scholarly journals Retroviruses drive the rapid evolution of mammalianAPOBEC3genes

2019 ◽  
Vol 117 (1) ◽  
pp. 610-618 ◽  
Author(s):  
Jumpei Ito ◽  
Robert J. Gifford ◽  
Kei Sato
Keyword(s):  
Gene Family ◽  
Fossil Record ◽  
Driving Force ◽  
Mammalian Species ◽  
Rapid Evolution ◽  
Endogenous Retroviruses ◽  
Mammalian Evolution ◽  
History Of ◽  
Mammalian Genomes

APOBEC3(A3) genes are members of theAID/APOBECgene family that are found exclusively in mammals.A3genes encode antiviral proteins that restrict the replication of retroviruses by inducing G-to-A mutations in their genomes and have undergone extensive amplification and diversification during mammalian evolution. Endogenous retroviruses (ERVs) are sequences derived from ancient retroviruses that are widespread mammalian genomes. In this study we characterize theA3repertoire and use the ERV fossil record to explore the long-term history of coevolutionary interaction between A3s and retroviruses. We examine the genomes of 160 mammalian species and identify 1,420AID/APOBEC-related genes, including representatives of previously uncharacterized lineages. We show thatA3genes have been amplified in mammals and that amplification is positively correlated with the extent of germline colonization by ERVs. Moreover, we demonstrate that the signatures of A3-mediated mutation can be detected in ERVs found throughout mammalian genomes and show that in mammalian species with expandedA3repertoires, ERVs are significantly enriched for G-to-A mutations. Finally, we show thatA3amplification occurred concurrently with prominent ERV invasions in primates. Our findings establish that conflict with retroviruses is a major driving force for the rapid evolution of mammalianA3genes.

scholarly journals Tracking interspecies transmission and long-term evolution of an ancient retrovirus using the genomes of modern mammals

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
William E Diehl ◽  
Nirali Patel ◽  
Kate Halm ◽  
Welkin E Johnson
Keyword(s):  
Fossil Record ◽  
Viral Infections ◽  
Endogenous Retroviruses ◽  
Interspecies Transmission ◽  
Viral Spread ◽  
Protein Functions ◽  
History Of ◽  
Mammalian Genomes ◽  
Retroviral Infections

Mammalian genomes typically contain hundreds of thousands of endogenous retroviruses (ERVs), derived from ancient retroviral infections. Using this molecular 'fossil' record, we reconstructed the natural history of a specific retrovirus lineage (ERV-Fc) that disseminated widely between ~33 and ~15 million years ago, corresponding to the Oligocene and early Miocene epochs. Intercontinental viral spread, numerous instances of interspecies transmission and emergence in hosts representing at least 11 mammalian orders, and a significant role for recombination in diversification of this viral lineage were also revealed. By reconstructing the canonical retroviral genes, we identified patterns of adaptation consistent with selection to maintain essential viral protein functions. Our results demonstrate the unique potential of the ERV fossil record for studying the processes of viral spread and emergence as they play out across macro-evolutionary timescales, such that looking back in time may prove insightful for predicting the long-term consequences of newly emerging viral infections.

scholarly journals Distribution, Diversity, and Evolution of Endogenous Retroviruses in Perissodactyl Genomes

2018 ◽  
Vol 92 (23) ◽  
Author(s):  
Henan Zhu ◽  
Robert James Gifford ◽  
Pablo Ramiro Murcia
Keyword(s):  
Germ Line ◽  
Mammalian Species ◽  
Endogenous Retroviruses ◽  
Functional Roles ◽  
Physiological Processes ◽  
Great Utility ◽  
White Rhinoceros ◽  
History Of ◽  
Mammalian Genomes

