Ahlgren, U., J. Jonsson and H. Edlund. 1996. The morphogenesis of the pancreatic mesenchyme is uncoupled from that of the pancreatic epithelium in IPF/PDX1-deficient mice. Development 122: 1409–1416.
PubMed Link

Apelqvist, A., U. Ahlgren and H. Edlund. 1997. Sonic hedgehog directs specialised mesoderm differentiation in the intestine and pancreas. Curr. Biol. 7: 801–804.
PubMed Link

Bayha, E., M. C. Jørgensen, P. Serup and A. Grapin-Botton. 2009. Retinoic acid signaling organizes endodermal organ specification along the entire antero-posterior axis. PLo S ONE 4: e5845.
PubMed Link

Bossard, P. and K. S. Zaret. 2000. Repressive and restrictive mesodermal interactions with gut endoderm: Possible relation to Meckel's diverticulum. Development 127: 4915–4923.
PubMed Link

Buczacki, S. J. and 6 others. 2013. Intestinal label-retaining cells are secretory precursors expressing Lgr5. Nature 495: 65–69.
PubMed Link

Burlison, J. S., Q. Long, Y. Fujitani, C. V. Wright and M. A. Magnuson. 2008. Pdx-1 and Ptf1a concurrently determine fate specification of pancreatic multipotent progenitor cells. Dev. Biol. 316: 74–86.
PubMed Link

Carlson, B. M. 1981. Patten’s Foundations of Embryology. McGraw-Hill, New York.

Cebra-Thomas, J. A., J. Bromer, R. Gardner. G. K. Lam, H. Sheipe and S. F. Gilbert. 2003. T-box gene products are required for mesenchymal induction of epithelial branching in the embryonic mouse lung. Dev. Dyn. 22: 82–90.
PubMed Link

Chevalier, N. R., N. Dacher, C. Jacques, L. Langlois, C. Guedj and O. Faklaris. 2019. Embryogenesis of the peristaltic reflex. J. Physiol. 597: 2785–2801.
PubMed Link

Chung, W.-S., C. H. Shin and D. Y. R. Stainier. 2008. Bmp2 signaling regulates the hepatic versus pancreatic fate decision. Dev. Cell. 15: 738–48.
PubMed Link

Crump, J. G., L. Maves, N. D. Lawson, B. M. Weinstein and C. B. Kimmel. 2004. An essential role for FGFs in endoderm pouch formation influences later craniofacial skeletal patterning. Development 131: 5703–5716.
PubMed Link

DeLeve, L. D. 2013. Liver sinusoidal endothelial cells and liver regeneration. J. Clin. Invest. 123: 1861–1866.
PubMed Link

Dhawan, S., S. Georgia, S. I. Tschen, G. Fan and A. Bhushan. 2011. Pancreatic β cell identity is maintained by DNA methylation-mediated repression of Arx. Dev. Cell 20: 419–429.
PubMed Link

Ding, B. S. and 12 others. 2010. Inductive angiocrine signals from sinusoidal endothelium are required for liver regeneration. Nature 468: 310–315.
PubMed Link

Dong, P. D., E. Provost, S. D. Leach and D. Y. Stainier. 2008. Graded levels of Ptf1a differentially regulate endocrine and exocrine fates in the developing pancreas. Genes Dev. 22: 1445–1450.
PubMed Link

Dunn, N. R., S. D. Vincent, L. Oxburgh, E. J. Robertson and E. K. Bikoff. 2004. Combinatorial activities of Smad2 and Smad3 regulate mesoderm formation and patterning in the mouse embryo. Development 131: 1717–1728.
PubMed Link

Fawkner-Corbett D. and 13 others. 2021. Spatiotemporal analysis of human intestinal development at single-cell resolution. Cell 184: 810–826.e23.
PubMed Link

Fishman, M. P. and D. A. Melton. 2002. Pancreatic lineage analysis using a retroviral vector in embryonic mice demonstrates a common progenitor for endocrine and exocrine cells. Int. J. Dev. Biol. 46: 201–207.
PubMed Link

Franklin, V., P. L. Khoo, H. Bildsoe, N. Wong, S. Lewis and P. P. Tam. 2008. Regionalisation of the endoderm progenitors and morphogenesis of the gut portals of the mouse embryo. Mech. Dev. 125: 587–600.
PubMed Link

