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Baker JN, Walker JA, Denham MW, Loupe CD, Batzer MA. Recently integrated Alu insertions in the squirrel monkey ( Saimiri) lineage and application for population analyses. Mob DNA 2018; 9:9. [PMID: 29449901 PMCID: PMC5808450 DOI: 10.1186/s13100-018-0114-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/05/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolution of Alu elements has been ongoing in primate lineages and Alu insertion polymorphisms are widely used in phylogenetic and population genetics studies. Alu subfamilies in the squirrel monkey (Saimiri), a New World Monkey (NWM), were recently reported. Squirrel monkeys are commonly used in biomedical research and often require species identification. The purpose of this study was two-fold: 1) Perform locus-specific PCR analyses on recently integrated Alu insertions in Saimiri to determine their amplification dynamics, and 2) Identify a subset of Alu insertion polymorphisms with species informative allele frequency distributions between the Saimiri sciureus and Saimiri boliviensis groups. RESULTS PCR analyses were performed on a DNA panel of 32 squirrel monkey individuals for 382 Alu insertion events ≤2% diverged from 46 different Alu subfamily consensus sequences, 25 Saimiri specific and 21 NWM specific Alu subfamilies. Of the 382 loci, 110 were polymorphic for presence / absence among squirrel monkey individuals, 35 elements from 14 different Saimiri specific Alu subfamilies and 75 elements from 19 different NWM specific Alu subfamilies (13 of 46 subfamilies analyzed did not contain polymorphic insertions). Of the 110 Alu insertion polymorphisms, 51 had species informative allele frequency distributions between Saimiri sciureus and Saimiri boliviensis groups. CONCLUSIONS This study confirms the evolution of Alu subfamilies in Saimiri and provides evidence for an ongoing and prolific expansion of these elements in Saimiri with many active subfamilies concurrently propagating. The subset of polymorphic Alu insertions with species informative allele frequency distribution between Saimiri sciureus and Saimiri boliviensis will be instructive for specimen identification and conservation biology.
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Affiliation(s)
- Jasmine N. Baker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803 USA
| | - Jerilyn A. Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803 USA
| | - Michael W. Denham
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803 USA
| | - Charles D. Loupe
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803 USA
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803 USA
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2
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Useful parasites: the evolutionary biology and biotechnology applications of transposable elements. J Genet 2017; 95:1039-1052. [PMID: 27994207 DOI: 10.1007/s12041-016-0702-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Transposable elements usually comprise the most abundant nongenic fraction of eukaryotic genomes. Because of their capacity to selfreplicate and to induce a wide range of mutations, transposable elements have long been considered as 'parasitic' or 'selfish'. Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work. Numerous studies have provided evidences that mobile elements have the potential to act as agents of evolution by increasing, rearranging and diversifying the genetic repertoire of their hosts. With large-scale sequencing becoming increasingly available, more and more scientists come across transposable element sequences in their data. I will provide examples that transposable elements, although having signatures of 'selfish' DNA, play a significant biological role in the maintainance of genome integrity and providing novel regulatoty networks. These features, along with the transpositional and mutagenic capacity to produce a raw genetic diversity, make the genome mobile fraction, a key player in species adaptation and microevolution. The last but not least, transposable elements stand as informative DNA markers that may complement other conventional DNA markers. Altogether, transposable elements represent a promising, but still largely unexplored research niche and deserve to be included into the agenda of molecular ecologists, evolutionary geneticists, conservation biologists and plant breeders.
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Jiang J, Yu J, Li J, Li P, Fan Z, Niu L, Deng J, Yue B, Li J. Mitochondrial Genome and Nuclear Markers Provide New Insight into the Evolutionary History of Macaques. PLoS One 2016; 11:e0154665. [PMID: 27135608 PMCID: PMC4852913 DOI: 10.1371/journal.pone.0154665] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/18/2016] [Indexed: 01/20/2023] Open
Abstract
The evolutionary history of macaques, genus Macaca, has been under debate due to the short times of divergence. In this study, maternal, paternal, and biparental genetic systems were applied to infer phylogenetic relationships among macaques and to trace ancient hybridization events in their evolutionary history. Using a PCR display method, 17 newly phylogenetically informative Alu insertions were identified from M. assamensis. We combined presence/absence analysis of 84 Alu elements with mitochondrial genomes as well as nuclear sequences (five autosomal genes, two Y chromosomal genes, and one X chromosomal fragment) to reconstruct a robust macaque phylogeny. Topologies generated from different inherited markers were similar supporting six well defined species groups and a close relationship of M. assamensis and M. thibetana, but differed in the placing of M. arctoides. Both Alu elements and nuclear genes supported that M. arctoides was close to the sinica group, whereas the mitochondrial data clustered it into the fascicularis/mulatta lineage. Our results reveal that a sex-biased hybridization most likely occurred in the evolutionary history of M. arctoides, and suggest an introgressive pattern of male-mediated gene flow from the ancestors of M. arctoides to the M. mulatta population followed by nuclear swamping. According to the estimation of divergence dates, the hybridization occurred around 0.88~1.77 mya (nuclear data) or 1.38~2.56 mya (mitochondrial data). In general, our study indicates that a combination of various molecular markers could help explain complicated evolutionary relationships. Our results have provided new insights into the evolutionary history of macaques and emphasize that hybridization might play an important role in macaque evolution.
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Affiliation(s)
- Juan Jiang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064 Sichuan, China
| | - Jianqiu Yu
- Chengdu Zoo, Institute of Chengdu Wildlife, Chengdu 610081, China
| | - Jing Li
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Peng Li
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064 Sichuan, China
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064 Sichuan, China
| | - Lili Niu
- Chengdu Zoo, Institute of Chengdu Wildlife, Chengdu 610081, China
| | - Jiabo Deng
- Chengdu Zoo, Institute of Chengdu Wildlife, Chengdu 610081, China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Jing Li
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064 Sichuan, China
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Guo H, Jiang J, Cui Y, Yi Y, Jia X, Wang H, Yue B, Li J. Identification and characterization of polymorphic Alu insertions in the Tibetan macaque (Macaca thibetana). EUR J WILDLIFE RES 2014. [DOI: 10.1007/s10344-014-0887-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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5
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Pattinson DJ, Thompson RS, Piotrowski AK, Asher RJ. Phylogeny, Paleontology, and Primates: Do Incomplete Fossils Bias the Tree of Life? Syst Biol 2014; 64:169-86. [DOI: 10.1093/sysbio/syu077] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- David J. Pattinson
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Richard S. Thompson
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Aleks K. Piotrowski
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Robert J. Asher
- Department of Zoology, Downing Street, Cambridge, CB2 3EJ; 2Division of Ecology and Evolution, Imperial College London, South Kensington Campus, London, SW7 2AZ; 3Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD; and 4Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
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Hartig G, Churakov G, Warren WC, Brosius J, Makałowski W, Schmitz J. Retrophylogenomics place tarsiers on the evolutionary branch of anthropoids. Sci Rep 2014; 3:1756. [PMID: 23629008 PMCID: PMC3639448 DOI: 10.1038/srep01756] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/02/2013] [Indexed: 11/15/2022] Open
Abstract
One of the most disputed issues in primate evolution and thus of our own primate roots, is the phylogenetic position of the Southeast Asian tarsier. While much molecular data indicate a basal place in the primate tree shared with strepsirrhines (prosimian monophyly hypothesis), data also exist supporting either an earlier divergence in primates (tarsier-first hypothesis) or a close relationship with anthropoid primates (Haplorrhini hypothesis). The use of retroposon insertions embedded in the Tarsius genome afforded us the unique opportunity to directly test all three hypotheses via three pairwise genome alignments. From millions of retroposons, we found 104 perfect orthologous insertions in both tarsiers and anthropoids to the exclusion of strepsirrhines, providing conflict-free evidence for the Haplorrhini hypothesis, and none supporting either of the other two positions. Thus, tarsiers are clearly the sister group to anthropoids in the clade Haplorrhini.
