general morphological and diversification patterns of the group. The diversification pulses analysis suggests variation on the rates of diversification on the different pleurodiran clades. The first shift detected is related to the great radiation of Bothremydidae and Podocnemoidae in the Late Cretaceous; the second shift, detected in the Miocene, is related to a diversification within the Stereogenyina, a Podocnemididae clade. Ongoing analysis will determine which factors could enforce those different diversification rates in the evolution of Pleurodira.

scholarly journals The evolutionary history of polycotylid plesiosaurians

2018 ◽  
Vol 5 (3) ◽  
pp. 172177 ◽  
Author(s):  
V. Fischer ◽  
R. B. J. Benson ◽  
P. S. Druckenmiller ◽  
H. F. Ketchum ◽  
N. Bardet
Keyword(s):  
Early Cretaceous ◽  
Late Cretaceous ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Neck Length ◽  
Ecological Release ◽  
Holotype Specimen ◽  
Low Diversity ◽  
History Of

Polycotylidae is a clade of plesiosaurians that appeared during the Early Cretaceous and became speciose and abundant early in the Late Cretaceous. However, this radiation is poorly understood. Thililua longicollis from the Middle Turonian of Morocco is an enigmatic taxon possessing an atypically long neck and, as originally reported, a series of unusual cranial features that cause unstable phylogenetic relationships for polycotylids. We reinterpret the holotype specimen of Thililua longicollis and clarify its cranial anatomy. Thililua longicollis possesses an extensive, foramina-bearing jugal, a premaxilla–parietal contact and carinated teeth. Phylogenetic analyses of a new cladistic dataset based on first-hand observation of most polycotylids recover Thililua and Mauriciosaurus as successive lineages at the base of the earliest Late Cretaceous polycotyline radiation. A new dataset summarizing the Bauplan of polycotylids reveals that their radiation produced an early burst of disparity during the Cenomanian–Turonian interval, with marked plasticity in relative neck length, but this did not arise as an ecological release following the extinction of ichthyosaurs and pliosaurids. This disparity vanished during and after the Turonian, which is consistent with a model of ‘early experimentation/late constraint’. Two polycotylid clades, Occultonectia clade nov. and Polycotylinae, survived up to the Maastrichtian, but with low diversity.

scholarly journals Diversification patterns based on the largest morphological phylogenetic analysis of Pleurodira

2015 ◽  
Author(s):  
Gabriel S Ferreira ◽  
Juliana Sterli ◽  
Mario Bronzati Filho ◽  
Max C Langer
Keyword(s):  
Early Cretaceous ◽  
Late Cretaceous ◽  
Evolutionary History ◽  
Feeding Habits ◽  
Phylogenetic Analyses ◽  
Morphological Data ◽  
Phylogenetic Hypothesis ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
History Of

Background. Most studies on pleurodiran turtles are about the behavior and/or feeding habits analyzes, description of new taxa or specimens (both extinct and extant), or phylogenetic analyzes of one of its subclades with extant taxa: Chelidae, Pelomedusidae or Podocnemididae. With the exception of some molecular phylogenies, there are no phylogenetic analyses of extant and extinct representatives of Pleurodira including all of its lineages. A broader understanding of the evolutionary history of Pleurodira requires a phylogenetic hypothesis based on more extensive taxonomic and character samplings.Methods. We constructed a taxon-character matrix including 227 morphological characters and 87 taxa from all the Pleurodira lineages, plus one stem Pan-Pleurodira, Notoemys laticentralis, and one stem-Testudinata, Proganochelys quenstedti, as outgroups. The resulting matrix was analyzed using parsimony, Tree Bisection and Reconnection (TBR) algorithms, with 5000 replicates, and a hold of 20. The obtained strict consensus tree was used as the basis of a diversification analysis using topology-based methods. A nestedgrowing tree approach was employed to create a corresponding tree for different intervals of the geological history of the group. Six distinct time bins were created for periods in which members of Pleurodira occur: Early Cretaceous, Late Cretaceous, Paleocene, Eocene, Miocene, and Recent. Results. All main pleurodiran clades were recovered in the strict consensus tree, but with some changes in their relationship compared to previous analyses, e.g. the inclusiveness of both Pelomedusoides and Bothremydidae. The diversification analysis shows that, after the establishment of the two major lineages (i.e. Chelidae and Pelomedusoides) in the Early Cretaceous, these subgroups diversified in distinct rates along their evolutionary history. Two main diversification shifts were identified: one at the early evolution of Podocnemoidea, during the Late Cretaceous, and another during the Miocene, deep nested in the Podocnemididae clade. Discussion. The resulting strict consensus tree is the largest exclusive phylogenetic hypothesis for Pleurodira, including both extant and extinct taxa. Based on morphological data, it allows more inclusive inferences on the general morphological and diversification patterns of the group. The diversification pulses analysis suggests variation on the rates of diversification on the different pleurodiran clades. The first shift detected is related to the great radiation of Bothremydidae and Podocnemoidae in the Late Cretaceous; the second shift, detected in the Miocene, is related to a diversification within the Stereogenyina, a Podocnemididae clade. Ongoing analysis will determine which factors could enforce those different diversification rates in the evolution of Pleurodira.