Fried, S. and 9 others. 2020. Extrahepatic cholangiocyte obstruction is mediated by decreased glutathione, Wnt and Notch signaling pathways in a toxic model of biliary atresia. Sci Rep. 10: 7 599.
PubMed Link

Fukumachi, H. and S. Takayama. 1980. Epithelial-mesenchymal interaction in differentiation of duodenal epithelium of fetal rats in organ culture. Experientia 36: 335–336.
PubMed Link

Goldman, O., S. Han, W. Hamou, V. Jodon de Villeroche, G. Uzan, H. Lickert and V. Gouon-Evans. 2014. Endoderm generates endothelial cells during liver development. Stem Cell Rep. 3: 556–565.
PubMed Link

Goldstein, A. M., K. C. Brewer, A. M. Doyle, N. Nagy and D. J. Roberts. 2005. BMP signaling is necessary for neural crest cell migration and ganglion formation in the enteric nervous system. Mech. Dev. 122: 821–833.
PubMed Link

Gordillo, M., T. Evans and V. Gouon-Evans. 2015. Orchestrating liver development. Development 142: 2094–2108.
PubMed Link

Goss, A. M. and 7 others. 2009. Wnt2/2b and beta-catenin signaling are necessary and sufficient to specify lung progenitors in the foregut. Dev. Cell 17: 290–298.
PubMed Link

Graham, A. and J. Richardson. 2012. Developmental and evolutionary origins of the pharyngeal apparatus. EvoDevo 3: 24.
PubMed Link

Grapin-Botton, A., A. R. Majithia and D. A. Melton. 2001. Key events of pancreas formation are triggered in gut endoderm by ectopic expression of pancreatic regulatory genes. Genes Dev. 15: 444–454.
PubMed Link

Gualdi, R., P. Bossard, M. Zheng, Y. Hamada, J. R. Coleman and K. S. Zaret. 1996. Hepatic specification of the gut endoderm in vitro: Cell signaling and transcriptional control. Genes Dev. 10: 1670–1682.
PubMed Link

Gumpel-Pinot, M., S. Yasugi and T. Mizuno. 1978. Différenciation d’épithéliums endodermiques associaés au mésoderme splanchnique. Comp. Rend. Acad. Sci. 286: 117–120.
PubMed Link

Harris-Johnson, K. S., E. T. Domyan, C. M. Vezina and X. Sun. 2009. Beta-catenin promotes respiratory progenitor identity in mouse foregut. Proc. Natl. Acad. Sci. USA 106: 16287–16292.
PubMed Link

Hebrok, M., S. Kim and D. A. Melton. 1998. Notochord repression of endodermal Sonic hedgehog permits pancreas development. Genes Dev. 12: 1705–1713.
PubMed Link

Henry, G. L. and D. A. Melton. 1998. Mixer, a homeobox gene required for endoderm development. Science 281: 91–96.
PubMed Link

Hirai, H., T. Tani and N. Kikyo . 2010. Structure and functions of powerful transactivators: VP16, MyoD and FoxA. Int. J. Dev. Biol. 54: 1589–1596
PubMed Link

Holland,, L. Z. and N. D. Holland. 2021. Cephalochordates: A window into vertebrate origins. Curr. Top. Dev. Biol. 141:119–147.
PubMed Link

Horb, M. E., C. N. Shen, D. Tosh and J. M. Slack. 2003. Experimental conversion of liver to pancreas. Curr. Biol. 13: 105–115.
PubMed Link

Hu, J. and 12 others. 2014. Endothelial cell-derived angiopoietin-2 controls liver regeneration as a spatiotemporal rheostat. Science 343: 416–419.
PubMed Link

Hudson, C., D. Clements, R. V. Friday, D. Stott and H. R. Woodland. 1997. Xsox17-a and -b mediate endoderm formation in Xenopus. Cell 91: 397–405.
PubMed Link

Huycke, T. R. and 6 others. 2019. Genetic and mechanical regulation of intestinal smooth muscle development. Cell 79: 90–105.
PubMed Link

Isaacson, D., J. Shen, D. McCreedy, M. Calvert, G. Cunha and L. Baskin. 2017. Dichotomous branching of human fetal lung demonstrated with light sheet fluorescence microscopy. Am. J. Respir. Crit. Care Med. 196: 1476–1477.
PubMed Link

Jonas, H. 1966. The Phenomenon of Life: Toward a Philosophical Biology. Evanston: Northwestern University Press.