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Affiliation(s)
- Gerrit Hartig
- Institute of Experimental Pathology, University of Münster, 48149 Münster, Germany
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Finstermeier K, Zinner D, Brameier M, Meyer M, Kreuz E, Hofreiter M, Roos C. A mitogenomic phylogeny of living primates. PLoS One 2013; 8:e69504. [PMID: 23874967 PMCID: PMC3713065 DOI: 10.1371/journal.pone.0069504] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 06/11/2013] [Indexed: 12/28/2022] Open
Abstract
Primates, the mammalian order including our own species, comprise 480 species in 78 genera. Thus, they represent the third largest of the 18 orders of eutherian mammals. Although recent phylogenetic studies on primates are increasingly built on molecular datasets, most of these studies have focused on taxonomic subgroups within the order. Complete mitochondrial (mt) genomes have proven to be extremely useful in deciphering within-order relationships even up to deep nodes. Using 454 sequencing, we sequenced 32 new complete mt genomes adding 20 previously not represented genera to the phylogenetic reconstruction of the primate tree. With 13 new sequences, the number of complete mt genomes within the parvorder Platyrrhini was widely extended, resulting in a largely resolved branching pattern among New World monkey families. We added 10 new Strepsirrhini mt genomes to the 15 previously available ones, thus almost doubling the number of mt genomes within this clade. Our data allow precise date estimates of all nodes and offer new insights into primate evolution. One major result is a relatively young date for the most recent common ancestor of all living primates which was estimated to 66-69 million years ago, suggesting that the divergence of extant primates started close to the K/T-boundary. Although some relationships remain unclear, the large number of mt genomes used allowed us to reconstruct a robust primate phylogeny which is largely in agreement with previous publications. Finally, we show that mt genomes are a useful tool for resolving primate phylogenetic relationships on various taxonomic levels.
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Affiliation(s)
- Knut Finstermeier
- Research Group Molecular Ecology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Markus Brameier
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Matthias Meyer
- Research Group Molecular Ecology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Eva Kreuz
- Research Group Molecular Ecology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Michael Hofreiter
- Research Group Molecular Ecology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- * E-mail:
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8
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Chang CH, Takai M, Ogino S. First discovery of colobine fossils from the early to middle Pleistocene of southern Taiwan. J Hum Evol 2012; 63:439-51. [DOI: 10.1016/j.jhevol.2012.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 03/01/2012] [Accepted: 03/14/2012] [Indexed: 11/30/2022]
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9
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Meyer TJ, McLain AT, Oldenburg JM, Faulk C, Bourgeois MG, Conlin EM, Mootnick AR, de Jong PJ, Roos C, Carbone L, Batzer MA. An Alu-based phylogeny of gibbons (hylobatidae). Mol Biol Evol 2012; 29:3441-50. [PMID: 22683814 DOI: 10.1093/molbev/mss149] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Gibbons (Hylobatidae) are small, arboreal apes indigenous to Southeast Asia that diverged from other apes ∼15-18 Ma. Extant lineages radiated rapidly 6-10 Ma and are organized into four genera (Hylobates, Hoolock, Symphalangus, and Nomascus) consisting of 12-19 species. The use of short interspersed elements (SINEs) as phylogenetic markers has seen recent popularity due to several desirable characteristics: the ancestral state of a locus is known to be the absence of an element, rare potentially homoplasious events are relatively easy to resolve, and samples can be quickly and inexpensively genotyped. During radiation of primates, one particular family of SINEs, the Alu family, has proliferated in primate genomes. Nomascus leucogenys (northern white-cheeked gibbon) sequences were analyzed for repetitive content with RepeatMasker using a custom library. The sequences containing Alu elements identified as members of a gibbon-specific subfamily were then compared with orthologous positions in other primate genomes. A primate phylogenetic panel consisting of 18 primate species, including 13 gibbon species representing all four extant genera, was assayed for all loci, and a total of 125 gibbon-specific Alu insertions were identified. The resulting amplification patterns were used to generate a phylogenetic tree. We demonstrate significant support for Symphalangus as the most basal lineage within the family. Our findings also place Nomascus as a derived lineage, sister to Hoolock, with the Nomascus-Hoolock clade sister to Hylobates. Further, our analysis groups N. leucogenys and Nomascus siki as sister taxa to the exclusion of the other Nomascus species assayed. This study represents the first use of SINEs to determine the genus level phylogenetic relationships within the family Hylobatidae. These relationships have been resolved with robust support at most internal nodes, demonstrating the utility of SINE-based phylogenetic analysis. We postulate that hybridization and rapid radiation may have contributed to the complex and contradictory findings of the previous studies. Our findings will aid in the conservation of these threatened primates and inform future studies of the biogeographical history and distribution of modern gibbon species.
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Affiliation(s)
- Thomas J Meyer
- Department of Biological Sciences, Louisiana State University
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10
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Rawal K, Priya A, Malik A, Bahl R, Ramaswamy R. Distribution of MGEs and their insertion sites in the Macaca mulatta genome. Mob Genet Elements 2012; 2:133-141. [PMID: 23061019 PMCID: PMC3463469 DOI: 10.4161/mge.21074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Mobile genetic elements (MGEs) are fragments of DNA that can move around within the genome through retrotransposition. These are responsible for various important events such as gene inactivation, transduction, regulation of gene expression and genome expansion. The present work involves the identification and study of the distribution of Alu and L1 retrotransposons in the genome of Macaca mulatta, an extensively used organism in biomedical studies. We also make comparisons with MGE distributions in other primate genomes and study the physicochemical properties of the local DNA structure around the transposon insertion site using ELAN. The present work also includes computational testing of the pre-insertion loci in order to detect unique features based on DNA structure, thermodynamic considerations and protein interaction measures. Although there is significant sequence divergence between the elements of M. mulatta and H. sapiens, their genome wide distribution is very similar; comparing the distribution of L1's in all available X chromosome sequences suggests a common mechanism behind the spread of MGE's in primate genomes.
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Affiliation(s)
- Kamal Rawal
- Department of Biotechnology; Jaypee Institute of Information Technology; Noida, India
| | - Avantika Priya
- Department of Biotechnology; Jaypee Institute of Information Technology; Noida, India
| | - Aman Malik
- Department of Biotechnology; Jaypee Institute of Information Technology; Noida, India
| | - Radhika Bahl
- Department of Biotechnology; Jaypee Institute of Information Technology; Noida, India
- University of Hyderabad; Central University; Gachibowli, Hyderaba, India
| | - Ram Ramaswamy
- University of Hyderabad; Central University; Gachibowli, Hyderaba, India
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11
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Cook DJ, Tymianski M. Translating promising preclinical neuroprotective therapies to human stroke trials. Expert Rev Cardiovasc Ther 2011; 9:433-49. [PMID: 21517728 DOI: 10.1586/erc.11.34] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Stroke is the third leading cause of mortality and carries the greatest socioeconomic burden of disease in North America. Despite several promising therapies discovered in the preclinical setting, there have been no positive results in human stroke clinical trials to date. In this article, we review the potential causes for failure and discuss strategies that have been proposed to overcome the barrier to translation of stroke therapies. To improve the chance of success in future human stroke trials, we propose that therapies be tested in stroke models that closely resemble the human condition with molecular, imaging and functional outcomes that relate to outcomes utilized in clinical trials. These strategies include higher-order, old-world, nonhuman primate models of stroke with clinically relevant outcome measures. Although stroke neuroprotection has been looked upon pessimistically given the many failures in clinical trials to date, we propose that neuroprotection in humans is feasible and will be realized with rigorous translational science.
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Affiliation(s)
- Douglas James Cook
- University of Toronto, Department of Surgery, Division of Neurosurgery, Toronto Western Research Institute Neuroprotection Laboratory, 11-414 MCl 399 Bathurst St, Toronto, ON, M5T 2S8, Canada
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12
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Schmitz J, Brosius J. Exonization of transposed elements: A challenge and opportunity for evolution. Biochimie 2011; 93:1928-34. [PMID: 21787833 DOI: 10.1016/j.biochi.2011.07.014] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 07/11/2011] [Indexed: 10/17/2022]
Abstract
Protein-coding genes are composed of exons and introns flanked by untranslated regions. Before the mRNA of a gene can be translated into protein, the splicing machinery removes all the intronic regions and joins the protein-coding exons together. Exonization is a process, whereby genes acquire new exons from non-protein-coding, primarily intronic, DNA sequences. Genomic insertions or point mutations within DNA sequences often generate alternative splice sites, causing the splicing system to include new sequences as exons or to elongate existing exons. Because the alternative splice sites are not as efficient as the originals the new variants usually constitute a minor fraction of mature mRNAs. While the prevailing original splice variant maintains functionality, the additional sequence, free from selection pressure, evolves a new function or eventually vanishes. If the new splice variant is advantageous, selection might operate to optimize the new splice sites and consequently increase the proportion of the alternative splice variant. In some instances, the original splice variant is completely replaced by constitutive splicing of the new form. Because of the fortuitous presence of internal splice site-like structures within their sequences, portions of transposed elements frequently serve as modules of exonization. Their recruitment requires a long and versatile optimization process involving multiple changes over a time span of millions, even hundreds of millions, of years. Comparisons of corresponding genes and mRNAs in phylogenetically related species enables one to chronologically reconstruct such changes, from ancient ancestors to living species, in a stepwise manner. We will review this process using three different exemplary cases: (1) the evolution of a constitutively spliced mammalian-wide repeat (MIR), (2) the evolution of an alternative exon 1 from an alternative 5'-extended primary transcript containing an Alu element, and (3) a rare case of the stepwise exoniztion of an Alu element-derived sequence mediated by A-to-I RNA editing.