ABSTRACTThe evolution of mammalian genomes has been shaped by interactions with endogenous retroviruses (ERVs). In this study, we investigated the distribution and diversity of ERVs in the mammalian orderPerissodactyla, with a view to understanding their impact on the evolution of modern equids (familyEquidae). We characterize the major ERV lineages in the horse genome in terms of their genomic distribution, ancestral genome organization, and time of activity. Our results show that subsequent to their ancestral divergence from rhinoceroses and tapirs, equids acquired four novel ERV lineages. We show that two of these ERV lineages proliferated extensively in the lineage leading to modern horses, and one contains loci that are actively transcribed in specific tissues. In addition, we show that the white rhinoceros has resisted germ line colonization by retroviruses for more than 54 million years—longer than any other extant mammalian species. The map of equine ERVs that we provide here will be of great utility to future studies aiming to investigate the potential functional roles of equine ERVs and their impact on equine evolution.IMPORTANCEERVs in the host genome are highly informative about the long-term interactions of retroviruses and hosts. They are also interesting because they have influenced the evolution of mammalian genomes in various ways. In this study, we derive a calibrated timeline describing the process through which ERV diversity has been generated in the equine germ line. We determined the distribution and diversity of perissodactyl ERV lineages and inferred their retrotranspositional activity during evolution, thereby gaining insight into the long-term coevolutionary history of retroviruses and mammals. Our study provides a platform for future investigations to identify equine ERV loci involved in physiological processes and/or pathological conditions.

Paleolimnology in Deep Time: The Evolution of Lacustrine Ecosystems

2003 ◽  
Author(s):  
Andrew S. Cohen
Keyword(s):  
Fossil Record ◽  
World Ocean ◽  
Biological Evolution ◽  
Body Distribution ◽  
Freshwater Organisms ◽  
History Of ◽  
Living Organisms ◽  
Lake Basins ◽  
Lake Beds

Most lakes are geologically ephemeral; even the longest-lived individual lakes persist only for tens of millions of years. However there is a continuity to lake systems that transcends the geologically short history of individual lake basins. This continuity comes from the long-term biological evolution of life in freshwater, and fittingly, forms the final subject of this treatment of paleolimnology. Like the oceans, lakes have provided habitats for living organisms for most of the earth’s history. Yet the patterns of aquatic ecosystem evolution in rivers and lakes have differed dramatically from those of the oceans. In large part this can be traced to the fundamentally ephemeral nature of most continental aquatic habitats and the ‘‘disconnectedness’’ in both time and space that exists between individual lakes and rivers compared with the world ocean. This pattern of temporal and spatial patchiness in water body distribution on the continents has shaped the evolution of lacustrine species and communities. Some understanding of this history can be gleaned from the study of modern ecology and molecular genetics of living freshwater organisms. But to understand long-term trends in lacustrine biodiversity and their relationship to the history of the lacustrine environment we must turn to the pre- Quaternary fossil record. Understanding this history, the timing and tempo of major species diversification and extinction events, and the evolution of key ecological innovations is critical for correctly interpreting ancient lake deposits. The fossil record of pre-Quaternary lakes is more difficult to interpret than that of more recent lake basins. Robust phylogenies are largely unavailable for clades of ancient lacustrine fossils, hindering our ability to test hypotheses of evolutionary ecology, although that situation hopefully will improve in coming years. Many major clades of fossil lacustrine organisms are extinct, and ecologies must be inferred from their depositional context. Even for organisms that have close-living relatives, our certainty in making inferences about habitat and relationship with other species weakens as we go back in time. Also the record we have to work with deteriorates with age, the result of (a) a declining volume of lake beds available for study with increasing age, (b) difficulties associated with processing lithified lake beds for their fossil content, and (c) an increasing likelihood of destruction by diagenesis with increasing age.

scholarly journals Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae

2016 ◽  
Author(s):  
Michael S. Barker ◽  
Zheng Li ◽  
Thomas I. Kidder ◽  
Chris R. Reardon ◽  
Zhao Lai ◽  
...  
Keyword(s):  
Gene Family ◽  
Linkage Map ◽  
Evolutionary History ◽  
Genome Duplication ◽  
Nuclear Gene ◽  
Flowering Plants ◽  
The Family ◽  
History Of ◽  
Phylogenomic Analyses

