Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers.

Abstract:

:To reconstruct modern human evolutionary history and identify loci that have shaped hunter-gatherer adaptation, we sequenced the whole genomes of five individuals in each of three different hunter-gatherer populations at > 60× coverage: Pygmies from Cameroon and Khoesan-speaking Hadza and Sandawe from Tanzania. We identify 13.4 million variants, substantially increasing the set of known human variation. We found evidence of archaic introgression in all three populations, and the distribution of time to most recent common ancestors from these regions is similar to that observed for introgressed regions in Europeans. Additionally, we identify numerous loci that harbor signatures of local adaptation, including genes involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing. Within the Pygmy population, we identify multiple highly differentiated loci that play a role in growth and anterior pituitary function and are associated with height.

journal_name

Cell

journal_title

Cell

authors

Lachance J,Vernot B,Elbers CC,Ferwerda B,Froment A,Bodo JM,Lema G,Fu W,Nyambo TB,Rebbeck TR,Zhang K,Akey JM,Tishkoff SA

doi

10.1016/j.cell.2012.07.009

subject

Has Abstract

pub_date

2012-08-03 00:00:00

pages

457-69

issue

3

eissn

0092-8674

issn

1097-4172

pii

S0092-8674(12)00831-8

journal_volume

150

pub_type

杂志文章

相关文献

CELL文献大全
  • Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences.

    abstract::Acquisition of the intestinal microbiota begins at birth, and a stable microbial community develops from a succession of key organisms. Disruption of the microbiota during maturation by low-dose antibiotic exposure can alter host metabolism and adiposity. We now show that low-dose penicillin (LDP), delivered from birt...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/j.cell.2014.05.052

    authors: Cox LM,Yamanishi S,Sohn J,Alekseyenko AV,Leung JM,Cho I,Kim SG,Li H,Gao Z,Mahana D,Zárate Rodriguez JG,Rogers AB,Robine N,Loke P,Blaser MJ

    更新日期:2014-08-14 00:00:00

  • On the nature of tetracycline resistance controlled by the plasmid pSC101.

    abstract::In vitro enzymatic alteration of plasmid phenotype and in vitro construction of recombinant plasmids containing genetic information derived from the plasmid pSC101 have been used to investigate the mechanism of function of tetracycline resistance determined by the plasmid pSC101. The resistance has been shown to be in...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/0092-8674(78)90139-3

    authors: Tait RC,Boyer HW

    更新日期:1978-01-01 00:00:00

  • Crossover/noncrossover differentiation, synaptonemal complex formation, and regulatory surveillance at the leptotene/zygotene transition of meiosis.

    abstract::Yeast mutants lacking meiotic proteins Zip1, Zip2, Zip3, Mer3, and/or Msh5 (ZMMs) were analyzed for recombination, synaptonemal complex (SC), and meiotic progression. At 33 degrees C, recombination-initiating double-strand breaks (DSBs) and noncrossover products (NCRs) form normally while formation of single-end invas...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/s0092-8674(04)00292-2

    authors: Börner GV,Kleckner N,Hunter N

    更新日期:2004-04-02 00:00:00

  • Gene organization and recombinational hotspots in the murine major histocompatibility complex.

    abstract::By chromosome walking in the major histocompatibility complex (MHC) of the BALB/c mouse, we have linked the K region to the I region at the molecular level. Forty-nine overlapping cosmid clones define a stretch of about 600 kb of DNA containing 2 class I and 7 class II genes. Eleven independent recombination events we...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/0092-8674(86)90012-7

    authors: Steinmetz M,Stephan D,Fischer Lindahl K

    更新日期:1986-03-28 00:00:00

  • Phosphoinositides in mitogenesis: neomycin inhibits thrombin-stimulated phosphoinositide turnover and initiation of cell proliferation.

    abstract::Thrombin stimulates 32Pi incorporation into phosphatidylinositol 4-phosphate (PIP), phosphatidylinositol 4,5-bis-phosphate (PIP2), and phosphatidylinositol (PI), and initiates DNA synthesis in hamster (NIL) fibroblasts at a half-maximal concentration of 125 ng/ml. Neomycin, which binds PIP2 and PIP, inhibits both thro...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/0092-8674(85)90105-9

    authors: Carney DH,Scott DL,Gordon EA,LaBelle EF

    更新日期:1985-09-01 00:00:00

  • Lineage tracing.

    abstract::Lineage tracing is the identification of all progeny of a single cell. Although its origins date back to developmental biology of invertebrates in the 19(th) century, lineage tracing is now an essential tool for studying stem cell properties in adult mammalian tissues. Lineage tracing provides a powerful means of unde...