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Affiliation(s)
- Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany.
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13
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Ray DA, Batzer MA. Reading TE leaves: new approaches to the identification of transposable element insertions. Genome Res 2011; 21:813-20. [PMID: 21632748 PMCID: PMC3106314 DOI: 10.1101/gr.110528.110] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Transposable elements (TEs) are a tremendous source of genome instability and genetic variation. Of particular interest to investigators of human biology and human evolution are retrotransposon insertions that are recent and/or polymorphic in the human population. As a consequence, the ability to assay large numbers of polymorphic TEs in a given genome is valuable. Five recent manuscripts each propose methods to scan whole human genomes to identify, map, and, in some cases, genotype polymorphic retrotransposon insertions in multiple human genomes simultaneously. These technologies promise to revolutionize our ability to analyze human genomes for TE-based variation important to studies of human variability and human disease. Furthermore, the approaches hold promise for researchers interested in nonhuman genomic variability. Herein, we explore the methods reported in the manuscripts and discuss their applications to aspects of human biology and the biology of other organisms.
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Affiliation(s)
- David A. Ray
- Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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14
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Roos C, Zinner D, Kubatko LS, Schwarz C, Yang M, Meyer D, Nash SD, Xing J, Batzer MA, Brameier M, Leendertz FH, Ziegler T, Perwitasari-Farajallah D, Nadler T, Walter L, Osterholz M. Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys. BMC Evol Biol 2011; 11:77. [PMID: 21435245 PMCID: PMC3068967 DOI: 10.1186/1471-2148-11-77] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 03/24/2011] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Colobine monkeys constitute a diverse group of primates with major radiations in Africa and Asia. However, phylogenetic relationships among genera are under debate, and recent molecular studies with incomplete taxon-sampling revealed discordant gene trees. To solve the evolutionary history of colobine genera and to determine causes for possible gene tree incongruences, we combined presence/absence analysis of mobile elements with autosomal, X chromosomal, Y chromosomal and mitochondrial sequence data from all recognized colobine genera. RESULTS Gene tree topologies and divergence age estimates derived from different markers were similar, but differed in placing Piliocolobus/Procolobus and langur genera among colobines. Although insufficient data, homoplasy and incomplete lineage sorting might all have contributed to the discordance among gene trees, hybridization is favored as the main cause of the observed discordance. We propose that African colobines are paraphyletic, but might later have experienced female introgression from Piliocolobus/Procolobus into Colobus. In the late Miocene, colobines invaded Eurasia and diversified into several lineages. Among Asian colobines, Semnopithecus diverged first, indicating langur paraphyly. However, unidirectional gene flow from Semnopithecus into Trachypithecus via male introgression followed by nuclear swamping might have occurred until the earliest Pleistocene. CONCLUSIONS Overall, our study provides the most comprehensive view on colobine evolution to date and emphasizes that analyses of various molecular markers, such as mobile elements and sequence data from multiple loci, are crucial to better understand evolutionary relationships and to trace hybridization events. Our results also suggest that sex-specific dispersal patterns, promoted by a respective social organization of the species involved, can result in different hybridization scenarios.
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Affiliation(s)
- Christian Roos
- Primate Genetics Laboratory, German Primate Center, Göttingen, Germany.
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Perelman P, Johnson WE, Roos C, Seuánez HN, Horvath JE, Moreira MAM, Kessing B, Pontius J, Roelke M, Rumpler Y, Schneider MPC, Silva A, O'Brien SJ, Pecon-Slattery J. A molecular phylogeny of living primates. PLoS Genet 2011; 7:e1001342. [PMID: 21436896 PMCID: PMC3060065 DOI: 10.1371/journal.pgen.1001342] [Citation(s) in RCA: 879] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 02/16/2011] [Indexed: 12/13/2022] Open
Abstract
Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (∼8 Mb) from 186 primates representing 61 (∼90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species. Advances in human biomedicine, including those focused on changes in genes triggered or disrupted in development, resistance/susceptibility to infectious disease, cancers, mechanisms of recombination, and genome plasticity, cannot be adequately interpreted in the absence of a precise evolutionary context or hierarchy. However, little is known about the genomes of other primate species, a situation exacerbated by a paucity of nuclear molecular sequence data necessary to resolve the complexities of primate divergence over time. We overcome this deficiency by sequencing 54 nuclear gene regions from DNA samples representing ∼90% of the diversity present in living primates. We conduct a phylogenetic analysis to determine the origin, evolution, patterns of speciation, and unique features in genome divergence among primate lineages. The resultant phylogenetic tree is remarkably robust and unambiguously resolves many long-standing issues in primate taxonomy. Our data provide a strong foundation for illuminating those genomic differences that are uniquely human and provide new insights on the breadth and richness of gene evolution across all primate lineages.
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Affiliation(s)
- Polina Perelman
- Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Warren E. Johnson
- Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Göttingen, Germany
| | - Hector N. Seuánez
- Division of Genetics, Instituto Nacional de Câncer and Department of Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Julie E. Horvath
- Department of Evolutionary Anthropology and Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America
| | - Miguel A. M. Moreira
- Division of Genetics, Instituto Nacional de Câncer and Department of Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bailey Kessing
- SAIC–Frederick, Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Joan Pontius
- SAIC–Frederick, Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Melody Roelke
- SAIC–Frederick, Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Yves Rumpler
- Physiopathologie et Médecine Translationnelle, Faculté de Médecine, Université Louis Pasteur, Strasbourg, France
| | | | | | - Stephen J. O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
| | - Jill Pecon-Slattery
- Laboratory of Genomic Diversity, National Cancer Institute–Frederick, Frederick, Maryland, United States of America
- * E-mail:
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16
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Affiliation(s)
- Miriam K Konkel
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803, USA
| | - Jerilyn A Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803, USA
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803, USA
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Churakov G, Grundmann N, Kuritzin A, Brosius J, Makałowski W, Schmitz J. A novel web-based TinT application and the chronology of the Primate Alu retroposon activity. BMC Evol Biol 2010; 10:376. [PMID: 21126360 PMCID: PMC3014933 DOI: 10.1186/1471-2148-10-376] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 12/02/2010] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND DNA sequences afford access to the evolutionary pathways of life. Particularly mobile elements that constantly co-evolve in genomes encrypt recent and ancient information of their host's history. In mammals there is an extraordinarily abundant activity of mobile elements that occurs in a dynamic succession of active families, subfamilies, types, and subtypes of retroposed elements. The high frequency of retroposons in mammals implies that, by chance, such elements also insert into each other. While inactive elements are no longer able to retropose, active elements retropose by chance into other active and inactive elements. Thousands of such directional, element-in-element insertions are found in present-day genomes. To help analyze these events, we developed a computational algorithm (Transpositions in Transpositions, or TinT) that examines the different frequencies of nested transpositions and reconstructs the chronological order of retroposon activities. RESULTS By examining the different frequencies of such nested transpositions, the TinT application reconstructs the chronological order of retroposon activities. We use such activity patterns as a comparative tool to (1) delineate the historical rise and fall of retroposons and their relations to each other, (2) understand the retroposon-induced complexity of recent genomes, and (3) find selective informative homoplasy-free markers of phylogeny. The efficiency of the new application is demonstrated by applying it to dimeric Alu Short INterspersed Elements (SINE) to derive a complete chronology of such elements in primates. CONCLUSION The user-friendly, web-based TinT interface presented here affords an easy, automated screening for nested transpositions from genome assemblies or trace data, assembles them in a frequency-matrix, and schematically displays their chronological activity history.
