Paleontological Evidence to Date the Tree of Life

Benton, Michael J.; Donoghue, Philip C. J.

doi:10.1093/molbev/msl150

Cited by 843 publications

(799 citation statements)

References 230 publications

(279 reference statements)

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“…Regarding the two eqA3Z1 genes, a homologous canine A3Z1 gene exists as a single gene (58). This suggests that the extant A3Z1a and A3Z1b genes in the horse genome appeared via duplication after the last common ancestor of Carnivora and Perissodactyla, which could be dated some 62.5 million years ago (2). With respect to origins of the five eqA3Z2 genes, they all also share a common ancestor that is more recent than the last common ancestor of Perissodactyla and Carnivora and should therefore be considered inparalogs compared with the rest of the tree terminal taxa (81).…”

Section: Discussionmentioning

confidence: 99%

Restriction of Equine Infectious Anemia Virus by Equine APOBEC3 Cytidine Deaminases

Zielonka

Bravo²,

Marino

et al. 2009

J Virol

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The mammalian APOBEC3 (A3) proteins comprise a multigene family of cytidine deaminases that act as potent inhibitors of retroviruses and retrotransposons. The A3 locus on the chromosome 28 of the horse genome contains multiple A3 genes: two copies of A3Z1, five copies of A3Z2, and a single copy of A3Z3, indicating a complex evolution of multiple gene duplications. We have cloned and analyzed for expression the different equine A3 genes and examined as well the subcellular distribution of the corresponding proteins. Additionally, we have tested the functional antiretroviral activity of the equine and of several of the human and nonprimate A3 proteins against the Equine infectious anemia virus (EIAV), the Simian immunodeficiency virus (SIV), and the Adeno-associated virus type 2 (AAV-2). Hematopoietic cells of horses express at least five different A3s: A3Z1b, A3Z2a-Z2b, A3Z2c-Z2d, A3Z2e, and A3Z3, whereas circulating macrophages, the natural target of EIAV, express only part of the A3 repertoire. The five A3Z2 tandem copies arose after three consecutive, recent duplication events in the horse lineage, after the split between Equidae and Carnivora. The duplicated genes show different antiviral activities against different viruses: equine A3Z3 and A3Z2c-Z2d are potent inhibitors of EIAV while equine A3Z1b, A3Z2a-Z2b, A3Z2e showed only weak anti-EIAV activity. Equine A3Z1b and A3Z3 restricted AAV and all equine A3s, except A3Z1b, inhibited SIV. We hypothesize that the horse A3 genes are undergoing a process of subfunctionalization in their respective viral specificities, which might provide the evolutionary advantage for keeping five copies of the original gene.The Equine infectious anemia virus (EIAV) (family Retroviridae, genus Lentivirus) infects equids almost worldwide, causing a persistent infection characterized by recurring viremia, fever, thrombocytopenia, and wasting symptoms (40). EIAV infections are used as a model for natural immunologic control of lentivirus replication and virus persistence and as a test system to improve vaccines against lentiviruses (10,40,41,82). In vivo EIAV replicates predominantly in macrophages (77). Interaction with the equine lentiviral receptor 1 (ELR1) has been demonstrated to be responsible for EIAV internalization (96). There have been no reported cases of EIAV infections in humans, suggesting that it is an intrinsically safe virus and of interest for use in a clinical setting. Therefore, EIAV-based lentiviral vectors for human gene therapy were recently developed (1, 67, 68).In the last few years, two cellular proteins that inhibit many different retroviruses have been characterized: tripartite motif protein 5 alpha (TRIM5␣) and apolipoprotein B mRNAediting enzyme-catalytic polypeptide 3 (APOBEC3 [A3]) (for a review, see reference 92). With respect to TRIM5␣ proteins, both human and nonhuman primate TRIM5␣ orthologues can restrict infection by EIAV (26,72). The activity of equine TRIM5␣ on EIAV infection, however, has not been described so far. With respect to A3 proteins...

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Section: Discussionmentioning

confidence: 99%

Restriction of Equine Infectious Anemia Virus by Equine APOBEC3 Cytidine Deaminases

Zielonka

Bravo²,

Marino

et al. 2009

J Virol

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“…Then we estimated divergence time and neutral substitution rate per year (branch/divergence time) among species. The PAML mcmctree 60 used to estimate the species divergence time referred to two fossil calibrations, including the divergence time of D. melanogaster and Culicidae (238.5-295.4 million years ago) and the divergence time of D. melanogaster and Hymenoptera (238.5-307.2 million years ago) 61,62 . T. urticae (Arachnida) was used as an outgroup, and a bootstrap value was set as 1000.…”

Section: Methodsmentioning

confidence: 99%

Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest

et al. 2017

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The tobacco cutworm, Spodoptera litura, is among the most widespread and destructive agricultural pests, feeding on over 100 crops throughout tropical and subtropical Asia. By genome sequencing, physical mapping and transcriptome analysis, we found that the gene families encoding receptors for bitter or toxic substances and detoxification enzymes, such as cytochrome P450, carboxylesterase and glutathione-S-transferase, were massively expanded in this polyphagous species, enabling its extraordinary ability to detect and detoxify many plant secondary compounds. Larval exposure to insecticidal toxins induced expression of detoxification genes, and knockdown of representative genes using short interfering RNA (siRNA) reduced larval survival, consistent with their contribution to the insect’s natural pesticide tolerance. A population genetics study indicated that this species expanded throughout southeast Asia by migrating along a South India–South China–Japan axis, adapting to wide-ranging ecological conditions with diverse host plants and insecticides, surviving and adapting with the aid of its expanded detoxification systems. The findings of this study will enable the development of new pest management strategies for the control of major agricultural pests such as S. litura.

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“…1). The finding that genes on the human X all lie also on the elephant X chromosome implies that the fusion occurred before the eutherian radiation about 105 MYA 63. And the finding that in elephants, XCR and XAR are separated by the centromere, suggests that the two ancestral blocks underwent centromere‐centromere (Robertsonian) fusion 64.…”

Section: Sex Chromosome‐autosome Fusion Accompanied Evolution Of Euthmentioning

confidence: 99%

Did sex chromosome turnover promote divergence of the major mammal groups?

Graves

2016

BioEssays

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Comparative mapping and sequencing show that turnover of sex determining genes and chromosomes, and sex chromosome rearrangements, accompany speciation in many vertebrates. Here I review the evidence and propose that the evolution of therian mammals was precipitated by evolution of the male‐determining SRY gene, defining a novel XY sex chromosome pair, and interposing a reproductive barrier with the ancestral population of synapsid reptiles 190 million years ago (MYA). Divergence was reinforced by multiple translocations in monotreme sex chromosomes, the first of which supplied a novel sex determining gene. A sex chromosome‐autosome fusion may have separated eutherians (placental mammals) from marsupials 160 MYA. Another burst of sex chromosome change and speciation is occurring in rodents, precipitated by the degradation of the Y. And although primates have a more stable Y chromosome, it may be just a matter of time before the same fate overtakes our own lineage.Also watch the video abstract.

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Paleontological Evidence to Date the Tree of Life

Cited by 843 publications

References 230 publications

Restriction of Equine Infectious Anemia Virus by Equine APOBEC3 Cytidine Deaminases

Restriction of Equine Infectious Anemia Virus by Equine APOBEC3 Cytidine Deaminases

Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest

Did sex chromosome turnover promote divergence of the major mammal groups?

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