    journal_title:Cell

    pub_type: 历史文章,杂志文章

    doi:10.1016/j.cell.2012.01.002

    authors: Kretzschmar K,Watt FM

    更新日期:2012-01-20 00:00:00

  • Suppressor mutations that restore export of a protein with a defective signal sequence.

    abstract::A selection procedure is described that should allow the genetic identification of cellular components involved in the process of protein localization in Escherichia coli. This procedure makes use of mutations that alter the signal sequence of the lambda receptor protein (product of the lamB gene), and prevent export ...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/0092-8674(81)90272-5

    authors: Emr SD,Hanley-Way S,Silhavy TJ

    更新日期:1981-01-01 00:00:00

  • Conversion of an extracellular Dpp/BMP morphogen gradient into an inverse transcriptional gradient.

    abstract::Morphogen gradients control body pattern by differentially regulating cellular behavior. Here, we analyze the molecular events underlying the primary response to the Dpp/BMP morphogen in Drosophila. Throughout development, Dpp transduction causes the graded transcriptional downregulation of the brinker (brk) gene. We ...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/s0092-8674(03)00241-1

    authors: Müller B,Hartmann B,Pyrowolakis G,Affolter M,Basler K

    更新日期:2003-04-18 00:00:00

  • Whence meiosis?

    abstract::Sexual reproduction predominates among eukaryotic organisms on our planet. While debate continues over why this should be so, burgeoning genomic and functional information now allows us to begin to think reasonably about some of the events that may have occurred to make sex possible in the first place. ...

    journal_title:Cell

    pub_type: 杂志文章,评审

    doi:10.1016/s0092-8674(01)00500-1

    authors: Villeneuve AM,Hillers KJ

    更新日期:2001-09-21 00:00:00

  • Structural basis for activation of ARF GTPase: mechanisms of guanine nucleotide exchange and GTP-myristoyl switching.

    abstract::Ras-related GTPases are positively regulated by guanine nucleotide exchange factors (GEFs) that promote the exchange of GDP for GTP. The crystal structure of the Sec7 domain GEF bound to nucleotide-free ARF1 GTPase has been determined at 2.8 A resolution and the structure of ARF1 in the GTP-analog form determined at 1...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/s0092-8674(00)81754-7

    authors: Goldberg J

    更新日期:1998-10-16 00:00:00

  • VEGF-induced adult neovascularization: recruitment, retention, and role of accessory cells.

    abstract::Adult neovascularization relies on the recruitment of circulating cells, but their angiogenic roles and recruitment mechanisms are unclear. We show that the endothelial growth factor VEGF is sufficient for organ homing of circulating mononuclear myeloid cells and is required for their perivascular positioning and rete...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/j.cell.2005.10.036

    authors: Grunewald M,Avraham I,Dor Y,Bachar-Lustig E,Itin A,Jung S,Chimenti S,Landsman L,Abramovitch R,Keshet E

    更新日期:2006-01-13 00:00:00

  • Isolation of two genes that affect mitotic chromosome transmission in S. cerevisiae.

    abstract::Two DNA sequences that reduce mitotic fidelity of chromosome transmission have been identified: MIF1 and MIF2. MIF1 is a unique sequence located on the right arm of chromosome XII that stimulates loss and recombination for both chromosomes V and VII when present in a high copy number plasmid. MIF1 is not essential for...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/0092-8674(86)90484-8

    authors: Meeks-Wagner D,Wood JS,Garvik B,Hartwell LH

    更新日期:1986-01-17 00:00:00

  • Cryptic and polar variation of the fragile X repeat could result in predisposing normal alleles.

    abstract::Fragile X syndrome results from the expansion of a CGG repeat that is normally interrupted by occasional AGG triplets. Linkage disequilibrium suggests that certain normal haplotypes may contribute unequally to the pool of fragile X chromosomes. Sequence analysis of normal alleles demonstrates haplotype-specific variat...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/0092-8674(94)90134-1

    authors: Kunst CB,Warren ST

    更新日期:1994-06-17 00:00:00

  • Germinal center dynamics revealed by multiphoton microscopy with a photoactivatable fluorescent reporter.

    abstract::The germinal center (GC) reaction produces high-affinity antibodies by random mutation and selective clonal expansion of B cells with high-affinity receptors. The mechanism by which B cells are selected remains unclear, as does the role of the two anatomically defined areas of the GC, light zone (LZ) and dark zone (DZ...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/j.cell.2010.10.032

    authors: Victora GD,Schwickert TA,Fooksman DR,Kamphorst AO,Meyer-Hermann M,Dustin ML,Nussenzweig MC

    更新日期:2010-11-12 00:00:00

  • Structure of a heterophilic adhesion complex between the human CD2 and CD58 (LFA-3) counterreceptors.