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Affiliation(s)
- Gennady Churakov
- Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany
| | - Norbert Grundmann
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Niels Stensen Str. 14, 48149 Münster, Germany
| | - Andrej Kuritzin
- Department of Physics and Mathematics, Saint Petersburg State Institute of Technology, 26 Moskovsky av., St.-Petersburg 198013, Russia
| | - Jürgen Brosius
- Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany
| | - Wojciech Makałowski
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Niels Stensen Str. 14, 48149 Münster, Germany
| | - Jürgen Schmitz
- Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany
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18
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Schwartz JH, Tattersall I. Fossil evidence for the origin of Homo sapiens. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 143 Suppl 51:94-121. [DOI: 10.1002/ajpa.21443] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Williams BA, Kay RF, Christopher Kirk E, Ross CF. Darwinius masillae is a strepsirrhine—a reply to Franzen et al. (2009). J Hum Evol 2010; 59:567-73; discussion 574-9. [DOI: 10.1016/j.jhevol.2010.01.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2009] [Revised: 10/21/2009] [Accepted: 11/02/2009] [Indexed: 10/19/2022]
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20
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Arnold C, Matthews LJ, Nunn CL. The 10kTrees website: A new online resource for primate phylogeny. Evol Anthropol 2010. [DOI: 10.1002/evan.20251] [Citation(s) in RCA: 488] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Heads M. Evolution and biogeography of primates: a new model based on molecular phylogenetics, vicariance and plate tectonics. ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2009.00411.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Meer MV, Kondrashov AS, Artzy-Randrup Y, Kondrashov FA. Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature 2010; 464:279-82. [PMID: 20182427 DOI: 10.1038/nature08691] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 11/16/2009] [Indexed: 12/25/2022]
Abstract
A long-standing controversy in evolutionary biology is whether or not evolving lineages can cross valleys on the fitness landscape that correspond to low-fitness genotypes, which can eventually enable them to reach isolated fitness peaks. Here we study the fitness landscapes traversed by switches between different AU and GC Watson-Crick nucleotide pairs at complementary sites of mitochondrial transfer RNA stem regions in 83 mammalian species. We find that such Watson-Crick switches occur 30-40 times more slowly than pairs of neutral substitutions, and that alleles corresponding to GU and AC non-Watson-Crick intermediate states segregate within human populations at low frequencies, similar to those of non-synonymous alleles. Substitutions leading to a Watson-Crick switch are strongly correlated, especially in mitochondrial tRNAs encoded on the GT-nucleotide-rich strand of the mitochondrial genome. Using these data we estimate that a typical Watson-Crick switch involves crossing a fitness valley of a depth of about 10(-3) or even about 10(-2), with AC intermediates being slightly more deleterious than GU intermediates. This compensatory evolution must proceed through rare intermediate variants that never reach fixation. The ubiquitous nature of compensatory evolution in mammalian mitochondrial tRNAs and other molecules implies that simultaneous fixation of two alleles that are individually deleterious may be a common phenomenon at the molecular level.
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Affiliation(s)
- Margarita V Meer
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, C/Dr Aiguader 88, Barcelona Biomedical Research Park Building, 08003 Barcelona, Spain
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Asher RJ, Bennett N, Lehmann T. The new framework for understanding placental mammal evolution. Bioessays 2010; 31:853-64. [PMID: 19582725 DOI: 10.1002/bies.200900053] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An unprecedented level of confidence has recently crystallized around a new hypothesis of how living placental mammals share a pattern of common descent. The major groups are afrotheres (e.g., aardvarks, elephants), xenarthrans (e.g., anteaters, sloths), laurasiatheres (e.g., horses, shrews), and euarchontoglires (e.g., humans, rodents). Compared with previous hypotheses this tree is remarkably stable; however, some uncertainty persists about the location of the placental root, and (for example) the position of bats within laurasiatheres, of sea cows and aardvarks within afrotheres, and of dermopterans within euarchontoglires. A variety of names for sub-clades within the new placental mammal tree have been proposed, not all of which follow conventions regarding priority and stability. More importantly, the new phylogenetic framework enables the formulation of new hypotheses and testing thereof, for example regarding the possible developmental dichotomy that seems to distinguish members of the newly identified southern and northern radiations of living placental mammals.
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Affiliation(s)
- Robert J Asher
- Department of Zoology, University of Cambridge, Downing St., Cambridge CB23EJ, UK.
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24
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Churakov G, Sadasivuni MK, Rosenbloom KR, Huchon D, Brosius J, Schmitz J. Rodent Evolution: Back to the Root. Mol Biol Evol 2010; 27:1315-26. [DOI: 10.1093/molbev/msq019] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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Chatterjee HJ, Ho SYW, Barnes I, Groves C. Estimating the phylogeny and divergence times of primates using a supermatrix approach. BMC Evol Biol 2009; 9:259. [PMID: 19860891 PMCID: PMC2774700 DOI: 10.1186/1471-2148-9-259] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Accepted: 10/27/2009] [Indexed: 12/05/2022] Open
Abstract
Background The primates are among the most broadly studied mammalian orders, with the published literature containing extensive analyses of their behavior, physiology, genetics and ecology. The importance of this group in medical and biological research is well appreciated, and explains the numerous molecular phylogenies that have been proposed for most primate families and genera. Composite estimates for the entire order have been infrequently attempted, with the last phylogenetic reconstruction spanning the full range of primate evolutionary relationships having been conducted over a decade ago. Results To estimate the structure and tempo of primate evolutionary history, we employed Bayesian phylogenetic methods to analyze data supermatrices comprising 7 mitochondrial genes (6,138 nucleotides) from 219 species across 67 genera and 3 nuclear genes (2,157 nucleotides) from 26 genera. Many taxa were only partially represented, with an average of 3.95 and 5.43 mitochondrial genes per species and per genus, respectively, and 2.23 nuclear genes per genus. Our analyses of mitochondrial DNA place Tarsiiformes as the sister group of Strepsirrhini. Within Haplorrhini, we find support for the primary divergence of Pitheciidae in Platyrrhini, and our results suggest a sister grouping of African and non-African colobines within Colobinae and of Cercopithecini and Papionini within Cercopthecinae. Date estimates for nodes within each family and genus are presented, with estimates for key splits including: Strepsirrhini-Haplorrhini 64 million years ago (MYA), Lemuriformes-Lorisiformes 52 MYA, Platyrrhini-Catarrhini 43 MYA and Cercopithecoidea-Hominoidea 29 MYA. Conclusion We present an up-to-date, comprehensive estimate of the structure and tempo of primate evolutionary history. Although considerable gaps remain in our knowledge of the primate phylogeny, increased data sampling, particularly from nuclear loci, will be able to provide further resolution.
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Affiliation(s)
- Helen J Chatterjee
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.
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26
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Averdam A, Petersen B, Rosner C, Neff J, Roos C, Eberle M, Aujard F, Münch C, Schempp W, Carrington M, Shiina T, Inoko H, Knaust F, Coggill P, Sehra H, Beck S, Abi-Rached L, Reinhardt R, Walter L. A novel system of polymorphic and diverse NK cell receptors in primates. PLoS Genet 2009; 5:e1000688. [PMID: 19834558 PMCID: PMC2757895 DOI: 10.1371/journal.pgen.1000688] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 09/17/2009] [Indexed: 11/21/2022] Open
Abstract
There are two main classes of natural killer (NK) cell receptors in mammals, the killer cell immunoglobulin-like receptors (KIR) and the structurally unrelated killer cell lectin-like receptors (KLR). While KIR represent the most diverse group of NK receptors in all primates studied to date, including humans, apes, and Old and New World monkeys, KLR represent the functional equivalent in rodents. Here, we report a first digression from this rule in lemurs, where the KLR (CD94/NKG2) rather than KIR constitute the most diverse group of NK cell receptors. We demonstrate that natural selection contributed to such diversification in lemurs and particularly targeted KLR residues interacting with the peptide presented by MHC class I ligands. We further show that lemurs lack a strict ortholog or functional equivalent of MHC-E, the ligands of non-polymorphic KLR in "higher" primates. Our data support the existence of a hitherto unknown system of polymorphic and diverse NK cell receptors in primates and of combinatorial diversity as a novel mechanism to increase NK cell receptor repertoire.
