scholarly journals Birth, School, Work, Death, and Resurrection: The Life Stages and Dynamics of Transposable Element Proliferation

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 336 ◽  
Author(s):  
Justin P. Blumenstiel
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Horizontal Transfer ◽  
Evolutionary Dynamics ◽  
Evolutionary Strategies ◽  
Species Boundaries ◽  
Life Stages ◽  
School Work

Transposable elements (TEs) can be maintained in sexually reproducing species even if they are harmful. However, the evolutionary strategies that TEs employ during proliferation can modulate their impact. In this review, I outline the different life stages of a TE lineage, from birth to proliferation to extinction. Through their interactions with the host, TEs can exploit diverse strategies that range from long-term coexistence to recurrent movement across species boundaries by horizontal transfer. TEs can also engage in a poorly understood phenomenon of TE resurrection, where TE lineages can apparently go extinct, only to proliferate again. By determining how this is possible, we may obtain new insights into the evolutionary dynamics of TEs and how they shape the genomes of their hosts.

scholarly journals Models of repression of transposition in P-M hybrid dysgenesis by P cytotype and by zygotically encoded repressor proteins.

Genetics ◽  
1991 ◽  
Vol 128 (2) ◽  
pp. 471-486 ◽  
Author(s):  
J F Brookfield
Keyword(s):  
Computer Simulation ◽  
Transposable Elements ◽  
Transposable Element ◽  
Evolutionary Dynamics ◽  
Hybrid Dysgenesis ◽  
P Elements ◽  
Infinite Population ◽  
Repressor Proteins ◽  
P Transposable Element ◽  
Harmful Effects

Abstract By analytical theory and computer simulation the expected evolutionary dynamics of P transposable element spread in an infinite population are investigated. The analysis is based on the assumption that, unlike transposable elements which move via RNA intermediates, the harmful effects of P elements arise primarily in the act of transposition, and that this causes their evolutionary dynamics to be unusual. It is suggested that a situation of transposition-selection balance will be superceded by the buildup of a cytoplasmically inherited repression or by the elimination of active transposase-encoding elements from the chromosomes, a process which may be accompanied by the evolution of elements which encode proteins which repress transposition.

scholarly journals Eukaryotic transposable elements as “cargo carriers”: the forging of metal resistance in the fungus Paecilomyces variotii

2020 ◽  
Author(s):  
Andrew S. Urquhart ◽  
Nicholas F. Chong ◽  
Yongqing Yang ◽  
Alexander Idnurm
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Horizontal Transfer ◽  
Gene Clusters ◽  
Environmental Stresses ◽  
Metal Resistance ◽  
Mobile Elements ◽  
Paecilomyces Variotii ◽  
Large Gene ◽  
Cadmium And Lead

ABSTRACTThe horizontal transfer of large gene clusters by mobile elements is a key driver of prokaryotic adaptation in response to environmental stresses. Eukaryotic microbes face similar environmental stresses yet a parallel role for mobile elements has not yet been established. A stress faced by all microorganisms is the prevalence of toxic metals in their environment. In fungi, identified mechanisms for protection against metals generally rely on genes that are dispersed within an organism’s genome. Here we have discovered a large (∼85 kb) region that confers resistance to several metals in the genomes of some, but not all, strains of a fungus, Paecilomyces variotii. We name this region HEPHAESTUS (Hϕ) and present evidence that this region is mobile within the P. variotii genome with features highly characteristic of a transposable element. While large gene clusters including those for the synthesis of secondary metabolites have been widely reported in fungi, these are not mobile within fungal genomes. HEPHAESTUS contains the greatest complement of host-beneficial genes carried by a transposable element in eukaryotes. This suggests that eukaryotic transposable elements might play a role analogous to their bacterial counterparts in the horizontal transfer of large regions of host-beneficial DNA. Genes within HEPHAESTUS responsible for individual metal resistances include those encoding a P-type ATPase transporter, PcaA, required for cadmium and lead resistance, a transporter, ZrcA, providing resistance to zinc, and a multicopper oxidase, McoA, conferring resistance to copper. Additionally, a subregion of Hϕ conferring resistance to arsenate was identified. The presence of a strikingly similar cluster in the genome of another fungus, Penicillium fuscoglaucum, suggests that HEPHAESTUS arrived in P. variotii via horizontal gene transfer.