    abstract::Interaction between CD2 and its counterreceptor, CD58 (LFA-3), on opposing cells optimizes immune recognition, facilitating contacts between helper T lymphocytes and antigen-presenting cells as well as between cytolytic effectors and target cells. Here, we report the crystal structure of the heterophilic adhesion comp...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/s0092-8674(00)80790-4

    authors: Wang JH,Smolyar A,Tan K,Liu JH,Kim M,Sun ZY,Wagner G,Reinherz EL

    更新日期:1999-06-11 00:00:00

  • EGFR-mediated Beclin 1 phosphorylation in autophagy suppression, tumor progression, and tumor chemoresistance.

    abstract::Cell surface growth factor receptors couple environmental cues to the regulation of cytoplasmic homeostatic processes, including autophagy, and aberrant activation of such receptors is a common feature of human malignancies. Here, we defined the molecular basis by which the epidermal growth factor receptor (EGFR) tyro...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/j.cell.2013.08.015

    authors: Wei Y,Zou Z,Becker N,Anderson M,Sumpter R,Xiao G,Kinch L,Koduru P,Christudass CS,Veltri RW,Grishin NV,Peyton M,Minna J,Bhagat G,Levine B

    更新日期:2013-09-12 00:00:00

  • N(6)-methyladenosine Modulates Messenger RNA Translation Efficiency.

    abstract::N(6)-methyladenosine (m(6)A) is the most abundant internal modification in mammalian mRNA. This modification is reversible and non-stoichiometric and adds another layer to the dynamic control of mRNA metabolism. The stability of m(6)A-modified mRNA is regulated by an m(6)A reader protein, human YTHDF2, which recognize...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/j.cell.2015.05.014

    authors: Wang X,Zhao BS,Roundtree IA,Lu Z,Han D,Ma H,Weng X,Chen K,Shi H,He C

    更新日期:2015-06-04 00:00:00

  • p53 and its 14 kDa C-terminal domain recognize primary DNA damage in the form of insertion/deletion mismatches.

    abstract::Insertion/deletion (IDL) mismatches in DNA are lesions consisting of extra bases on one strand. Here, the binding of p53 and its 14 kDa C-terminal domain to DNAs containing one or three 3-cytosine IDL mismatches was examined. Electron microscopy showed that both p53 forms bound predominantly as tetramers at the lesion...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/s0092-8674(05)80006-6

    authors: Lee S,Elenbaas B,Levine A,Griffith J

    更新日期:1995-06-30 00:00:00

  • Mutations in the human Ca(2+)-sensing receptor gene cause familial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism.

    abstract::We demonstrate that mutations in the human Ca(2+)-sensing receptor gene cause familial hypocalciuric hypercalcemia (FHH) and neonatal severe hyperparathyroidism (NSHPT), two inherited conditions characterized by altered calcium homeostasis. The Ca(2+)-sensing receptor belongs to the superfamily of seven membrane-spann...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/0092-8674(93)90617-y

    authors: Pollak MR,Brown EM,Chou YH,Hebert SC,Marx SJ,Steinmann B,Levi T,Seidman CE,Seidman JG

    更新日期:1993-12-31 00:00:00

  • Nucleosome arrangement on tRNA genes of Xenopus laevis.

    abstract::We have examined the chromatin structure of a repeated cluster of tRNA genes of Xenopus laevis, with particular attention to possible phase relationships between nucleosomes and the underlying tDNA sequence. In transcriptionally active liver and cultured kidney cells, essentially all tDNA is packaged into regularly sp...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/0092-8674(81)90387-1

    authors: Bryan PN,Hofstetter H,Birnstiel ML

    更新日期:1981-12-01 00:00:00

  • A Viral Immunoevasin Controls Innate Immunity by Targeting the Prototypical Natural Killer Cell Receptor Family.

    abstract::Natural killer (NK) cells play a key role in innate immunity by detecting alterations in self and non-self ligands via paired NK cell receptors (NKRs). Despite identification of numerous NKR-ligand interactions, physiological ligands for the prototypical NK1.1 orphan receptor remain elusive. Here, we identify a viral ...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/j.cell.2017.03.002

    authors: Aguilar OA,Berry R,Rahim MMA,Reichel JJ,Popović B,Tanaka M,Fu Z,Balaji GR,Lau TNH,Tu MM,Kirkham CL,Mahmoud AB,Mesci A,Krmpotić A,Allan DSJ,Makrigiannis AP,Jonjić S,Rossjohn J,Carlyle JR

    更新日期:2017-03-23 00:00:00

  • Suppressor of Hairless, the Drosophila homolog of the mouse recombination signal-binding protein gene, controls sensory organ cell fates.