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Affiliation(s)
- Anne Averdam
- Department of Primate Genetics, German Primate Centre, Göttingen, Germany
| | - Beatrix Petersen
- Department of Primate Genetics, German Primate Centre, Göttingen, Germany
| | - Cornelia Rosner
- Department of Primate Genetics, German Primate Centre, Göttingen, Germany
| | - Jennifer Neff
- Department of Primate Genetics, German Primate Centre, Göttingen, Germany
| | - Christian Roos
- Department of Primate Genetics, German Primate Centre, Göttingen, Germany
- Gene Bank of Primates, German Primate Centre, Göttingen, Germany
| | - Manfred Eberle
- Department of Behavioural Ecology and Sociobiology, German Primate Centre, Göttingen, Germany
| | - Fabienne Aujard
- Adaptive Mechanisms and Evolution, UMR CNRS/MNHN 7179, Brunoy, France
| | - Claudia Münch
- Institute for Human Genetics, University of Freiburg, Freiburg, Germany
| | - Werner Schempp
- Institute for Human Genetics, University of Freiburg, Freiburg, Germany
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | | | | | - Florian Knaust
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Penny Coggill
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Stephan Beck
- University College London Cancer Institute, University College London, London, United Kingdom
| | - Laurent Abi-Rached
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | | | - Lutz Walter
- Department of Primate Genetics, German Primate Centre, Göttingen, Germany
- Gene Bank of Primates, German Primate Centre, Göttingen, Germany
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Fabre PH, Rodrigues A, Douzery EJP. Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA. Mol Phylogenet Evol 2009; 53:808-25. [PMID: 19682589 DOI: 10.1016/j.ympev.2009.08.004] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 07/08/2009] [Accepted: 08/03/2009] [Indexed: 11/18/2022]
Abstract
Here, we present a new primate phylogeny inferred from molecular supermatrix analyses of size 42 kb containing 70% of missing data, and representing 75% of primate species diversity. The supermatrix was analysed using a gene-partitioned maximum likelihood approach to obtain an exhaustive molecular phylogenetic framework. All clades recovered from recent molecular works were upheld in our analyses demonstrating that the presence of missing data did not bias our supermatrix inference. The resulting phylogenetic tree was subsequently dated with a molecular dating method to provide a timescale for speciation events. Results obtained from our relaxed molecular clock analyses concurred with previous works based on the same fossil constraints. The resulting dated tree allowed to infer of macroevolutionary processes among the primates. Shifts in diversification rate and speciation rates were determined using the SymmeTREE method and a birthdeath process. No significant asymmetry was detected for the primate clade, but significant shifts in diversification rate were identified for seven clades: Anthropoidea, Lemuriformes, Lemuridae, Galagidae, Callithrix genus, the Cercopithecinae and Asian Macaca. Comparisons with previous primate supertree results reveal that (i) there was a diversification event at the root of the Lemuriformes, (ii) a higher diversification rate is detected for Cercopithecidae and Anthropoidea and (iii) a shift in diversification is always recovered for Macaca genus. Macroevolutionary inferences and primate divergence dates show that major primate diversification events occurred after the Paleogene, suggesting the extinction of ancient primate lineages.
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Affiliation(s)
- P-H Fabre
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Université Montpellier II, Place E. Bataillon, CC 064, 34095 Montpellier Cedex 5, France.
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Abstract
Primate models are essential tools for translational research in stroke but are reportedly inconsistent in their ability to produce cortical infarcts of reproducible size. Here, we report a new stroke model using a transorbital, reversible, two-vessel occlusion approach in male rhesus macaques that produces consistent and reproducible cortical infarcts. The right middle cerebral artery (distal to the orbitofrontal branch) and both anterior cerebral arteries were occluded with vascular clips. Bilateral occlusion of the anterior cerebral artery was critical for reducing collateral flow to the ipsilateral cortex. Reversible ischemia was induced for 45, 60, or 90 mins (n=2/timepoint) and infarct volume and neurologic outcome were evaluated. The infarcts were located predominantly in the cortex and increased in size with extended duration of ischemia determined by T(2)-weighted magnetic resonance imaging . Infarct volume measured by 2,3,5-triphenyl tetrazolium chloride and cresyl violet staining corroborated magnetic resonance imaging results. Neurologic deficit scores worsened gradually with longer occlusion times. A subset of animals (n=5) underwent 60 mins of ischemia resulting in consistent infarct volumes primarily located to the cortex that correlated well with neurologic deficit scores. This approach offers promise for evaluating therapeutic interventions in stroke.
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Osterholz M, Vermeer J, Walter L, Roos C. A PCR-based marker to simply identify Saimiri sciureus and S. boliviensis boliviensis. Am J Primatol 2009; 70:1177-80. [PMID: 18831057 DOI: 10.1002/ajp.20606] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Squirrel monkeys, mainly Saimiri sciureus and S. boliviensis, are common in zoos and widely used in biomedical research. However, an exact species identification based on morphological characteristics is difficult. Hence, several molecular methods were proposed, but all of them are expensive and require extensive laboratory work. In contrast, we describe an Alu integration, which is present in S. boliviensis boliviensis and absent in S. sciureus. Among analyzed S. b. peruviensis specimens various presence/absence patterns of the integration were detected indicating that this study population might have originated from a natural hybrid zone. Based on the size of the Alu element ( approximately 300 bp), the presence/absence pattern of the integration can easily be traced by PCR and followed by agarose gel electrophoresis.
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Osterholz M, Walter L, Roos C. Retropositional events consolidate the branching order among New World monkey genera. Mol Phylogenet Evol 2008; 50:507-13. [PMID: 19135536 DOI: 10.1016/j.ympev.2008.12.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Revised: 11/10/2008] [Accepted: 12/16/2008] [Indexed: 11/28/2022]
Abstract
Due to contradicting relationships obtained from various morphological and genetic studies, phylogenetic relationships among New World monkey genera are highly disputed. In the present study, we analyzed the presence/absence pattern of 128 SINE integrations in all New World monkey genera. Among them, 70 were specific for only a single genus, whereas another 18 were present in all New World monkey genera. The 40 remaining insertions were informative to elucidate phylogenetic relationships among genera. Several of them confirmed the monophyly of the three families Cebidae, Atelidae and Pitheciidae as well as of the subfamily Callithrichinae. Further markers provided evidence for a sister grouping of Cebidae and Atelidae to the exclusion of Pitheciidae as well as for relationships among genera belonging to Callithrichinae and Atelidae. Although a close affiliation of Saimiri, Aotus and Cebus to Callithrichinae was shown, the relationships among the three genera remained unresolved due to three contradicting insertions.
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Affiliation(s)
- Martin Osterholz
- Primate Genetics, German Primate Center, Kellnerweg 4, 37077 Goettingen, Germany.
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31
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Vittori K, Delbem AC, Pereira SL. Ant-Based Phylogenetic Reconstruction (ABPR): A new distance algorithm for phylogenetic estimation based on ant colony optimization. Genet Mol Biol 2008. [DOI: 10.1590/s1415-47572008000500027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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32
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Asher RJ, Geisler JH, Sánchez-Villagra MR. Morphology, paleontology, and placental mammal phylogeny. Syst Biol 2008; 57:311-7. [PMID: 18432551 DOI: 10.1080/10635150802033022] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Robert J Asher
- Department of Zoology, University of Cambridge, Downing Street, UK
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33
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Mitogenomic relationships of placental mammals and molecular estimates of their divergences. Gene 2008; 421:37-51. [DOI: 10.1016/j.gene.2008.05.024] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Revised: 04/01/2008] [Accepted: 05/26/2008] [Indexed: 11/22/2022]
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Abstract
In 1992 the Japanese macaque was the first species for which the homology of the entire karyotype was established by cross-species chromosome painting. Today, there are chromosome painting data on more than 50 species of primates. Although chromosome painting is a rapid and economical method for tracking translocations, it has limited utility for revealing intrachromosomal rearrangements. Fortunately, the use of BAC-FISH in the last few years has allowed remarkable progress in determining marker order along primate chromosomes and there are now marker order data on an array of primate species for a good number of chromosomes. These data reveal inversions, but also show that centromeres of many orthologous chromosomes are embedded in different genomic contexts. Even if the mechanisms of neocentromere formation and progression are just beginning to be understood, it is clear that these phenomena had a significant impact on shaping the primate genome and are fundamental to our understanding of genome evolution. In this report we complete and integrate the dataset of BAC-FISH marker order for human syntenies 1, 2, 4, 5, 8, 12, 17, 18, 19, 21, 22 and the X. These results allowed us to develop hypotheses about the content, marker order and centromere position in ancestral karyotypes at five major branching points on the primate evolutionary tree: ancestral primate, ancestral anthropoid, ancestral platyrrhine, ancestral catarrhine and ancestral hominoid. Current models suggest that between-species structural rearrangements are often intimately related to speciation. Comparative primate cytogenetics has become an important tool for elucidating the phylogeny and the taxonomy of primates. It has become increasingly apparent that molecular cytogenetic data in the future can be fruitfully combined with whole-genome assemblies to advance our understanding of primate genome evolution as well as the mechanisms and processes that have led to the origin of the human genome.
