Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals.

Abstract:

:As a consequence of recent developments in molecular phylogenomics, all extant orders of placental mammals have been grouped into 3 lineages: Afrotheria, Xenarthra, and Boreotheria, which originated in Africa, South America, and Laurasia, respectively. Despite this advancement, the order of divergence of these 3 lineages remains unresolved. Here, we performed extensive retroposon analysis with mammalian genomic data. Surprisingly, we identified a similar number of informative retroposon loci that support each of 3 possible phylogenetic hypotheses: the basal position for Afrotheria (22 loci), Xenarthra (25 loci), and Boreotheria (21 loci). This result indicates that the divergence of the placental common ancestor into the 3 lineages occurred nearly simultaneously. Thus, we examined whether these molecular data could be integrated into the geological context by incorporating recent geological data. We obtained firm evidence that complete separation of Gondwana into Africa and South America occurred 120 +/- 10 Ma. Accordingly, the previous reported time frame (division of Pangea into Gondwana and Laurasia at 148-138 Ma and division of Gondwana at 105 Ma) cannot be used to validate mammalian divergence order. Instead, we use our retroposon results and the recent geological data to propose that near-simultaneous divisions of continents leading to isolated Africa, South America, and Laurasia caused nearly concomitant divergence of the ancient placental ancestor into 3 lineages, Afrotheria, Xenarthra, and Boreotheria, approximately 120 Ma.

authors

Nishihara H,Maruyama S,Okada N

doi

10.1073/pnas.0809297106

subject

Has Abstract

pub_date

2009-03-31 00:00:00

pages

5235-40

issue

13

eissn

0027-8424

issn

1091-6490

pii

0809297106

journal_volume

106

pub_type

杂志文章
  • Specificity of diffusion channels produced by lambda phage receptor protein of Escherichia coli.

    abstract::The lamB protein, the receptor for phage lambda, was purified from the outer membrane of Escherichia coli K-12 by extraction with Triton X-100 and EDTA, chromatography on DEAE-Sephacel in Triton X-100, exchange of Triton for cholate by gel filtration, and chromatography on Sephacryl S-200 in cholate, NaCl, and EDTA. T...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.77.1.167

    authors: Luckey M,Nikaido H

    更新日期:1980-01-01 00:00:00

  • Nitric oxide stimulates the ADP-ribosylation of a 41-kDa cytosolic protein in Dictyostelium discoideum.

    abstract::Nitric oxide-releasing compounds were shown to activate an ADP-ribosyltransferase activity in the cytosol of Dictyostelium discoideum. The enzyme ADP-ribosylated a cytosolic protein of approximately 41 kDa, p41. Neither cGMP nor GTP and its analogues affected this ADP-ribosylation. p41 differs from other substrates AD...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.89.13.5902

    authors: Tao Y,Howlett A,Klein C

    更新日期:1992-07-01 00:00:00

  • Frequency of DNA end joining in trans is not determined by the predamage spatial proximity of double-strand breaks in yeast.

    abstract::DNA double-strand breaks (DSBs) are serious genomic insults that can lead to chromosomal rearrangements if repaired incorrectly. To gain insight into the nuclear mechanisms contributing to these rearrangements, we developed an assay in yeast to measure cis (same site) vs. trans (different site) repair for the majority...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1818595116

    authors: Sunder S,Wilson TE

    更新日期:2019-05-07 00:00:00

  • Nerve growth factor is an autocrine factor essential for the survival of macrophages infected with HIV.

    abstract::Nerve growth factor (NGF) is a neurotrophin with the ability to exert specific effects on cells of the immune system. Human monocytes/macrophages (M/M) infected in vitro with HIV type 1 (HIV-1) are able to produce substantial levels of NGF that are associated with enhanced expression of the high-affinity NGF receptor ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.96.24.14013

    authors: Garaci E,Caroleo MC,Aloe L,Aquaro S,Piacentini M,Costa N,Amendola A,Micera A,Caliò R,Perno CF,Levi-Montalcini R

    更新日期:1999-11-23 00:00:00

  • Epimorphic regeneration approach to tissue replacement in adult mammals.

    abstract::Urodeles and fetal mammals are capable of impressive epimorphic regeneration in a variety of tissues, whereas the typical default response to injury in adult mammals consists of inflammation and scar tissue formation. One component of epimorphic regeneration is the recruitment of resident progenitor and stem cells to ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0905851106

    authors: Agrawal V,Johnson SA,Reing J,Zhang L,Tottey S,Wang G,Hirschi KK,Braunhut S,Gudas LJ,Badylak SF