Adaptive convergent evolution of genome proofreading in SARS-CoV2: insights into the Eigen’s paradox

2021 ◽  
Author(s):  
Keerthic Aswin ◽  
Srinivasan Ramachandran ◽  
Vivek T Natarajan
Keyword(s):  
Convergent Evolution ◽  
Genome Stability ◽  
Evolutionary History ◽  
Rna Binding ◽  
Phylogenetic Analyses ◽  
Comparative Genome Analysis ◽  
The Family ◽  
History Of ◽  
Key Residues

AbstractEvolutionary history of coronaviruses holds the key to understand mutational behavior and prepare for possible future outbreaks. By performing comparative genome analysis of nidovirales that contain the family of coronaviruses, we traced the origin of proofreading, surprisingly to the eukaryotic antiviral component ZNFX1. This common recent ancestor contributes two zinc finger (ZnF) motifs that are unique to viral exonuclease, segregating them from DNA proof-readers. Phylogenetic analyses indicate that following acquisition, genomes of coronaviruses retained and further fine-tuned proofreading exonuclease, whereas related families harbor substitution of key residues in ZnF1 motif concomitant to a reduction in their genome sizes. Structural modelling followed by simulation suggests the role of ZnF in RNA binding. Key ZnF residues strongly coevolve with replicase, and the helicase involved in duplex RNA unwinding. Hence, fidelity of replication in coronaviruses is a result of convergent evolution, that enables maintenance of genome stability akin to cellular proofreading systems.

scholarly journals The study of host–microbiome (co)evolution across levels of selection

2020 ◽  
Vol 375 (1808) ◽  
pp. 20190604 ◽  
Author(s):  
Britt Koskella ◽  
Joy Bergelson
Keyword(s):  
Paradigm Shift ◽  
Dynamic Nature ◽  
Theme Issue ◽  
Critical Question ◽  
Microbiome Composition ◽  
Single Host ◽  
Host Evolution ◽  
Existing Data ◽  
Over Time

Microorganismal diversity can be explained in large part by selection imposed from both the abiotic and biotic environments, including—in the case of host-associated microbiomes—interactions with eukaryotes. As such, the diversity of host-associated microbiomes can be usefully studied across a variety of scales: within a single host over time, among host genotypes within a population, between populations and among host species. A plethora of recent studies across these scales and across diverse systems are: (i) exemplifying the importance of the host genetics in shaping microbiome composition; (ii) uncovering the role of the microbiome in shaping key host phenotypes; and (iii) highlighting the dynamic nature of the microbiome. They have also raised a critical question: do these complex associations fit within our existing understanding of evolution and coevolution, or do these often intimate and seemingly cross-generational interactions follow novel evolutionary rules from those previously identified? Herein, we describe the known importance of (co)evolution in host–microbiome systems, placing the existing data within extant frameworks that have been developed over decades of study, and ask whether there are unique properties of host–microbiome systems that require a paradigm shift. By examining when and how selection can act on the host and its microbiome as a unit (termed, the holobiont), we find that the existing conceptual framework, which focuses on individuals, as well as interactions among individuals and groups, is generally well suited for understanding (co)evolutionary change in these intimate assemblages. This article is part of the theme issue ‘The role of the microbiome in host evolution’.

scholarly journals Tempo and mode of antibat ultrasound production and sonar jamming in the diverse hawkmoth radiation