Jonnson, J., L. Carlsson, T. Edlund and H. Edlund. 1994. Insulin-promote-factor 1 is required for pancreas development in mice. Nature 371: 606–609.
PubMed Link

Jung, J., M. Zheng, M. Goldfarb and K. S. Zaret. 1999. Initiation of mammalian liver development from endoderm by fibroblast growth factors. Science 284: 1998–2003.
PubMed Link

Kanai-Azuma, M. and 10 others. 2002. Depletion of definitive gut endoderm in Sox17-null mutant mice. Development 129: 2367–2379.
PubMed Link

Karolak, J. A., T. Gambin, P. Szafranski and P. Stankiewicz. 2021. Potential interactions between the TBX4-FGF10 and SHH-FOXF1 signaling during human lung development revealed using ChIP-seq. Respir. Res. 22: 26
PubMed Link

Kedinger, M., P. M. Simon-Assman, F. Bouziges, C. Arnold, E. Alexandre and K. Haffen. 1990. Smooth muscle actin expression during rat gut development and induction in fetal skin fibroblastic cells associated with intestinal embryonic epithelium. Differentiation 43: 87–97.
PubMed Link

Kim, B.-M., G. Buchner, I. Miletich, P. T. Sharpe and R. A. Shivdasani. 2005. The stomach mesenchymal transcription factor Barx1 specifies gastric epithelial identity through inhibition of transient Wnt signaling. Dev. Cell 8: 611–622.
PubMed Link

Kim, H. Y., M. F. Pang, V. D. Varner, L. Kojima, E. Miller, D. C. Radisky and C. M. Nelson. 2015. Localized smooth muscle differentiation is essential for epithelial bifurcation during branching morphogenesis of the mammalian lung. Dev. Cell 34: 719–726.
PubMed Link

Kim, H. Y., V. D. Varner and C. M. Nelson. 2013 Apical constriction initiates new bud formation during monopodial branching of the embryonic chicken lung. Development 140: 3146–3155.
PubMed Link

Kishimoto K. and 8 others. 2020. Bidirectional Wnt signaling between endoderm and mesoderm confers tracheal identity in mouse and human cells. Nat. Commun. 11: 4159.
PubMed Link

Kishimoto, K. and 7 others. 2018. Synchronized mesenchymal cell polarization and differentiation shape the formation of the murine trachea and esophagus. Nat. Commun. 9: 2816.
PubMed Link

Kwon, G. S., M. Viotti and A. K. Hadjantonakis. 2008. The endoderm of the mouse embryo arises by dynamic widespread intercalation of embryonic and extraembryonic lineages. Dev. Cell. 15: 509–520.
PubMed Link

Lammert, E., O. Cleaver and D. A. Melton. 2001. Induction of pancreatic differentiation by signals from blood vessels. Science 294: 564–567.
PubMed Link

Langman, J. 1981. Medical Embryology, 4th Ed. Williams & Wilkins, Baltimore, MD.

Lawson, K. A., J. J. Meneses and R. A. Pedersen. 1986. Cell fate and cell lineage in the endoderm of the presomite mouse embryo, studied with an intracellular tracer. Dev. Biol. 115: 325–339.
PubMed Link

Le Douarin, N. 1975. An experimental analysis of liver development. Med. Biol. 53: 427–455.
PubMed Link

Lee, C. D., J. R. Friedman, J. T. Fulmer and K. H. Kaestner. 2005. The initiation of liver development is dependent on Foxa transcription factors. Nature 435: 944–947.
PubMed Link

Lorent, K. and 13 others. 2015. Identification of a plant isoflavonoid that causes biliary atresia. Sci. Transl. Med. 7: 286ra67.
PubMed Link

Lowe, C. J. 2021. Molecular insights into deuterostome evolution from hemichordate developmental biology. Curr. Top. Dev. Biol. 141: 75–117.
PubMed Link