    更新日期:2010-02-23 00:00:00

  • Replication initiator protein of plasmid R6K autoregulates its own synthesis at the transcriptional step.

    abstract::The replication initiator protein of plasmid R6K preferentially repressed transcription initiated in vitro from the promoter of the initiator protein cistron. DNase I protection experiments revealed that the sequences in the region of the promoter recognized by the initiator protein partially overlapped the sequences ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.82.9.2574

    authors: Kelley W,Bastia D

    更新日期:1985-05-01 00:00:00

  • Relationship between the intra and intermolecular cross-links of collagen.

    abstract::Spontaneous cross-linking in vitro, during incubation of purified collagen in nonstriated and native type fibrils, was studied to elucidate the relationship between intra and intermolecular cross-links. In nonbanded fibrils, the aldol condensation products of two allysyl residues, previously shown to constitute the in...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.67.3.1307

    authors: Kang AH,Gross J

    更新日期:1970-11-01 00:00:00

  • Lysosomal storage disease upon disruption of the neuronal chloride transport protein ClC-6.

    abstract::Mammalian CLC proteins function as Cl(-) channels or as electrogenic Cl(-)/H(+) exchangers and are present in the plasma membrane and intracellular vesicles. We now show that the ClC-6 protein is almost exclusively expressed in neurons of the central and peripheral nervous systems, with a particularly high expression ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0606137103

    authors: Poët M,Kornak U,Schweizer M,Zdebik AA,Scheel O,Hoelter S,Wurst W,Schmitt A,Fuhrmann JC,Planells-Cases R,Mole SE,Hübner CA,Jentsch TJ

    更新日期:2006-09-12 00:00:00

  • SLP-76-ADAP adaptor module regulates LFA-1 mediated costimulation and T cell motility.

    abstract::Although adaptor ADAP (FYB) and its binding to SLP-76 has been implicated in TcR-induced "inside-out" signaling for LFA-1 activation in T cells, little is known regarding its role in LFA-1-mediated "outside-in" signaling. In this study, we demonstrate that ADAP and SLP-76-ADAP binding are coupled to LFA-1 costimulatio...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0900510106

    authors: Wang H,Wei B,Bismuth G,Rudd CE

    更新日期:2009-07-28 00:00:00

  • Rationing social contact during the COVID-19 pandemic: Transmission risk and social benefits of US locations.

    abstract::To prevent the spread of coronavirus disease 2019 (COVID-19), some types of public spaces have been shut down while others remain open. These decisions constitute a judgment about the relative danger and benefits of those locations. Using mobility data from a large sample of smartphones, nationally representative cons...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2008025117

    authors: Benzell SG,Collis A,Nicolaides C

    更新日期:2020-06-30 00:00:00

  • Analyzing variation in egg-to-adult viability in experimental populations of Drosophila melanogaster.

    abstract::Selective culling in populations of most organisms is rank-order: individuals of low rank on a scale of potential fitnesses tend to be eliminated during early development, whereas surviving adults (whose number reflects the carrying capacity of the environment) are generally drawn from the distribution's upper end. Ha...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.86.6.2117

    authors: Wallace B

    更新日期:1989-03-01 00:00:00

  • Bax degradation by the ubiquitin/proteasome-dependent pathway: involvement in tumor survival and progression.

    abstract::Previously we reported that proteasome inhibitors were able to overcome Bcl-2-mediated protection from apoptosis. Here we show that inhibition of the proteasome activity in Bcl-2-overexpressing cells accumulates the proapoptotic Bax protein to mitochondria/cytoplasm, where it interacts to Bcl-2 protein. This event was...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.070047997

    authors: Li B,Dou QP

    更新日期:2000-04-11 00:00:00

  • Glycosylation of ovalbumin in a heterologous cell: analysis of oligosaccharide chains of the cloned glycoprotein in mouse L cells.

    abstract::In an effort to understand the factors that influence protein glycosylation, we are studying the expression of the chicken ovalbumin gene in a heterologous cell. Ovalbumin synthesized in mouse L-353 cells is glycosylated, as judged by incorporation of [3H]mannose and susceptibility to endo-beta-N-acetylglucosaminidase...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.7.1993

    authors: Sheares BT,Robbins PW

    更新日期:1986-04-01 00:00:00

  • The immune response attenuates growth and nutrient storage in Drosophila by reducing insulin signaling.

