Identification and sequencing of chimpanzee BACs We screened high-density filters from the RPCI-43 male chimpanzee BAC library 22 (BACPAC resources) using hybridization probes designed to detect sequences (1) near the inner boundaries of palindromes P1–P6 and P8; (2) near P7; and (3) from a non- ampliconic region of the human MSY. STS content and BAC-end sequences confirmed that, among the candidate BACs identified by hybridization, six contained the central portions of orthologues to human MSY palindromes. The BACs were sequenced as previously described 2 . Supplementary Table 4 provides descriptions of the sequenced BACs and their GenBank accession numbers. Sequence analysis Sequences were aligned with CLUSTAL W using default parameters 23 . In a few cases, the resulting alignments were adjusted manually. All alignments are provided as Supplementary Information. Typing nucleotide variants in palindrome arms The sites studied were CDY1þ381 (Fig. 2 and Supplementary Fig. 1), CDY1284 (Supplementary Fig. 2), and sY586 (Supplementary Fig. 3). sY586 was genotyped as previously described 24 . PCR primers and conditions for amplifying CDY1þ381 (sY1313) and CDY1284 (sY1314) have been deposited in GenBank (accession numbers G73596 and G73597, respectively). When typing CDY1þ381 by sequencing, ‘primer A’ in GenBank G73596 served as the sequencing primer. CDY1284 was typed by sequencing using ‘primer B’ in GenBank G73597. For the samples that showed evidence of gene conversion (Fig. 2 and Supplementary Figs 1–3), we excluded the possibility of deletion of one copy of the variant site as discussed in Supplementary Note 1. Steady-state balance between mutations and gene-conversion To show that the combined action of mutation and gene conversion results in a steady- state level of arm-to-arm divergence, we use the following recursion: d nþ1 ¼ð1 2 c g Þd n þ 2m g where d n is the sequence divergence between repeat copies at generation n, m g is the mutation rate per nucleotide per generation, and c g is the gene conversion rate per duplicated nucleotide per generation. We presume that d 0 ¼ 0, corresponding to no differences between sequence copies immediately after the initial duplication event. However, as 1 2 c g , 1, lim n!1 d n ¼ 2m g /c g , for any value of d 0 small enough to support c g . Because m g and d are very small, mutations almost never occur at sites that already differ between the two palindrome arms, and this possibility can be ignored. As shown in Supplementary Note 2, our analysis is a special case of Ohta’s analysis 25 . 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Four DAZ genes in two clusters found in AZFc region of human Y chromosome. Genomics 67, 256–267 (2000). 25. Ohta, T. Allelic and nonallelic homology of a supergene family. Proc. Natl Acad. Sci. USA 79, 3251–3254 (1982). 26. Casanova, M. et al. A human Y-linked DNA polymorphism and its potential for estimating genetic and evolutionary distance. Science 230, 1403–1406 (1985). 27. Underhill, P. A. et al. Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. Genome Res. 7, 996–1005 (1997). 28. Shen, P. et al. Population genetic implications from sequence variation in four Y chromosome genes. Proc. Natl Acad. Sci. USA 97, 7354–7359 (2000). Supplementary Information accompanies the paper on www.nature.com/nature. Acknowledgements We thank R. K. Alagappan and L. G. Brown for technical contributions; N. A. Ellis, M. F. Hammer, T. Jenkins and P. A. Underhill for assistance with genealogical studies; H. M. McClure and Yerkes Regional Primate Research Center for samples; C. Disteche, A. E. Donnenfeld, J. H. Hersh, T. Jenkins, P. G. McDonough, B. McGillivray, R. D. Oates, P. Patrizio, R. Rosenfield, L. Shapiro, S. Silber, M. C. Summers, J. Weissenbach, B. Whitmire and S. Yang for patient samples; and J. E. Alfoldi, B.Charlesworth, A. G. Clark, J. Koubova, J. Lange, B. Levy, T. L. Orr-Weaver, S. Repping, W. R. Rice and J. Saionz for comments on the manuscript. This work was supported by the National Institutes of Health and the Howard Hughes Medical Institute. Competing interests statement The authors declare that they have no competing financial interests. Correspondence and requests for materials should be addressed to D.C.P. (page_admin@wi.mit.edu). All new DNA sequences and STSs were submitted to GenBank with accession numbers AC139189–AC139194 (chimpanzeeBACs), AY090860–AY090881 (palindrome boundary sequences in apes), and G73582–G73595 (STS for amplifying palindrome boundaries); see Supplementary Information for details. .............................................................. Fibronectin requirement in branching morphogenesis Takayoshi Sakai, Melinda Larsen & Kenneth M. Yamada Craniofacial Developmental Biology and Regeneration Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892-4370, USA ............................................................................................................................................................................. Many organs, including salivary glands, lung and kidney, are formed during embryonic development by epithelial branching. In branching morphogenesis, repetitive epithelial cleft and bud formation create the complex three-dimensional branching structures characteristic of many organs 1–3 . Although the mech- anisms are poorly understood, one might involve the site-specific accumulation of some regulatory protein. Here we show that the extracellular matrix protein fibronectin 4,5 is essential for cleft formation during the initiation of epithelial branching. Fibro- nectin messenger RNA and fibrils appeared transiently and focally in forming cleft regions of submandibular salivary- gland epithelia, accompanied by an adjacent loss of cadherin localization. Decreasing the fibronectin concentration by using small interfering RNA and inhibition by anti-fibronectin or anti- integrin antibodies blocked cleft formation and branching. Exogenous fibronectin accelerated cleft formation and branch- ing. Similar effects of fibronectin suppression and augmentation were observed in developing lung and kidney. Mechanistic studies revealed that fibrillar fibronectin can induce cell–matrix adhesions on cultured human salivary epithelial cells with a local loss of cadherins at cell–cell junctions. Thus, fibro- nectin expression is required for cleft formation in branching letters to nature NATURE | VOL 423 | 19 JUNE 2003 | www.nature.com/nature 876 © 2003 Nature Publishing Group