Lüdtke, T. H. and 9 others. 2016. Tbx2 and Tbx3 act downstream of Shh to maintain canonical Wnt Signaling during branching morphogenesis of the murine lung. Dev. Cell. 39: 239–253.
PubMed Link

Matsumoto, K., H. Yoshitomi, J. Rossant and K. S. Zaret. 2001. Liver organogenesis promoted by endothelial cells prior to vascular function. Science 294: 559–563.
PubMed Link

McLin, V. A., S. A. Rankin and A. M. Zorn. 2007. Repression of Wnt/beta-catenin signaling in the anterior endoderm is essential for liver and pancreas development. Development 134: 2207–2217.
PubMed Link

Metzger, R. J., O. D. Klein, G. R. Martin and M. A. Krasnow. 2008. The branching programme of mouse lung development. Nature 453: 745–750.
PubMed Link

Montalbano, A. P., S. Hawgood and C. R. Mendelson. 2013. Mice deficient in surfactant protein A (SP-A) and SP-D or in TLR2 manifest delayed parturition and decreased expression of inflammatory and contractile genes. Endocrinology 154: 483–498.
PubMed Link

Moore-Scott, B. A. and N. R. Manley. 2005. Differential expression of sonic hedgehog along the anterior-posterior axis regulates patterning of pharyngeal pouch endoderm and pharyngeal endoderm-derived organs. Dev. Biol. 278: 323–335.
PubMed Link

Mu, T. and 22 others. 2020. Embryonic liver developmental trajectory revealed by single-cell RNA sequencing in the Foxa2eGFP mouse. Commun. Biol. 3: 642.
PubMed Link

Nerurkar, N. L., C. Lee, L. Mahadevan and C. J. Tabin. 2019. Molecular control of macroscopic forces drives formation of the vertebrate hindgut. Nature 565: 480–484.
PubMed Link

Nowotschin, S. and 13 others. 2019. The emergent landscape of the mouse gut endoderm at single-cell resolution. Nature 569: 361–367.
PubMed Link

Ober, E. A., H. Verkade, H. A. Field and D. Y. Stainier. 2006. Mesodermal Wnt2b signalling positively regulates liver specification. Nature 442: 688–691.
PubMed Link

Odom, D. T. and 12 others. 2004. Control of pancreas and liver gene expression by HNF transcription factors. Science 303: 1378–1381.
PubMed Link

Offield, M. F. and 7 others. 1996. PDX-1 is required for pancreatic outgrowth and differentiation of the rostral duodenum. Development 122: 983–995.
PubMed Link

Okada, T. S. 1960. Epithelio-mesenchymal interactions in the regional differentiation of the digestive tract in the amphibian embryo. Roux Arch. Entwick. Mech. 152: 1–21.

Pagliuca, F. W. and 8 others. 2014. Generation of functional human pancreatic beta cells in vitro. Cell 159: 428–439.
PubMed Link

Pander, C. H. 1817. Beiträge zur Entwicklungsgeschichte des Hühnchens im Eye. Brönner, Würzburg.

Pardo-Saganta, A., P. R. Tata, B. M. Law, B. Saez, R. D. Chow, M. Prabhu, T. Gridley and J. Rajagopal. 2015. Parent stem cells can serve as niches for their daughter cells. Nature 523: 597–601.
PubMed Link

Parviz, F., C. Matullo, W. D. Garrison, L. Savatski, J. W. Adamson, G. Ning, K. H. Kaestner, J. M. Rossi, K. S. Zaret and S. A. Duncan. 2003. Hepatocyte nuclear factor 4a controls the development of the hepatic diverticulum and liver morphogenesis. Nat. Genet. 34: 292–296.
PubMed Link

Reizel, Y. and 9 others. 2021. FoxA-dependent demethylation of DNA initiates epigenetic memory of cellular identity. Dev. Cell. 56: 602–612.e4.
PubMed Link

Rezania, A. and 12 others. 2014. Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells. Nat. Biotechnol. 32: 1121–1133.
PubMed Link

Roberts, D. J., D. M. Smith, D. J. Goff and C. J. Tabin. 1998. Epithelial-mesenchymal signaling during the regionalization of the chick gut. Development 125: 2791–2801.
PubMed Link