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35
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Munshi-South J. Colugo: The Flying Lemur of South-East Asia. J Mammal 2008. [DOI: 10.1644/07-mamm-r-337.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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36
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Osterholz M, Walter L, Roos C. Phylogenetic position of the langur genera Semnopithecus and Trachypithecus among Asian colobines, and genus affiliations of their species groups. BMC Evol Biol 2008; 8:58. [PMID: 18298809 PMCID: PMC2268674 DOI: 10.1186/1471-2148-8-58] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Accepted: 02/25/2008] [Indexed: 11/16/2022] Open
Abstract
Background The evolutionary history of the Asian colobines is less understood. Although monophyly of the odd-nosed monkeys was recently confirmed, the relationships among the langur genera Presbytis, Semnopithecus and Trachypithecus and their position among Asian colobines remained unclear. Moreover, in Trachypithecus various species groups are recognized, but their affiliations are still disputed. To address these issues, mitochondrial and Y chromosomal sequence data were phylogenetically related and combined with presence/absence analyses of retroposon integrations. Results The analysed 5 kb fragment of the mitochondrial genome allows no resolution of the phylogenetic relationships among langur genera, but five retroposon integrations were detected which link Trachypithecus and Semnopithecus. According to Y chromosomal data and a 573 bp fragment of the mitochondrial cytochrome b gene, a common origin of the species groups T. [cristatus], T. [obscurus] and T. [francoisi] and their reciprocal monophyly is supported, which is also underpinned by an orthologous retroposon insertion. T. [vetulus] clusters within Semnopithecus, which is confirmed by two retroposon integrations. Moreover, this species group is paraphyletic, with T. vetulus forming a clade with the Sri Lankan, and T. johnii with the South Indian form of S. entellus. Incongruence between gene trees was detected for T. [pileatus], in that Y chromosomal data link it with T. [cristatus], T. [obscurus] and T. [francoisi], whereas mitochondrial data affiliates it with the Semnopithecus clade. Conclusion Neither relationships among the three langur genera nor their position within Asian colobines can be settled with 5 kb mitochondrial sequence data, but retroposon integrations confirm at least a common origin of Semnopithecus and Trachypithecus. According to Y chromosomal and 573 bp mitochondrial sequence data, T. [cristatus], T. [obscurus] and T. [francoisi] represent true members of the genus Trachypithecus, whereas T. [vetulus] clusters within Semnopithecus. Due to paraphyly of T. [vetulus] and polyphyly of Semnopithecus, a split of the genus into three species groups (S. entellus - North India, S. entellus - South India + T. johnii, S. entellus - Sri Lanka + T. vetulus) seems to be appropriate. T. [pileatus] posses an intermediate position between both genera, indicating that the species group might be the result of ancestral hybridization.
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Affiliation(s)
- Martin Osterholz
- Department of Primate Genetics, German Primate Center, Kellnerweg 4, 37077 Goettingen, Germany.
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Xing J, Witherspoon DJ, Ray DA, Batzer MA, Jorde LB. Mobile DNA elements in primate and human evolution. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2008; Suppl 45:2-19. [PMID: 18046749 DOI: 10.1002/ajpa.20722] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Roughly 50% of the primate genome consists of mobile, repetitive DNA sequences such as Alu and LINE1 elements. The causes and evolutionary consequences of mobile element insertion, which have received considerable attention during the past decade, are reviewed in this article. Because of their unique mutational mechanisms, these elements are highly useful for answering phylogenetic questions. We demonstrate how they have been used to help resolve a number of questions in primate phylogeny, including the human-chimpanzee-gorilla trichotomy and New World primate phylogeny. Alu and LINE1 element insertion polymorphisms have also been analyzed in human populations to test hypotheses about human evolution and population affinities and to address forensic issues. Finally, these elements have had impacts on the genome itself. We review how they have influenced fundamental ongoing processes like nonhomologous recombination, genomic deletion, and X chromosome inactivation.
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Affiliation(s)
- Jinchuan Xing
- Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
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Dumas F, Stanyon R, Sineo L, Stone G, Bigoni F. Phylogenomics of species from four genera of New World monkeys by flow sorting and reciprocal chromosome painting. BMC Evol Biol 2007; 7 Suppl 2:S11. [PMID: 17767727 PMCID: PMC1963484 DOI: 10.1186/1471-2148-7-s2-s11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Background The taxonomic and phylogenetic relationships of New World monkeys (Platyrrhini) are difficult to distinguish on the basis of morphology and because diagnostic fossils are rare. Recently, molecular data have led to a radical revision of the traditional taxonomy and phylogeny of these primates. Here we examine new hypotheses of platyrrhine evolutionary relationships by reciprocal chromosome painting after chromosome flow sorting of species belonging to four genera of platyrrhines included in the Cebidae family: Callithrix argentata (silvered-marmoset), Cebuella pygmaea (pygmy marmoset), Callimico goeldii (Goeldi's marmoset) and Saimiri sciureus (squirrel monkey). This is the first report of reciprocal painting in marmosets. Results The paints made from chromosome flow sorting of the four platyrrhine monkeys provided from 42 to 45 hybridization signals on human metaphases. The reciprocal painting of monkey probes on human chromosomes revealed that 21 breakpoints are common to all four studied species. There are only three additional breakpoints. A breakpoint on human chromosome 13 was found in Callithrix argentata, Cebuella pygmaea and Callimico goeldii, but not in Saimiri sciureus. There are two additional breakpoints on human chromosome 5: one is specific to squirrel monkeys, and the other to Goeldi's marmoset. Conclusion The reciprocal painting results support the molecular genomic assemblage of Cebidae. We demonstrated that the five chromosome associations previously hypothesized to phylogenetically link tamarins and marmosets are homologous and represent derived chromosome rearrangements. Four of these derived homologous associations tightly nest Callimico goeldii with marmosets. One derived association 2/15 may place squirrel monkeys within the Cebidae assemblage. An apparently common breakpoint on chromosome 5q33 found in both Saimiri and Aotus nancymae could be evidence of a phylogenetic link between these species. Comparison with previous reports shows that many syntenic associations found in platyrrhines have the same breakpoints and are homologous, derived rearrangements showing that the New World monkeys are a closely related group of species. Our data support the hypothesis that the ancestral karyotype of the Platyrrhini has a diploid number of 2n = 54 and is almost identical to that found today in capuchin monkeys; congruent with a basal position of the Cebidae among platyrrhine families.