scholarly journals High frequency of horizontal transfer in Jockey families (LINE order) of drosophilids

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Izabella L. Tambones ◽  
Annabelle Haudry ◽  
Maryanna C. Simão ◽  
Claudia M. A. Carareto
Keyword(s):  
Transposable Element ◽  
Horizontal Transfer ◽  
Large Scale ◽  
Evolutionary Dynamics ◽  
Phylogenetic Analyses ◽  
Genetic Material ◽  
Long Terminal Repeat Retrotransposons ◽  
Spatio Temporal ◽  
Line Elements ◽  
Horizontal Transfers

Abstract Background The use of large-scale genomic analyses has resulted in an improvement of transposable element sampling and a significant increase in the number of reported HTT (horizontal transfer of transposable elements) events by expanding the sampling of transposable element sequences in general and of specific families of these elements in particular, which were previously poorly sampled. In this study, we investigated the occurrence of HTT events in a group of elements that, until recently, were uncommon among the HTT records in Drosophila – the Jockey elements, members of the LINE (long interspersed nuclear element) order of non-LTR (long terminal repeat) retrotransposons. The sequences of 111 Jockey families deposited in Repbase that met the criteria of the analysis were used to identify Jockey sequences in 48 genomes of Drosophilidae (genus Drosophila, subgenus Sophophora: melanogaster, obscura and willistoni groups; subgenus Drosophila: immigrans, melanica, repleta, robusta, virilis and grimshawi groups; subgenus Dorsilopha: busckii group; genus/subgenus Zaprionus and genus Scaptodrosophila). Results Phylogenetic analyses revealed 72 Jockey families in 41 genomes. Combined analyses revealed 15 potential HTT events between species belonging to different genera and species groups of Drosophilidae, providing evidence for the flow of genetic material favoured by the spatio-temporal sharing of these species present in the Palaeartic or Afrotropical region. Conclusions Our results provide phylogenetic, biogeographic and temporal evidence of horizontal transfers of the Jockey elements, increase the number of rare records of HTT in specific families of LINE elements, increase the number of known occurrences of these events, and enable a broad understanding of the evolutionary dynamics of these elements and the host species.

scholarly journals Strong and Fluctuating Sequence Constraints Drive Alu_ Evolution

2016 ◽  
Author(s):  
Aaron C. Wacholder ◽  
David D. Pollock
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Human Genome ◽  
Evolutionary Dynamics ◽  
Phylogenetic Network ◽  
Reconstruction Method ◽  
Ancestral Reconstruction ◽  
Computationally Efficient ◽  
Whole Genome Analysis ◽  
Sequence Constraints

AbstractThough Alu elements are the most common and well-studied transposable elements in the primate genome, Alu evolutionary dynamics remain poorly understood. To better understand these dynamics, we improved our recently introduced Bayesian transposable element ancestral reconstruction method to incorporate automated alignment and be more computationally efficient. We then used it to reconstruct the relationships among almost 800,000 Alu elements in the human genome. We identified the phylogenetic network relating 154 ancestral replicative Alu sequences, and found that the aligned ancestors vary at only 56 out of ~300 sites. We show that the limited number of variable sites among replicative Alu ancestors is best explained by strong sequence constraints on Alu replicative capacity. Moreover, the pattern of variation suggests that sequence constraints fluctuated over the course of Alu evolution, driving the extinction of older Alu subfamilies and the birth of newer ones. Previous analyses have taken the tight clustering of Alu sequences with age as evidence that all Alu sequences are descended from a small number of "master elements." Our results imply instead that the clustering of Alu sequences with age results from fluctuating sequence constraints, and that there were over 4,000 replicative loci during the course of Alu evolution, most of which were disabled by mutation before mutating to new replicative sequences. We also predict which sites have been functionally important for replication, and how these sites have changed over time. The newly clarified dynamics of Alu evolution invalidate assumptions used in common method of transposable element classification and phylogenetics.Significance StatementTransposable elements are genomic sequences that can insert copies of themselves elsewhere in the genome. Alu is the most abundant transposable element in primates, making up 10% of the human genome. Due to its ubiquity and tendency to cause genomic instability, Alu has played a major role in shaping primate genomes. Characterizing the trajectory of Alu evolution is important for understanding how the human genome evolved.Previous analyses of Alu concluded that a tiny number of elements generated all copies, and existing classifications of Alu reflect that conclusion. In a whole-genome analysis, we determine that many more elements were replicative than previously understood, indicating that current classifications of Alu are flawed. We develop an alternative reconstruction of Alu evolutionary history.