    abstract::Innate immunity is the primary and most ancient defense against infection. Although critical to survival, coordinating protection against a foreign organism is energetically costly, creating the need to reallocate substrates from nonessential functions, such as growth and nutrient storage. However, the mechanism by wh...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0906749106

    authors: DiAngelo JR,Bland ML,Bambina S,Cherry S,Birnbaum MJ

    更新日期:2009-12-08 00:00:00

  • Spiking activity in the human hippocampus prior to encoding predicts subsequent memory.

    abstract::Encoding activity in the medial temporal lobe, presumably evoked by the presentation of stimuli (postonset activity), is known to predict subsequent memory. However, several independent lines of research suggest that preonset activity also affects subsequent memory. We investigated the role of preonset and postonset s...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2001338117

    authors: Urgolites ZJ,Wixted JT,Goldinger SD,Papesh MH,Treiman DM,Squire LR,Steinmetz PN

    更新日期:2020-06-16 00:00:00

  • Assignment of the human gene for galactose-1-phosphate uridyltransferase to chromosome 9: studies with Chinese hamster-human somatic cell hybrids.

    abstract::Chinese hamster-human somatic cell hybrids were analyzed for the expression of human galactose-1-phosphate uridyltransferase (GALT; UDPglucose:alpha-D-galactose-1-phosphate uridyltransferase, EC 2.7.7.12) by electrophoresis and for the presence of human chromosomes cytogenetically with the aid of Q-banding. Three of t...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.74.12.5628

    authors: Mohandas T,Sparkes RS,Sparkes MC,Shulkin JD

    更新日期:1977-12-01 00:00:00

  • Structural and biochemical studies of p21Ras S-nitrosylation and nitric oxide-mediated guanine nucleotide exchange.

    abstract::Ras is a guanine nucleotide-binding protein that cycles between inactive GDP-bound and active GTP-bound states to regulate a diverse array of cellular processes, including cell growth, apoptosis, and differentiation. The guanine nucleotide-bound state of Ras is tightly maintained by regulatory factors to promote regul...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1037299100

    authors: Williams JG,Pappu K,Campbell SL

    更新日期:2003-05-27 00:00:00

  • Ataxia telangiectasia-mutated protein and DNA-dependent protein kinase have complementary V(D)J recombination functions.

    abstract::Antigen receptor variable region exons are assembled during lymphocyte development from variable (V), diversity (D), and joining (J) gene segments. Each germ-line gene segment is flanked by recombination signal sequences (RSs). Recombination-activating gene endonuclease initiates V(D)J recombination by cleaving a pair...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1019293108

    authors: Zha S,Jiang W,Fujiwara Y,Patel H,Goff PH,Brush JW,Dubois RL,Alt FW

    更新日期:2011-02-01 00:00:00

  • Immunocytochemical localization of prosomatostatin fragments in maturing and mature secretory granules of pancreatic and gastrointestinal D cells.

    abstract::Pancreatic and gastrointestinal D cells were examined by immunocytochemistry using antisera against somatostatin-28 (SS28) and its NH2-terminal fragment SS28-(1-12), followed by the staphylococcal protein A-gold (pAg) complex. In pancreatic and gastric D cells incubated with antiserum against SS28-(1-12) the gold part...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.80.1.215

    authors: Ravazzola M,Benoit R,Ling N,Guillemin R,Orci L

    更新日期:1983-01-01 00:00:00

  • Molecular recognition and self-assembly special feature: A general protocol for creating high-throughput screening assays for reaction yield and enantiomeric excess applied to hydrobenzoin.

    abstract::A general approach to high-throughput screening of enantiomeric excess (ee) and concentration was developed by using indicator displacement assays (IDAs), and the protocol was then applied to the vicinal diol hydrobenzoin. The method involves the sequential utilization of what we define herein as screening, training, ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0809530106

    authors: Shabbir SH,Regan CJ,Anslyn EV

    更新日期:2009-06-30 00:00:00

  • Geometric interpretation of vertex operator algebras.

    abstract::In this paper, Vafa's approach to the formulation of conformal field theories is combined with the formal calculus developed in Frenkel, Lepowsky, and Meurman's work on the vertex operator construction of the Monster to give a geometric definition of vertex operator algebras. The main result announced is the equivalen...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.22.9964

    authors: Huang YZ

    更新日期:1991-11-15 00:00:00

  • Compression of the DNA substrate by a viral packaging motor is supported by removal of intercalating dye during translocation.

    abstract::Viral genome packaging into capsids is powered by high-force-generating motor proteins. In the presence of all packaging components, ATP-powered translocation in vitro expels all detectable tightly bound YOYO-1 dye from packaged short dsDNA substrates and removes all aminoacridine dye from packaged genomic DNA in vivo...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1214318109

    authors: Dixit AB,Ray K,Black LW

    更新日期:2012-12-11 00:00:00

  • Recombinant rabies virus as potential live-viral vaccines for HIV-1.