AbstractPremise of the studyLike many other flowering plants, members of the Compositae (Asteraceae) have a polyploid ancestry. Previous analyses found evidence for an ancient duplication or possibly triplication in the early evolutionary history of the family. We sought to better place this paleopolyploidy in the phylogeny and assess its nature.MethodsWe sequenced new transcriptomes for Barnadesia, the lineage sister to all other Compositae, and four representatives of closely related families. Using a recently developed algorithm, MAPS, we analyzed nuclear gene family phylogenies for evidence of paleopolyploidy.Key resultsWe found that the previously recognized Compositae paleopolyploidy is also in the ancestry of the Calyceraceae. Our phylogenomic analyses uncovered evidence for a successive second round of genome duplication among all sampled Compositae except Barnadesia.ConclusionsOur analyses of new samples with new tools provide a revised view of paleopolyploidy in the Compositae. Together with results from a high density Lactuca linkage map, our results suggest that the Compositae and Calyceraceae have a common paleotetraploid ancestor and most Compositae are descendants of a paleohexaploid. Although paleohexaploids have been previously identified, this is the first example where the paleotetraploid and paleohexaploid lineages have survived over tens of millions of years. The complex polyploidy in the ancestry of the Compositae and Calyceraceae represents a unique opportunity to study the long-term evolutionary fates and consequences of different ploidal levels.

scholarly journals Deep time diversity and the early radiations of birds

2021 ◽  
Vol 118 (10) ◽  
pp. e2019865118
Author(s):  
Yilun Yu ◽  
Chi Zhang ◽  
Xing Xu
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Evolutionary Rate ◽  
Rapid Evolution ◽  
Morphological Data ◽  
Deep Time ◽  
The Third ◽  
Time Diversity ◽  
History Of

Reconstructing the history of biodiversity has been hindered by often-separate analyses of stem and crown groups of the clades in question that are not easily understood within the same unified evolutionary framework. Here, we investigate the evolutionary history of birds by analyzing three supertrees that combine published phylogenies of both stem and crown birds. Our analyses reveal three distinct large-scale increases in the diversification rate across bird evolutionary history. The first increase, which began between 160 and 170 Ma and reached its peak between 130 and 135 Ma, corresponds to an accelerated morphological evolutionary rate associated with the locomotory systems among early stem birds. This radiation resulted in morphospace occupation that is larger and different from their close dinosaurian relatives, demonstrating the occurrence of a radiation among early stem birds. The second increase, which started ∼90 Ma and reached its peak between 65 and 55 Ma, is associated with rapid evolution of the cranial skeleton among early crown birds, driven differently from the first radiation. The third increase, which occurred after ∼40 to 45 Ma, has yet to be supported by quantitative morphological data but gains some support from the fossil record. Our analyses indicate that the bird biodiversity evolution was influenced mainly by long-term climatic changes and also by major paleobiological events such as the Cretaceous–Paleogene (K–Pg) extinction.

Pteridophyte success and past biota—a palaeobotanist's approach

1985 ◽  
Vol 86 ◽  
pp. 423-430
Author(s):  
B. A. Thomas
Keyword(s):  
Fossil Record ◽  
Geological History ◽  
Term Survival ◽  
Long Term Survival ◽  
Amount Of Information ◽  
The Past ◽  
History Of

SynopsisThe success of plants which lived in the past should be assessed differently from that of living plants as time is an additional important factor. Success may therefore be judged in one period of time or throughout the whole geological history of the plants.Limitations of the fossil record through plant fragmentation, lack of preservation and incomplete preservation severely restrict the amount of information available. However, accepting these problems, there are four major ways in which plants may be judged: long term survival, repeated specialisation, dominance and adaptability. Examples are given of pteridophytes that exhibit success in these four ways.

scholarly journals Territories in Time: Mapping Palimpsest Horizons

2020 ◽  
Vol 5 (2) ◽  
pp. 94-98 ◽  
Author(s):  
Chiara Cavalieri ◽  
Elena Cogato Lanza
Keyword(s):  
Rapid Evolution ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Data Recording ◽  
New Paradigm ◽  
Dimensional Matrix ◽  
History Of ◽  
Theoretical Question

In the early 80s André Corboz, in describing the territory as being the result of slow and long-term processes involving multiple transformations, implicitly declares the onset of a new paradigm for understanding cities and territories: a new gaze attentive to the chronological dimension of spaces, aware of the long history of places, interested in that ensemble of signs, traces and voids so tangible, and yet ignored by the paradigm of tabula rasa. To describe this complexity, Corboz proposes the metaphor of territory as palimpsest: A palimpsest is a two-dimensional writing board bearing a three-dimensional matrix of signs, which, as a metaphor, allows for a contextual, four-dimensional apprehension of territory, portraying space in its chronological evolution. This text re-contextualizes the notion of palimpsest—both as a methodological and a theoretical question—in the light of two main conceptual ‘shifts’: the ‘territorial turn,’ which increased interest among different disciplines, projects, and policies for the dimension of cities as territory, and the ‘digital turn,’ namely the rapid evolution of data recording, archiving, and mapping technologies.

scholarly journals Is there a role for endogenous retroviruses to mediate long-term adaptive phenotypic response upon environmental inputs?