scholarly journals Evolutionary dynamics of transposable elements in bdelloid rotifers

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Reuben W Nowell ◽  
Christopher G Wilson ◽  
Pedro Almeida ◽  
Philipp H Schiffer ◽  
Diego Fontaneto ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Evolutionary Dynamics ◽  
Sequence Data ◽  
Gene Families ◽  
Current Theory ◽  
Whole Genome Sequence ◽  
Term Outcome ◽  
Long Term Outcome ◽  
Bdelloid Rotifers

Transposable elements (TEs) are selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. If hosts become obligately asexual, TE frequencies and dynamics are predicted to change dramatically, but the long-term outcome is unclear. Here, we test current theory using whole-genome sequence data from eight species of bdelloid rotifers, a class of invertebrates in which males are thus far unknown. Contrary to expectations, we find a variety of active TEs in bdelloid genomes, at an overall frequency within the range seen in sexual species. We find no evidence that TEs are spread by cryptic recombination or restrained by unusual DNA repair mechanisms. Instead, we find that that TE content evolves relatively slowly in bdelloids and that gene families involved in RNAi-mediated TE suppression have undergone significant expansion, which might mitigate the deleterious effects of active TEs and compensate for the consequences of long-term asexuality.

scholarly journals Evolutionary dynamics of transposable elements in bdelloid rotifers

2020 ◽  
Author(s):  
Reuben W. Nowell ◽  
Christopher G. Wilson ◽  
Pedro Almeida ◽  
Philipp H. Schiffer ◽  
Diego Fontaneto ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Evolutionary Dynamics ◽  
Sequence Data ◽  
Current Theory ◽  
Whole Genome Sequence ◽  
Term Outcome ◽  
Diverse Range ◽  
Long Term Outcome ◽  
Bdelloid Rotifers

AbstractTransposable elements (TEs) are selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. If hosts become obligately asexual, TE frequencies and dynamics are predicted to change dramatically, but the long-term outcome is unclear. Here, we test current theory using whole-genome sequence data from eight species of bdelloid rotifers, a class of invertebrates where males are thus far unknown. Contrary to expectations, we find a diverse range of active TEs in bdelloid genomes, at an overall frequency within the range seen in sexual species. We find no evidence that TEs are spread by cryptic recombination or restrained by unusual DNA repair mechanisms, but we report that bdelloids share a large and unusual expansion of genes involved in RNAi-mediated TE suppression. This suggests that enhanced cellular defence mechanisms might mitigate the deleterious effects of active TEs and compensate for the consequences of long-term asexuality.

scholarly journals Long-Term Cocirculation of Two Strains of Pepino Mosaic Virus in Tomato Crops and Its Effect on Population Genetic Variability

2020 ◽  
Vol 110 (1) ◽  
pp. 49-57 ◽  
Author(s):  
C. Alcaide ◽  
M. P. Rabadán ◽  
M. Juárez ◽  
P. Gómez
Keyword(s):  
Genetic Variability ◽  
Mosaic Virus ◽  
Evolutionary Dynamics ◽  
Geographical Area ◽  
Viral Fitness ◽  
Mixed Infections ◽  
Supporting Evidence ◽  
Pepino Mosaic Virus ◽  
Nucleotide Variability