2015 ◽  
Vol 112 (20) ◽  
pp. 6407-6412 ◽  
Author(s):  
Akito Y. Kawahara ◽  
Jesse R. Barber
Keyword(s):  
Evolutionary History ◽  
Tactile Stimulation ◽  
Phylogenetic Analyses ◽  
Physical Contact ◽  
Divergence Times ◽  
Entire Group ◽  
Multigene Phylogeny ◽  
Late Oligocene ◽  
Entire Family ◽  
Big Brown Bats

The bat–moth arms race has existed for over 60 million y, with moths evolving ultrasonically sensitive ears and ultrasound-producing organs to combat bat predation. The evolution of these defenses has never been thoroughly examined because of limitations in simultaneously conducting behavioral and phylogenetic analyses across an entire group. Hawkmoths include >1,500 species worldwide, some of which produce ultrasound using genital stridulatory structures. However, the function and evolution of this behavior remain largely unknown. We built a comprehensive behavioral dataset of hawkmoth hearing and ultrasonic reply to sonar attack using high-throughput field assays. Nearly half of the species tested (57 of 124 species) produced ultrasound to tactile stimulation or playback of bat echolocation attack. To test the function of ultrasound, we pitted big brown bats (Eptesicus fuscus) against hawkmoths over multiple nights and show that hawkmoths jam bat sonar. Ultrasound production was immediately and consistently effective at thwarting attack and bats regularly performed catching behavior without capturing moths. We also constructed a fossil-calibrated, multigene phylogeny to study the evolutionary history and divergence times of these antibat strategies across the entire family. We show that ultrasound production arose in multiple groups, starting in the late Oligocene (∼26 Ma) after the emergence of insectivorous bats. Sonar jamming and bat-detecting ears arose twice, independently, in the Miocene (18–14 Ma) either from earless hawkmoths that produced ultrasound in response to physical contact only, or from species that did not respond to touch or bat echolocation attack.

The role of Central Asia in dinosaurian biogeography

1993 ◽  
Vol 30 (10) ◽  
pp. 2002-2012 ◽  
Author(s):  
Dale A. Russell
Keyword(s):  
North America ◽  
Central Asia ◽  
Early Cretaceous ◽  
Late Cretaceous ◽  
Middle Jurassic ◽  
Late Jurassic ◽  
Late Triassic ◽  
Globally Distributed ◽  
Northern And Southern Hemispheres

Dinosaurian biogeography may have been largely controlled by the Mesozoic fragmentation of Pangea and the reassembly of its fragments into a new, boreal supercontinent (Laurasia). Although Late Triassic and Early Jurassic dinosaurs were globally distributed, Chinese assemblages were dominated by endemic forms from Middle Jurassic into Early Cretaceous time. The affinities of Aptian – Albian immigrants to Asia were strongest with North America and Europe rather than Gondwana, indicating that the northern and southern hemispheres had by then attained their biogeographic identity. This distinctiveness was maintained through Cretaceous time. Europe seems to have been a buffer area between Paleolaurasia and Gondwana; of the northern continents it was the most strongly influenced by Gondwana dispersants. Late Jurassic dinosaur assemblages in North America exhibited Gondwana affinities, but by Late Cretaceous time they were dominated by forms of Asian ancestry.

scholarly journals Why is Amazonia a ‘source’ of biodiversity? Climate-mediated dispersal and synchronous speciation across the Andes in an avian group (Tityrinae)

2019 ◽  
Vol 286 (1900) ◽  
pp. 20182343 ◽  
Author(s):  
Lukas J. Musher ◽  
Mateus Ferreira ◽  
Anya L. Auerbach ◽  
Jessica McKay ◽  
Joel Cracraft
Keyword(s):  
Evolutionary History ◽  
Divergence Times ◽  
The Andes ◽  
Heterogeneous Landscape ◽  
Habitat Corridors ◽  
High Utility ◽  
Dispersal Events ◽  
Avian Group ◽  
Over Time