2013 ◽  
Vol 368 (1609) ◽  
pp. 20110340 ◽  
Author(s):  
Jafar Sharif ◽  
Yoichi Shinkai ◽  
Haruhiko Koseki
Keyword(s):  
Gene Regulation ◽  
Endogenous Retroviruses ◽  
Highly Active ◽  
Global Gene Regulation ◽  
Mammalian Genomes ◽  
Insertion Sites ◽  
Genomic Locations ◽  
The Impact ◽  
Evolutionary Role

Endogenous retroviruses (ERVs) are long terminal repeat-containing virus-like elements that have colonized approximately 10 per cent of the present day mammalian genomes. The intracisternal A particles (IAPs) are a class of ERVs that is currently highly active in the rodents. IAP elements can influence the transcription profile of nearby genes by providing functional promoter elements and modulating local epigenetic landscape through changes in DNA methylation and histone (H3K9) modifications. Despite the potential role for IAPs in gene regulation, the precise genomic locations where these elements are integrated are not well understood. To address this issue, we have identified more than 400 novel IAP insertion sites within/near annotated genes by searching the murine genome, which suggests that the impact of IAP elements on local and/or global gene regulation could be more profound than was previously expected. On the basis of our independent analyses and already published reports, here we argue that IAPs and ERV elements in general could have an evolutionary role for modulating phenotypic plasticity upon environmental inputs, and that this could be mediated through specific stages of embryonic development such as placentation during which the epigenetic constraints on IAP elements are partially relaxed.

scholarly journals Deltaretroviruses have circulated since at least the Paleogene and infected a broad range of mammalian species

Retrovirology ◽  
2019 ◽  
Vol 16 (1) ◽  
Author(s):  
Tomáš Hron ◽  
Daniel Elleder ◽  
Robert J. Gifford
Keyword(s):  
Gene Regulation ◽  
Bovine Leukemia Virus ◽  
Fossil Record ◽  
Leukemia Virus ◽  
Mammalian Species ◽  
Endogenous Retroviruses ◽  
Cell Leukemia ◽  
Coding Regions ◽  
Human T Cell ◽  
Leukemia Viruses

AbstractThe Deltaretrovirus genus of retroviruses (family Retroviridae) includes the human T cell leukemia viruses and bovine leukemia virus (BLV). Relatively little is known about the biology and evolution of these viruses, because only a few species have been identified and the genomic ‘fossil record’ is relatively sparse. Here, we report the discovery of multiple novel endogenous retroviruses (ERVs) derived from ancestral deltaretroviruses. These sequences—two of which contain complete or near complete internal coding regions—reside in genomes of several distinct mammalian orders, including bats, carnivores, cetaceans, and insectivores. We demonstrate that two of these ERVs contain unambiguous homologs of the tax gene, indicating that complex gene regulation has ancient origins within the Deltaretrovirus genus. ERVs demonstrate that the host range of the deltaretrovirus genus is much more extensive than suggested by the relatively small number of exogenous deltaretroviruses described so far, and allow the evolutionary timeline of deltaretrovirus-mammal interaction to be more accurately calibrated.

scholarly journals Reference genome and demographic history of the most endangered marine mammal, the vaquita

2020 ◽  
Author(s):  
Phillip A. Morin ◽  
Frederick I. Archer ◽  
Catherine D. Avila ◽  
Jennifer R. Balacco ◽  
Yury V. Bukhman ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Marine Mammal ◽  
Reference Genome ◽  
Demographic History ◽  
Mammalian Species ◽  
Small Population ◽  
Chromosome Length ◽  
Rapid Decline ◽  
History Of

AbstractThe vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline resulting from inadvertent deaths due to the increasing use of large-mesh gillnets for more than 20 years. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analyzed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

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