Mixed viral infections are common in plants, and the evolutionary dynamics of viral populations may differ depending on whether the infection is caused by single or multiple viral strains. However, comparative studies of single and mixed infections using viral populations in comparable agricultural and geographical locations are lacking. Here, we monitored the occurrence of pepino mosaic virus (PepMV) in tomato crops in two major tomato-producing areas in Murcia (southeastern Spain), supporting evidence showing that PepMV disease-affected plants had single infections of the Chilean 2 (CH2) strain in one area and the other area exhibited long-term (13 years) coexistence of the CH2 and European (EU) strains. We hypothesized that circulating strains of PepMV might be modulating the differentiation between them and shaping the evolutionary dynamics of PepMV populations. Our phylogenetic analysis of 106 CH2 isolates randomly selected from both areas showed a remarkable divergence between the CH2 isolates, with increased nucleotide variability in the geographical area where both strains cocirculate. Furthermore, the potential virus–virus interaction was studied further by constructing six full-length infectious CH2 clones from both areas, and assessing their viral fitness in the presence and absence of an EU-type isolate. All CH2 clones showed decreased fitness in mixed infections and although complete genome sequencing indicated a nucleotide divergence of those CH2 clones by area, the magnitude of the fitness response was irrespective of the CH2 origin. Overall, these results suggest that although agroecological cropping practices may be particularly important for explaining the evolutionary dynamics of PepMV in tomato crops, the cocirculation of both strains may have implications on the genetic variability of PepMV populations.

Introgression between non-sister species of honeyeaters (Aves: Meliphagidae) several million years after speciation

2019 ◽  
Vol 128 (3) ◽  
pp. 583-591
Author(s):  
Leo Joseph ◽  
Alex Drew ◽  
Ian J Mason ◽  
Jeffrey L Peters
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Sex Chromosomes ◽  
Common Ancestor ◽  
Sister Species ◽  
Species Boundaries ◽  
North Eastern ◽  
The City

Abstract We reassessed whether two parapatric non-sister Australian honeyeater species (Aves: Meliphagidae), varied and mangrove honeyeaters (Gavicalis versicolor and G. fasciogularis, respectively), that diverged from a common ancestor c. 2.5 Mya intergrade in the Townsville area of north-eastern Queensland. Consistent with a previous specimen-based study, by using genomics methods we show one-way gene flow for autosomal but not Z-linked markers from varied into mangrove honeyeaters. Introgression barely extends south of the area of parapatry in and around the city of Townsville. While demonstrating the long-term porosity of species boundaries over several million years, our data also suggest a clear role of sex chromosomes in maintaining reproductive isolation.

scholarly journals Dinosaurs in decline tens of millions of years before their final extinction

2016 ◽  
Vol 113 (18) ◽  
pp. 5036-5040 ◽  
Author(s):  
Manabu Sakamoto ◽  
Michael J. Benton ◽  
Chris Venditti
Keyword(s):  
Mass Extinction ◽  
Marked Reduction ◽  
Evolutionary Dynamics ◽  
General Pattern ◽  
Extinction Rate ◽  
Catastrophic Event ◽  
Extinction Event ◽  
Mass Extinction Event ◽  
First Time

Whether dinosaurs were in a long-term decline or whether they were reigning strong right up to their final disappearance at the Cretaceous–Paleogene (K-Pg) mass extinction event 66 Mya has been debated for decades with no clear resolution. The dispute has continued unresolved because of a lack of statistical rigor and appropriate evolutionary framework. Here, for the first time to our knowledge, we apply a Bayesian phylogenetic approach to model the evolutionary dynamics of speciation and extinction through time in Mesozoic dinosaurs, properly taking account of previously ignored statistical violations. We find overwhelming support for a long-term decline across all dinosaurs and within all three dinosaurian subclades (Ornithischia, Sauropodomorpha, and Theropoda), where speciation rate slowed down through time and was ultimately exceeded by extinction rate tens of millions of years before the K-Pg boundary. The only exceptions to this general pattern are the morphologically specialized herbivores, the Hadrosauriformes and Ceratopsidae, which show rapid species proliferations throughout the Late Cretaceous instead. Our results highlight that, despite some heterogeneity in speciation dynamics, dinosaurs showed a marked reduction in their ability to replace extinct species with new ones, making them vulnerable to extinction and unable to respond quickly to and recover from the final catastrophic event.

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