Roberts, D. J., R. L. Johnson, A. C. Burke, C. E. Nelson, B. A. Morgan and C. Tabin. 1995. Sonic hedgehog is an endodermal signal inducing Bmp-4 and Hox genes during induction and regionalization of the chick hindgut. Development 121: 3163–3174.
PubMed Link

Rossi, J. M., N. R. Dunn, B. I. Hogan and K. S. Zaret. 2001. Distinct mesodermal signals, including BMPs from the septum transversum mesenchyme, are required in combination for hepatogenesis from the endoderm. Genes Dev. 15: 998–2009.
PubMed Link

Rothova, M., M. Thompson, H. Lickert and A. S. Tucker. 2012. Lineage tracing of the endoderm during oral development. Dev. Dyn. 241:1183–1191.
PubMed Link

Sadler, T. W. 2009. Langman’s Medical Embryology. Lippincott, Williams & Wilkins, Hagerstown, MD.

Savin, T., N. A. Kurpios, A. E. Shyer, P. Florescu, H. Liang, L. Mahadevan and C. J. Tabin. 2011. On the growth and form of the gut. Nature 476: 57–62.
PubMed Link

Schmidt, C., F. Bladt, S. Goedecke, V. Brinkmann, W. Zschiesche, M. Sharpe, E. Gherardi and C. Birchmeier. 1995. Scatter factor/hepatocyte growth factor is essential for liver development. Nature 373: 699–702.
PubMed Link

Shannon, J. M., L. D. Nielsen, S. A. Gebb and S. H. Randell. 1998. Mesenchyme specifies epithelial differentiation in reciprocal recombinants of embryonic lung and trachea. Dev. Dyn. 212: 482–494.
PubMed Link

Sherwood, R. I., R. Maehr, E. O. Mazzoni and D. A. Melton. 2011. Wnt signaling specifies and patterns intestinal endoderm. Mech. Dev. 128: 387–400.
PubMed Link

Shikaya, Y., Y.Takase, R. Tadokoro, R. Nakamura, M. Inaba and Y. Takahashi. 2021. Distribution map of peristaltic waves in the chicken embryonic gut reveals importance of ENS and inter-region cross talks along the gut axis. BioRxiv Dec. 9 2021 (preprint).
Link

Shyer, A. E., T. R. Huycke, C. Lee, L. Mahadevan and C. J. Tabin. 2015. Bending gradients: How the intestinal stem cell gets its home. Cell 161: 569–580.
PubMed Link

Shyer, A. E. and 7 others. 2013. Villification: How the gut gets its villi. Science 342: 212–218.
PubMed Link

Smith, A. B. 2005. The pre-radial history of the echinoderms. Geological Journal 40: 255–280.
Link

Spurlin, J. W. and C. M. Nelson. 2017. Building branched tissue structures: From single cell guidance to coordinated construction. Philos. Trans. R. Soc. London B 372: 20150527.

Stange, D. E. and 14 others. 2013. Differentiated Troy+ chief cells act as reserve stem cells to generate all lineages of the stomach epithelium. Cell 155: 357–368.
PubMed Link

Stringer, E. J. and 13 others. 2012. Cdx2 determines the fate of postnatal intestinal endoderm. Development 139: 465–474.
PubMed Link

Takayama, K. and 8 others. 2011. Efficient and directive generation of two distinct endoderm lineages from human ESCs and iPSCs by differentiation stage-specific SOX17 transduction. PLoS ONE 6: e21780.
PubMed Link

Tata, P. R. and 11 others. 2013. Dedifferentiation of committed epithelial cells into stem cells in vivo. Nature 503: 218–223.
PubMed Link

Theodosiou, A. and C. J. Tabin. 2005. Sox9 and Nkx2.5 determine the pyloric sphincter epithelium under the control of BMP signaling. Dev. Biol. 279: 481–490.
PubMed Link

Tremblay, K. D. and K. S. Zaret. 2005. Distinct populations of endoderm cells converge to generate the embryonic liver bud and ventral foregut tissues. Dev. Biol. 280: 87–99.
PubMed Link