Amazonia is a ‘source’ of biodiversity for other Neotropical ecosystems, but which conditions trigger in situ speciation and emigration is contentious. Three hypotheses for how communities have assembled include (1) a stochastic model wherein chance dispersal events lead to gradual emigration and species accumulation, (2) diversity-dependence wherein successful dispersal events decline through time due to ecological limits, and (3) barrier displacement wherein environmental change facilitates dispersal to other biomes via transient habitat corridors. We sequenced thousands of molecular markers for the Neotropical Tityrinae (Aves) and applied a novel filtering protocol to identify loci with high utility for dated phylogenomics. We used these loci to estimate divergence times and model Tityrinae's evolutionary history. We detected a prominent role for speciation driven by barriers including synchronous speciation across the Andes and found that dispersal increased toward the present. Because diversification was continuous but dispersal was non-random over time, we show that barrier displacement better explains Tityrinae's history than stochasticity or diversity-dependence. We propose that Amazonia is a source of biodiversity because (1) it is a relic of a biome that was once more extensive, (2) environmentally mediated corridors facilitated emigration and (3) constant diversification is attributed to a spatially heterogeneous landscape that is perpetually dynamic through time.

scholarly journals Discovery of viral myosin genes with complex evolutionary history within plankton

2021 ◽  
Author(s):  
Soichiro Kijima ◽  
Tom O. Delmont ◽  
Urara Miyazaki ◽  
Morgan Gaia ◽  
Hisashi Endo ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Viral Particle ◽  
Phylogenetic Analyses ◽  
Viral Proteins ◽  
The Other ◽  
Dna Viruses ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
The One ◽  
Complex Evolutionary History

AbstractNucleocytoplasmic large DNA viruses (NCLDVs) infect diverse eukaryotes and form a group of viruses with capsids encapsulating large genomes. Recent studies are increasingly revealing a spectacular array of functions encoded in their genomes, including genes for energy metabolisms, nutrient uptake, as well as cytoskeleton. Here, we report the discovery of genes homologous to myosins, the major eukaryotic motor proteins previously unrecognized in the virosphere, in environmental genomes of NCLDVs from the surface of the oceans. Interestingly, these genes were often accompanied by kinesin genes in the environmental genomes, suggesting a role of these viral proteins in the intracellular viral particle transport. Phylogenetic analyses indicate that most viral myosins (named “virmyosins”) belong to the Imitervirales order, except for one belonging to the Phycodnaviridae family. On the one hand, the phylogenetic positions of virmyosin-encoding Imitervirales are scattered within the Imitervirales. On the other hand, Imitervirales virmyosin genes form a monophyletic group in the phylogeny of diverse myosin sequences. Furthermore, phylogenetic trends for the virmyosin genes and viruses containing them were incongruent. Based on these results, we argue that multiple transfers of myosin homologs have occurred not only from eukaryotes to viruses but also between viruses, supposedly during co-infections of the same host.

Historical Biogeography of Holarctic Cymbiodyta Water Scavenger Beetles in the Times of Cenozoic Land Bridge Dispersal Routes

2019 ◽  
Vol 3 (5) ◽  
Author(s):  
Emmanuel F A Toussaint ◽  
Andrew E Z Short
Keyword(s):  
Evolutionary History ◽  
New Combination ◽  
Divergence Times ◽  
Range Estimation ◽  
Land Bridge ◽  
Palearctic Species ◽  
History Of ◽  
The Times ◽  
Ancestral Range Estimation

Abstract The genus Cymbiodyta Bedel, 1881 (Coleoptera: Hydrophilidae: Enochrinae) comprises 31 species distributed in both the Old and New World portions of the Holarctic realm. Although the species and taxonomy are relatively well known, the phylogenetic relationships among Cymbiodyta and the evolutionary history of the genus remain unexplored. To understand the systematics and evolution of this lineage, we sequenced five gene fragments for about half of the species in the genus, including most major morphological groups. We also estimated divergence times to test the hypothesis that Cymbiodyta beetles took advantage of the different land bridges connecting the Palearctic and Nearctic regions, that became subaerial in the Cretaceous and Paleocene. Our results recover the eastern Nearctic genus Helocombus Horn, 1890 nesting within Cymbiodyta. Therefore, we synonymize Helocombus syn. n. with Cymbiodyta, resulting in one new combination, Cymbiodyta bifidus (LeConte 1855) comb. n. Our dating analyses and ancestral range estimation support a Nearctic origin of Cymbiodyta in the late Cretaceous about 100 million year ago. The placement of the unique Palearctic species on a long branch as sister to the rest of the clade and the dating results cannot reject a role of the De Geer and/or Thulean routes in the colonization of the Palearctic region from the Nearctic; however, they do not support a role for Beringia in the more recent colonization of the Oriental region.

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