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Affiliation(s)
- Francesca Dumas
- Dipartimento di Biologia animale (DBA) Università degli Studi di Palermo, via Archirafi 18. Palermo, Italy
| | - Roscoe Stanyon
- Dipartimento di Biologia Animale e Genetica, Laboratori di Antropologia, Via del Proconsolo 12, 50122 Firenze, Italy
| | - Luca Sineo
- Dipartimento di Biologia animale (DBA) Università degli Studi di Palermo, via Archirafi 18. Palermo, Italy
| | - Gary Stone
- Comparative Molecular Cytogenetics Core, National Cancer Institute, Frederick Maryland, USA
| | - Francesca Bigoni
- Dipartimento di Biologia Animale e Genetica, Laboratori di Antropologia, Via del Proconsolo 12, 50122 Firenze, Italy
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Piskurek O, Okada N. Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals. Proc Natl Acad Sci U S A 2007; 104:12046-51. [PMID: 17623783 PMCID: PMC1924541 DOI: 10.1073/pnas.0700531104] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Indexed: 11/18/2022] Open
Abstract
Poxviruses (Poxviridae) are a family of double-stranded DNA viruses with no RNA stage. Members of the genus Orthopoxvirus (OPV) are highly invasive and virulent. It was recently shown that the taterapox virus (TATV) from a West African rodent is the sister of camelpox virus and therefore belongs to the clade closest to the variola virus (VARV), the etiological agent of smallpox. Although these OPVs are among the most dreaded pathogens on Earth, our current knowledge of their genomes, their origins, and their possible hosts is still very limited. Here, we report the horizontal transfer of a retroposon (known only from reptilian genomes) to the TATV genome. After isolating and analyzing different subfamilies of short interspersed elements (SINEs) from lizards and snakes, we identified a highly poisonous snake (Echis ocellatus) from West Africa as the closest species from which the SINE sequence discovered in the TATV genome (TATV-SINE) was transferred to the virus. We discovered direct repeats derived from the virus flanking the TATV-SINE, and the absence of any snake-derived DNA flanking the SINE. These data provide strong evidence that the TATV-SINE was actually transferred within the snake to the viral genome by retrotransposition and not by any horizontal transfer at the DNA level. We propose that the snake is another host for TATV, suggesting that VARV-related epidemiologically relevant viruses may have derived from our cold-blooded ancestors and that poxviruses are possible vectors for horizontal transfer of retroposons from reptiles to mammals.
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Affiliation(s)
- Oliver Piskurek
- Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B21 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Norihiro Okada
- Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B21 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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Hallström BM, Kullberg M, Nilsson MA, Janke A. Phylogenomic data analyses provide evidence that Xenarthra and Afrotheria are sister groups. Mol Biol Evol 2007; 24:2059-68. [PMID: 17630282 DOI: 10.1093/molbev/msm136] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The phylogenetic positions of the 4 clades, Euarchontoglires, Laurasiatheria, Afrotheria, and Xenarthra, have been major issues in the recent discussion of basal relationships among placental mammals. However, despite considerable efforts these relationships, crucial to the understanding of eutherian evolution and biogeography, have remained essentially unresolved. Euarchontoglires and Laurasiatheria are generally joined into a common clade (Boreoeutheria), whereas the position of Afrotheria and Xenarthra relative to Boreoeutheria has been equivocal in spite of the use of comprehensive amounts of nuclear encoded sequences or the application of genome-level characters such as retroposons. The probable reason for this uncertainty is that the divergences took place long time ago and within a narrow temporal window, leaving only short common branches. With the aim of further examining basal eutherian relationships, we have collected conserved protein-coding sequences from 11 placental mammals, a marsupial and a bird, whose nuclear genomes have been largely sequenced. The length of the alignment of homologous sequences representing each individual species is 2,168,859 nt. This number of sites, representing 2840 protein-coding genes, exceeds by a considerable margin that of any previous study. The phylogenetic analysis joined Xenarthra and Afrotheria on a common branch, Atlantogenata. This topology was found to fit the data significantly better than the alternative trees.
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Affiliation(s)
- Björn M Hallström
- Department of Cell and Organism Biology, Division of Evolutionary Molecular Systematics, University of Lund, Lund, Sweden
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Gu W, Ray DA, Walker JA, Barnes EW, Gentles AJ, Samollow PB, Jurka J, Batzer MA, Pollock DD. SINEs, evolution and genome structure in the opossum. Gene 2007; 396:46-58. [PMID: 17442506 DOI: 10.1016/j.gene.2007.02.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2006] [Revised: 02/15/2007] [Accepted: 02/19/2007] [Indexed: 10/23/2022]
Abstract
Short INterspersed Elements (SINEs) are non-autonomous retrotransposons, usually between 100 and 500 base pairs (bp) in length, which are ubiquitous components of eukaryotic genomes. Their activity, distribution, and evolution can be highly informative on genomic structure and evolutionary processes. To determine recent activity, we amplified more than one hundred SINE1 loci in a panel of 43 M. domestica individuals derived from five diverse geographic locations. The SINE1 family has expanded recently enough that many loci were polymorphic, and the SINE1 insertion-based genetic distances among populations reflected geographic distance. Genome-wide comparisons of SINE1 densities and GC content revealed that high SINE1 density is associated with high GC content in a few long and many short spans. Young SINE1s, whether fixed or polymorphic, showed an unbiased GC content preference for insertion, indicating that the GC preference accumulates over long time periods, possibly in periodic bursts. SINE1 evolution is thus broadly similar to human Alu evolution, although it has an independent origin. High GC content adjacent to SINE1s is strongly correlated with bias towards higher AT to GC substitutions and lower GC to AT substitutions. This is consistent with biased gene conversion, and also indicates that like chickens, but unlike eutherian mammals, GC content heterogeneity (isochore structure) is reinforced by substitution processes in the M. domestica genome. Nevertheless, both high and low GC content regions are apparently headed towards lower GC content equilibria, possibly due to a relative shift to lower recombination rates in the recent Monodelphis ancestral lineage. Like eutherians, metatherian (marsupial) mammals have evolved high CpG substitution rates, but this is apparently a convergence in process rather than a shared ancestral state.
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Affiliation(s)
- Wanjun Gu
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
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Abstract
Mobile elements have been recognized as powerful tools for phylogenetic and population-level analyses. However, issues regarding potential sources of homoplasy and other misleading events have been raised. We have collected available data for all phylogenetic and population level studies of primates utilizing Alu insertion data and examined them for potentially homoplasious and other misleading events. Very low levels of each potential confounding factor in a phylogenetic or population analysis (i.e., lineage sorting, parallel insertions, and precise excision) were found. Although taxa known to be subject to high levels of these types of events may indeed be subject to problems when using SINE analysis, we propose that most taxa will respond as the order Primates has--by the resolution of several long-standing problems observed using sequence-based methods.
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Affiliation(s)
- David A Ray
- Department of Biology, West Virginia University, PO Box 6057, Morgantown, West Virginia 26506, USA
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Farwick A, Jordan U, Fuellen G, Huchon D, Catzeflis F, Brosius J, Schmitz J. Automated scanning for phylogenetically informative transposed elements in rodents. Syst Biol 2007; 55:936-48. [PMID: 17345675 DOI: 10.1080/10635150601064806] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Transposed elements constitute an attractive, useful source of phylogenetic markers to elucidate the evolutionary history of their hosts. Frequent and successive amplifications over evolutionary time are important requirements for utilizing their presence or absence as landmarks of evolution. Although transposed elements are well distributed in rodent taxa, the generally high degree of genomic sequence divergence among species complicates our access to presence/absence data. With this in mind we developed a novel, high-throughput computational strategy, called CPAL (Conserved Presence/Absence Locus-finder), to identify genome-wide distributed, phylogenetically informative transposed elements flanked by highly conserved regions. From a total of 232 extracted chromosomal mouse loci we randomly selected 14 of these plus 2 others from previous test screens and attempted to amplify them via PCR in representative rodent species. All loci were amplifiable and ultimately contributed 31 phylogenetically informative markers distributed throughout the major groups of Rodentia.
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Affiliation(s)
- Astrid Farwick
- Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany
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Rylands AB. Primate Genetics — Is Taxonomy a Trivial Pursuit? Review ofPrimate Cytogenetics, edited by Stefan Müller, Ludwig Maximilian University, Munich, Germany. S. Karger, Basel, Switzerland. 268pp. ISSN: 1424–8581. 111 Figures, 56 Tables. Hardcover: 122.00 Swiss francs, Eur87.00, US$ 111.00. 2005. A reprint ofCytogenetic and Genome Research, Volume 108(1–3). ACTA ACUST UNITED AC 2007. [DOI: 10.1896/052.022.0117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
Mobile elements represent a unique and under-utilized set of tools for molecular ecologists. They are essentially homoplasy-free characters with the ability to be genotyped in a simple and efficient manner. Interpretation of the data generated using mobile elements can be simple compared to other genetic markers. They exist in a wide variety of taxa and are useful over a wide selection of temporal ranges within those taxa. Furthermore, their mode of evolution instills them with another advantage over other types of multilocus genotype data: the ability to determine loci applicable to a range of time spans in the history of a taxon. In this review, I discuss the application of mobile element markers, especially short interspersed elements (SINEs), to phylogenetic and population data, with an emphasis on potential applications to molecular ecology.