Uemura, M., H. Igarashi, A. Ozawa, N. Tsunekawa, M. Kurohmaru, M. Kanai-Azuma and Y. Kanai. 2015. Fate mapping of gallbladder progenitors in posteroventral foregut endoderm of mouse early somite-stage embryos. J. Vet. Med. Sci. 77: 587–591.
PubMed Link

Veitch, E., J. Begbie, T. F. Schilling, M. M. Smith and A. Graham. 1999. Pharyngeal arch patterning in the absence of neural crest. Curr. Biol. 9: 1481–1484.
PubMed Link

Vincent, S. D., N. R. Dunn, S. Hayashi, D. P. Norris and E. J. Robertson. 2003. Cell fate decisions within the mouse organizer are governed by graded Nodal signals. Genes Dev. 17: 1646–1662.
PubMed Link

Viotti, M., A. C. Foley and A. K. Hadjantonakis. 2014a. Gutsy moves in mice: Cellular and molecular dynamics of endoderm morphogenesis. Philos. Trans. R. Soc. London 369B: 20130547.
PubMed Link

Viotti, M., S. Nowotschin and A. K. Hadjantonakis. 2014b. SOX17 links gut endoderm morphogenesis and germ layer segregation. Nat. Cell Biol. 16: 1146–1156.
PubMed Link

Wallace, K. N. and M. Pack. 2003. Unique and conserved aspects of gut development in zebrafish. Dev. Biol. 255: 12–29.
PubMed Link

Walton, K. D. and 8 others. 2012. Hedgehog-responsive mesenchymal clusters direct patterning and emergence of intestinal villi. Proc. Natl. Acad. Sci. USA 109: 15817–15822.
PubMed Link

Walton, K. D. and 10 others. 2016. Villification in the mouse: BMP signals control intestinal villus patterning. Development 143: 427–436.
PubMed Link

Weaver, M., N. R. Dunn and B. L. Hogan. 2000. Bmp4 and Fgf10 play opposing roles during lung bud morphogenesis. Development 127: 2695–2704
PubMed Link

Wessells, N. K. 1970. Mammalian lung development: Interactions in formulation and morphogenesis of tracheal buds. J. Exp. Zool. 175: 455–466.
PubMed Link

Woo, J., I. Miletich, B.-M. Kim, P. T. Sharpe and R. A. Shivdasani. 2011. Barx1-mediated inhibition of Wnt signaling in the mouse thoracic foregut controls tracheo-esophageal septation and epithelial differentiation. PLOS ONE 6: e22493.
PubMed Link

Xu, C. R., P. A. Cole, D. J. Meyers, J. Kormish, S. Dent and K. S. Zaret. 2011. Chromatin “prepattern” and histone modifiers in a fate choice for liver and pancreas. Science 332: 963–966.
PubMed Link

Yokouchi, Y., J. Sakiyama and A. Kuroiwa. 1995. Coordinate expression of Abd-B subfamily genes of the HoxA cluster in developing digestive tract of the chick embryo. Dev. Biol. 169: 76–89.
PubMed Link

Yoshitomi, H. and K. S. Zaret. 2004. Endothelial cell interactions initiate dorsal pancreas development by selectively inducing transcription factor Ptf1a. Development 131: 807–814.
PubMed Link

Zaret, K. S. 2016. From endoderm to liver bud: Paradigms of cell type specification and tissue morphogenesis. Curr. Top. Dev. Biol. 117: 647–669.
PubMed Link

Zaret, K. S. 2016. From endoderm to liver bud: Paradigms of cell type specification and tissue morphogenesis. Curr. Top. Dev. Biol. 117: 647–669.
PubMed Link

Zhang, W., T. A. Yatskievych, R. K. Baker and P. B. Antin. 2004. Regulation of Hex gene expression and initial stages of avian hepatogenesis by BMP and FGF signaling. Dev. Biol. 268: 312–326.
PubMed Link

Zhou, Q., A. C. Law, J. Rajagopal, W. J. Anderson, P. A. Gray and D. A. Melton. 2007. A multipotent progenitor domain guides pancreatic organogenesis. Dev. Cell 13: 103–114.
PubMed Link

Zhou, Y. and 12 others. 2011. Latent TGF-b binding protein 3 identifies a second heart field in zebrafish. Nature 474: 645–648.
PubMed Link

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