    abstract::Suppressor of Hairless (Su(H)) is required at two stages of adult sensory organ development in Drosophila. Complete loss of Su(H) function results in a "neurogenic" phenotype in imaginal discs, in which too many cells adopt the sensory organ precursor cell fate. Su(H) is also involved in controlling the fates of sensi...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/0092-8674(92)90641-o

    authors: Schweisguth F,Posakony JW

    更新日期:1992-06-26 00:00:00

  • The timing of developmental transitions in plants.

    abstract::Plants rely heavily on environmental cues to control the timing of developmental transitions. We are beginning to better understand what determines the timing of two of these transitions, the switch from juvenile to adult vegetative development and the transition to flowering. In this review, we discuss how RNA silenc...

    journal_title:Cell

    pub_type: 杂志文章,评审

    doi:10.1016/j.cell.2006.05.005

    authors: Bäurle I,Dean C

    更新日期:2006-05-19 00:00:00

  • Mouse development and cell proliferation in the absence of D-cyclins.

    abstract::D-type cyclins (cyclins D1, D2, and D3) are regarded as essential links between cell environment and the core cell cycle machinery. We tested the requirement for D-cyclins in mouse development and in proliferation by generating mice lacking all D-cyclins. We found that these cyclin D1(-/-)D2(-/-)D3(-/-) mice develop u...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/j.cell.2004.07.025

    authors: Kozar K,Ciemerych MA,Rebel VI,Shigematsu H,Zagozdzon A,Sicinska E,Geng Y,Yu Q,Bhattacharya S,Bronson RT,Akashi K,Sicinski P

    更新日期:2004-08-20 00:00:00

  • Substrate selectivity APPLies to Akt.

    abstract::The protein kinase Akt occupies a central position in multiple signaling pathways. Although numerous Akt substrates have been identified, less is known about the factors that regulate specific cellular responses to Akt signaling. In this issue, Schenck et al. (2008) demonstrate that the endosomal protein Appl1 modulat...

    journal_title:Cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.cell.2008.04.015

    authors: Zhao S,Guan KL

    更新日期:2008-05-02 00:00:00

  • A novel all helix fold of the AP180 amino-terminal domain for phosphoinositide binding and clathrin assembly in synaptic vesicle endocytosis.

    abstract::Clathrin-mediated endocytosis plays a major role in retrieving synaptic vesicles from the plasma membrane following exocytosis. This endocytic process requires AP180 (or a homolog), which promotes the assembly and restricts the size of clathrin-coated vesicles. The highly conserved 33 kDa amino-terminal domain of AP18...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/s0092-8674(01)00230-6

    authors: Mao Y,Chen J,Maynard JA,Zhang B,Quiocho FA

    更新日期:2001-02-09 00:00:00

  • Identification of a promoter for transcription of the heavy strand of human mtDNA: in vitro transcription and deletion mutagenesis.

    abstract::Plasmids containing the origin region of human mtDNA are specifically transcribed by the partially purified homologous mtRNA polymerase in vitro. Transcription of both the light and heavy strands initiates at the same sites previously identified as in vivo transcription start sites. The sequences responsible for initi...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/0092-8674(84)90061-8

    authors: Bogenhagen DF,Applegate EF,Yoza BK

    更新日期:1984-04-01 00:00:00

  • Loss of T-bet sends host-microbe mutualism awry.

    abstract::Immune homeostasis in the intestine involves complex interactions between microbial organisms and host cells. In this issue, Garrett et al. (2007) describe a communicable form of colitis that is induced by deficiency of the transcription factor T-bet in cells of the innate immune system. ...

    journal_title:Cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.cell.2007.09.030

    authors: Ma A

    更新日期:2007-10-05 00:00:00

  • TGFbeta primes breast tumors for lung metastasis seeding through angiopoietin-like 4.

    abstract::Cells released from primary tumors seed metastases to specific organs by a nonrandom process, implying the involvement of biologically selective mechanisms. Based on clinical, functional, and molecular evidence, we show that the cytokine TGFbeta in the breast tumor microenvironment primes cancer cells for metastasis t...

    journal_title:Cell

    pub_type: 杂志文章

    doi:10.1016/j.cell.2008.01.046

    authors: Padua D,Zhang XH,Wang Q,Nadal C,Gerald WL,Gomis RR,Massagué J

    更新日期:2008-04-04 00:00:00

  • Gut microbiota: the link to your second brain.

    abstract::Serotonin is a highly ubiquitous signaling molecule that plays a role in the regulation of various physiological functions. Several lines of evidence, including the present work from Hsiao and colleagues, demonstrate that, in the gut, microbial-derived metabolites affect the production of serotonin that in turn impact...

    journal_title:Cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.cell.2015.03.033

    authors: Ridaura V,Belkaid Y

    更新日期:2015-04-09 00:00:00