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The Drifting Human Genome,’’ by BIOCHEMISTRY Corrections COMMENTARY. For the article ‘‘The drifting human genome,’’ by BIOCHEMISTRY. For the article ‘‘Crystal structure and functional Jianzhi Zhang, which appeared in issue 51, December 18, 2007, analysis of tetracenomycin ARO/CYC: Implications for cycliza- of Proc Natl Acad Sci USA (104:20147–20148; first published tion specificity of aromatic polyketides,’’ by Brian Douglas Ames, December 10, 2007; 10.1073͞pnas.0710524105), the authors note Tyler Paz Korman, Wenjun Zhang, Peter Smith, Thanh Vu, Yi that, due to a printer’s error, the DOI appeared incorrectly. The Tang, and Shiou-Chuan Tsai, which appeared in issue 14, April DOI 10.1073/pnas.0710524105 should have appeared as 10.1073/ 8, 2008, of Proc Natl Acad Sci USA (105:5349–5354; first pnas.0710524104. The online version has been corrected. published April 3, 2008; 10.1073͞pnas.0709223105), the authors note that on page 5353, left column, in Biological Significance and ͞ ͞ ͞ ͞ www.pnas.org cgi doi 10.1073 pnas.0804195105 Proposed Mechanism, line 5, ‘‘intercalculating’’ should have appeared as ‘‘intercalating.’’ Additionally, on page 5354, left column, in Gene Expression and Protein Purification, in the last BIOCHEMISTRY. For the article ‘‘Heterogeneity in EGF-binding line, ‘‘10 mM Hepes (pH 7.0) and NaOH’’ should instead read: affinities arises from negative cooperativity in an aggregating ‘‘10 mM Hepes (pH 7.0)/NaOH.’’ Finally, in the main article text, system,’’ by Jennifer L. Macdonald and Linda J. Pike, which the numbering and links to some supporting information (SI) appeared in issue 1, January 8, 2008, of Proc Natl Acad Sci USA ͞ figures and tables were incorrect and have been corrected. These (105:112–117; first published December 28, 2007; 10.1073 errors were printer’s errors and do not affect the conclusions of pnas.0707080105), the authors note that in Fig. 3, in the param- the article. eter list inset at lower right, the labels K21 and L20 are reversed. The correct values for all four parameters are K11 ϭ 4.6 Ϯ 0.6 ϫ www.pnas.org͞cgi͞doi͞10.1073͞pnas.0804020105 9 11 9 10 , L20 ϭ 5.3 Ϯ 2.2 ϫ 10 , K21 ϭ 5.3 Ϯ 0.4 ϫ 10 , and K22 ϭ 3.4 Ϯ 1.1 ϫ 108. This error does not affect the conclusions of the article. The corrected figure and its legend appear below. BIOCHEMISTRY. For the article ‘‘EB1 promotes Aurora-B kinase activity through blocking its inactivation by protein phosphatase 2A,’’ by Lei Sun, Jinmin Gao, Xin Dong, Min Liu, Dengwen Li, Xingjuan Shi, Jin-Tang Dong, Xianyu Lu, Chunyong Liu, and Jun Zhou, which appeared in issue 20, May 20, 2008, of Proc Natl Acad Sci USA (105:7153–7158; first published May 13, 2008; 10.1073͞pnas.0710018105), the authors note that Jinmin Gao (J.G.), and not Jun Zhou (J.Z.), should have been included among those credited with contributing equally to this work. The corrected author contributions footnote appears below. In ad- dition, in the Acknowledgments, a grant number was inadver- tently omitted. ‘‘This work was supported by grants from the National Key Scientific Program of China (2007CB914503 and CORRECTION 2007CB914802),’’ should instead read: ‘‘This work was sup- ported by grants from the National Key Scientific Program of China (2006CB910103, 2007CB914503, and 2007CB914802).’’ Author contributions: L.S., J.G., and X.D. contributed equally to this work; J.Z. designed research; L.S., J.G., X.D., M.L., D.L., X.S., and J.Z. performed research; J.-T.D., X.L., and C.L. contributed new reagents/analytic tools; L.S., J.G., and J.Z. analyzed data; and J.Z. wrote the Fig. 3. Binding of EGF to cells expressing increasing levels of wild-type EGF paper. receptors. CHO-K1 tet-on EGFR cells were induced to express EGF receptors by www.pnas.org͞cgi͞doi͞10.1073͞pnas.0804731105 using increasing doses of doxycycline. 125I-EGF-binding isotherms were gen- erated from each set of cells, and all six isotherms were globally fit to Eq. 1, with only the value of R0 varying among curves. Data points represent the mean Ϯ SD of triplicate determinations. Solid lines represent the fitted curve through the data points of the same color. www.pnas.org͞cgi͞doi͞10.1073͞pnas.0804457105 www.pnas.org PNAS ͉ July 1, 2008 ͉ vol. 105 ͉ no. 26 ͉ 9129–9130 Downloaded by guest on September 23, 2021 COMMENTARY The drifting human genome Jianzhi Zhang* Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 round the time of the comple- more, they found a normal distribution and Old World monkeys because of the tion of the draft human ge- of gene copy number among human in- inactivation of TRPC2, a crucial channel nome sequence, biologists dividuals, with a standard deviation of protein gene, in the common ancestor of heatedly debated the number 54. Between any two individuals, the hominoids and Old World monkeys (9). Aof genes contained in the human ge- average gene copy