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Affiliation(s)
- David A Ray
- Department of Biology, West Virginia University, 53 Campus Dr, Morgantown, WV 26506, USA.
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Herke SW, Xing J, Ray DA, Zimmerman JW, Cordaux R, Batzer MA. A SINE-based dichotomous key for primate identification. Gene 2006; 390:39-51. [PMID: 17056208 DOI: 10.1016/j.gene.2006.08.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Revised: 08/01/2006] [Accepted: 08/02/2006] [Indexed: 11/22/2022]
Abstract
For DNA samples or 'divorced' tissues, identifying the organism from which they were taken generally requires some type of analytical method. The ideal approach would be robust even in the hands of a novice, requiring minimal equipment, time, and effort. Genotyping SINEs (Short INterspersed Elements) is such an approach as it requires only PCR-related equipment, and the analysis consists solely of interpreting fragment sizes in agarose gels. Modern primate genomes are known to contain lineage-specific insertions of Alu elements (a primate-specific SINE); thus, to demonstrate the utility of this approach, we used members of the Alu family to identify DNA samples from evolutionarily divergent primate species. For each node of a combined phylogenetic tree (56 species; n=8 [Hominids]; 11 [New World monkeys]; 21 [Old World monkeys]; 2 [Tarsiformes]; and, 14 [Strepsirrhines]), we tested loci (>400 in total) from prior phylogenetic studies as well as newly identified elements for their ability to amplify in all 56 species. Ultimately, 195 loci were selected for inclusion in this Alu-based key for primate identification. This dichotomous SINE-based key is best used through hierarchical amplification, with the starting point determined by the level of initial uncertainty regarding sample origin. With newly emerging genome databases, finding informative retrotransposon insertions is becoming much more rapid; thus, the general principle of using SINEs to identify organisms is broadly applicable.
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Affiliation(s)
- Scott W Herke
- Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Microsystems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, United States
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Stanyon R, Dumas F, Stone G, Bigoni F. Multidirectional chromosome painting reveals a remarkable syntenic homology between the greater galagos and the slow loris. Am J Primatol 2006; 68:349-59. [PMID: 16534804 DOI: 10.1002/ajp.20229] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We report on the first reciprocal chromosome painting of lorisoids and humans. The chromosome painting showed a remarkable syntenic homology between Otolemur and Nycticebus. Eight derived syntenic associations of human segments are common to both Otolemur and Nycticebus, indicative of a considerable period of common evolution between the greater galago and the slow loris. Five additional Robertsonian translocations form the slow loris karyotype, while the remaining chromosomes are syntenically equivalent, although some differ in terms of centromere position and heterochromatin additions. Strikingly, the breakpoints of the human chromosomes found fragmented in these two species are apparently identical. Only fissions of homologs to human chromosomes 1 and 15 provide significant evidence of a cytogenetic link between Lemuriformes and Lorisiformes. The association of human chromosomes 7/16 in both lorisoids strongly suggests that this chromosome was present in the ancestral primate genome.
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Affiliation(s)
- R Stanyon
- Comparative Molecular Cytogenetics Core, MCGP, National Cancer Institute-Frederick, Frederick, Maryland, USA.
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Abstract
Background Alu elements are Short INterspersed Elements (SINEs) in primate genomes that have proven useful as markers for studying genome evolution, population biology and phylogenetics. Most of these applications, however, have been limited to humans and their nearest relatives, chimpanzees. In an effort to expand our understanding of Alu sequence evolution and to increase the applicability of these markers to non-human primate biology, we have analyzed available Alu sequences for loci specific to platyrrhine (New World) primates. Results Branching patterns along an Alu sequence phylogeny indicate three major classes of platyrrhine-specific Alu sequences. Sequence comparisons further reveal at least three New World monkey-specific subfamilies; AluTa7, AluTa10, and AluTa15. Two of these subfamilies appear to be derived from a gene conversion event that has produced a recently active fusion of AluSc- and AluSp-type elements. This is a novel mode of origin for new Alu subfamilies. Conclusion The use of Alu elements as genetic markers in studies of genome evolution, phylogenetics, and population biology has been very productive when applied to humans. The characterization of these three new Alu subfamilies not only increases our understanding of Alu sequence evolution in primates, but also opens the door to the application of these genetic markers outside the hominid lineage.
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Affiliation(s)
- David A Ray
- Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multiscale Systems, Louisiana State University, Baton Rouge, LA, 70803, USA
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Mark A Batzer
- Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multiscale Systems, Louisiana State University, Baton Rouge, LA, 70803, USA
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Ludwig A, Rozhdestvensky TS, Kuryshev VY, Schmitz J, Brosius J. An Unusual Primate Locus that Attracted Two Independent Alu Insertions and Facilitates their Transcription. J Mol Biol 2005; 350:200-14. [PMID: 15922354 DOI: 10.1016/j.jmb.2005.03.058] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2005] [Revised: 03/18/2005] [Accepted: 03/21/2005] [Indexed: 10/25/2022]
Abstract
BC200 RNA, a neuronal, small non-messenger RNA that originated from a monomeric Alu element is specific to anthropoid primates. Tarsiers lack an insert at the orthologous genomic position, whereas strepsirrhines (Lemuriformes and Lorisiformes) acquired a dimeric Alu element, independently from anthropoids. In Galago moholi, the CpG dinucleotides are conspicuously conserved, while in Eulemur coronatus a large proportion is changed, indicating that the G.moholi Alu is under purifying selection and might be transcribed. Indeed, Northern blot analysis of total brain RNA from G.moholi with a specific probe revealed a prominent signal. In contrast, a corresponding signal was absent from brain RNA from E.coronatus. Isolation and sequence analysis of additional strepsirrhine loci confirmed the differential sequence conservation including CpG patterns of the orthologous dimeric Alu elements in Lorisiformes and Lemuriformes. Interestingly, all examined Alu elements from Lorisiformes were transcribed, while all from Lemuriformes were silent when transiently transfected into HeLa cells. Upstream sequences, especially those between the transcriptional start site and -22 upstream, were important for basal transcriptional activity. Thus, the BC200 RNA gene locus attracted two independent Alu insertions during its evolutionary history and provided upstream promoter elements required for their transcription.
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Affiliation(s)
- A Ludwig
- Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
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Schmitz J, Piskurek O, Zischler H. Forty million years of independent evolution: a mitochondrial gene and its corresponding nuclear pseudogene in primates. J Mol Evol 2005; 61:1-11. [PMID: 16007490 DOI: 10.1007/s00239-004-0293-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2004] [Accepted: 02/25/2005] [Indexed: 10/25/2022]
Abstract
Sequences from nuclear mitochondrial pseudogenes (numts) that originated by transfer of genetic information from mitochondria to the nucleus offer a unique opportunity to compare different regimes of molecular evolution. Analyzing a 1621-nt-long numt of the rRNA specifying mitochondrial DNA residing on human chromosome 3 and its corresponding mitochondrial gene in 18 anthropoid primates, we were able to retrace about 40 MY of primate rDNA evolutionary history. The results illustrate strengths and weaknesses of mtDNA data sets in reconstructing and dating the phylogenetic history of primates. We were able to show the following. In contrast to numt-DNA, (1) the nucleotide composition of mtDNA changed dramatically in the different primate lineages. This is assumed to lead to significant misinterpretations of the mitochondrial evolutionary history. (2) Due to the nucleotide compositional plasticity of primate mtDNA, the phylogenetic reconstruction combining mitochondrial and nuclear sequences is unlikely to yield reliable information for either tree topologies or branch lengths. This is because a major part of the underlying sequence evolution model--the nucleotide composition--is undergoing dramatic change in different mitochondrial lineages. We propose that this problem is also expressed in the occasional unexpected long branches leading to the "common ancestor" of orthologous numt sequences of different primate taxa. (3) The heterogeneous and lineage-specific evolution of mitochondrial sequences in primates renders molecular dating based on primate mtDNA problematic, whereas the numt sequences provide a much more reliable base for dating.
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Affiliation(s)
- Jürgen Schmitz
- Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56,, D-48149 , Münster, Germany.
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