    abstract::Recombinant, replication-competent rabies virus (RV) vaccine strain-based vectors were developed expressing HIV type I (HIV-1) envelope glycoprotein (gp160) from both a laboratory-adapted (CXCR4-tropic) and a primary (dual-tropic) HIV-1 isolate. An additional transcription stop/start unit within the RV genome was used...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.050589197

    authors: Schnell MJ,Foley HD,Siler CA,McGettigan JP,Dietzschold B,Pomerantz RJ

    更新日期:2000-03-28 00:00:00

  • Antibodies against a synthetic peptide identify the Epstein-Barr virus-determined nuclear antigen.

    abstract::Five peptides corresponding to amino acid sequences predicted from all three reading frames of the nucleotide sequence of the third internal repeat array (IR3) of the Epstein-Barr virus (EBV) genome were synthesized chemically. All five peptides elicited antipeptide antibodies in rabbits. The antiserum raised against ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.81.15.4652

    authors: Dillner J,Sternås L,Kallin B,Alexander H,Ehlin-Henriksson B,Jörnvall H,Klein G,Lerner R

    更新日期:1984-08-01 00:00:00

  • Specific interaction between a Saccharomyces cerevisiae protein and a DNA element associated with certain autonomously replicating sequences.

    abstract::We have isolated a protein from Saccharomyces cerevisiae that binds specifically to a nucleotide sequence associated with the autonomously replicating sequence (ARS) ARS120, located in the telomeric region of a yeast chromosome. "Footprinting" analysis revealed that a 26-base-pair DNA sequence, 5'-CAAGTGCCGTGCATAATGAT...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.85.3.743

    authors: Eisenberg S,Civalier C,Tye BK

    更新日期:1988-02-01 00:00:00

  • Atomistic structure and dynamics of the human MHC-I peptide-loading complex.

    abstract::The major histocompatibility complex class-I (MHC-I) peptide-loading complex (PLC) is a cornerstone of the human adaptive immune system, being responsible for processing antigens that allow killer T cells to distinguish between healthy and compromised cells. Based on a recent low-resolution cryo-electron microscopy (c...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2004445117

    authors: Fisette O,Schröder GF,Schäfer LV

    更新日期:2020-08-25 00:00:00

  • Aquaporin 5-deficient mouse lungs are hyperresponsive to cholinergic stimulation.

    abstract::Although aquaporin 5 (AQP5) is the major water channel expressed in alveolar type I cells in the lung, its actual role in the lung is a matter of considerable speculation. By using immunohistochemical staining, we show that AQP5 expression in mouse lung is not restricted to type I cells, but is also detected in alveol...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.231273398

    authors: Krane CM,Fortner CN,Hand AR,McGraw DW,Lorenz JN,Wert SE,Towne JE,Paul RJ,Whitsett JA,Menon AG

    更新日期:2001-11-20 00:00:00

  • Repair of O6-ethylguanine in DNA by a chromatin fraction from rat liver: transfer of the ethyl group to an acceptor protein.

    abstract::Incubation of O6-[3H]ethylguanine-containing DNA with a rat liver chromatin fraction resulted in a decrease in the O6-ethylguanine content of the DNA. Analysis of the products of this reaction showed that the ethyl group had been transferred from the O6-ethylguanine to a protein acceptor. When the incubation mixture w...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.78.11.6766

    authors: Mehta JR,Ludlum DB,Renard A,Verly WG

    更新日期:1981-11-01 00:00:00

  • Apparent failure of the Born-Oppenheimer static surface model for vibrational excitation of molecular hydrogen on copper.

    abstract::The accuracy of dynamical models for reactive scattering of molecular hydrogen, H(2), from metal surfaces is relevant to the validation of first principles electronic structure methods for molecules interacting with metal surfaces. The ability to validate such methods is important to progress in modeling heterogeneous...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1001098107

    authors: Kroes GJ,Díaz C,Pijper E,Olsen RA,Auerbach DJ

    更新日期:2010-12-07 00:00:00

  • Successive-signal biasing for a learned sound sequence.

    abstract::Adult rats were trained to detect the occurrence of a two-element sound sequence in a background of nine other nontarget sound pairs. Training resulted in a modest, enduring, static expansion of the cortical areas of representation of both target stimulus sounds. More importantly, once the initial stimulus A in the ta...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1009433107

    authors: Zhou X,de Villers-Sidani E,Panizzutti R,Merzenich MM

    更新日期:2010-08-17 00:00:00