number difference is Nozawa et al. (2) further extended nome. In 2003, GeneSweep, an informal as high as 61.5. When Africans, Asians, their analysis from within populations to gene-count betting pool that began at and Europeans were analyzed sepa- between populations and between spe- the 2000 Cold Spring Harbor Labora- rately, Africans showed greater variation cies. This type of analysis is in principle tory Genome Meeting, announced Lee than Asians and Europeans, consistent similar to the Hudson–Kreitman– Rowen of the Institute of Systems Biol- with the out-of-Africa model of modern Aguade´ (HKA) test of neutrality of sin- ogy in Seattle to be the winner. His bet human origins. gle nucleotide changes (10). The HKA (25,946) was the lowest and was closest Their subsequent analysis focused on test compares the ratios of the intraspe- to what many computer programs pre- three families of chemosensory genes cific polymorphism level and the inter- dicted from the then draft human ge- that encode odorant receptors (ORs), specific divergence level between two nome sequence (1). But, in this issue of type 1 vomeronasal (pheromone) recep- loci, which are expected to be identical PNAS, Nozawa, Kawahara, and Nei (2) tors (V1Rs), and bitter taste receptors under neutrality. When one of the loci tell us that asking about the exact num- (T2Rs), respectively, because chemosen- is a functional gene and the other is a ber of human genes is meaningless, be- sory genes have particularly high levels cause different human individuals have pseudogene, rejection of the null hy- different numbers of genes, and it is not pothesis by the HKA test suggests non- uncommon for one person to have 100 It is not uncommon for neutral evolution of the functional gene, more gene copies than another person. caused by positive or negative selection. They argue that this large variation re- one person to have 100 Nozawa et al. measured the intraspecific flects genomic drift, random changes of polymorphism of OR gene copy number gene copy number in evolution. more gene copies than by its standard deviation among human Genetic variation among humans individuals and measured the interspe- takes many forms. In the past two de- another person. cific divergence of OR gene copy num- cades, most studies have focused on ber by the absolute difference in OR single-nucleotide polymorphisms. For gene number between the reference ge- example, the International HapMap of CNV (2, 4, 8). It is important to note nome sequences of humans and chim- Consortium recently published HapMap panzees. Similar measures were used for Ͼ that chemosensation is apparently im- II, which characterizes 3 million portant and highly refined in mammals, OR pseudogenes. However, they did not single-nucleotide polymorphisms geno- as Ͼ5% of all genes in a mammalian formally test the neutral hypothesis, pre- typed in 270 individuals from four hu- genome are devoted to the detection of sumably because it is not possible to man populations of African, Asian, and odorants, pheromones, and tastants. The compare polymorphism and divergence European origins (3). In the last few most interesting analysis Nozawa et al. statistically when one is measured by years, multiple groups reported a high (2) conducted is a comparison of CNV standard deviation and the other is mea- prevalence of copy number variation between functional and nonfunctional sured by difference. Inspired by their (CNV) of DNA segments ranging in size attempt, I designed a neutrality test in from 103 to 106 nucleotides in humans chemosensory genes. They found that the proportion of genes that have CNV which polymorphism is measured by the (4, 5), chimpanzees (6), and mice (7). number of OR loci that show CNV and CNV is generated by segmental duplica- is not significantly different between functional and nonfunctional OR genes. divergence is measured by the difference tion and deletion mutations that are ap- in OR gene number between the refer- parently quite frequent. Thanks to the Furthermore, the distribution of OR ence genome sequences of humans and rapid advance of genomic technologies, gene copy number among human indi- chimpanzees. Although some informa- genome-wide human CNV data recently viduals is normal for both functional tion about the intraspecific variation is became available, but studies of CNV genes and pseudogenes, with almost have been largely descriptive. The work identical standard deviations. Because lost in this treatment as the quantitative of Nozawa et al. (2) puts CNV into the pseudogenes are not subject to natural level of CNV at each locus is not con- framework of population and evolution- selection, the simplest explanation of sidered, I can now compare polymor- ary genetics and is thus an exciting ad- this observation is that the CNV of phism and divergence directly.
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