The Human Cell Atlas (HCA) initiative was set up to create comprehensive reference maps of all the body’s cells in a bid to increase understanding of human health and disease. This week, the HCA consortium presents early drafts of a number of maps alongside analytical tools in a collection of papers published across Nature Portfolio and Genome Biology. In Nature, Ken To and colleagues map early fetal skeletal development, identifying gene networks that drive bone formation. In a second paper, Bao Zhang and co-workers reveal gene programs that orchestrate the differentiation of bone, muscle and neural tissue in a map of human embryonic limb development. In a third paper, Nusayhah Gopee and colleagues map the fetal development of skin, identifying the role played by immune cells in the formation of hair follicles and the vascular network. A fourth paper sees Zhisong He and co-workers present an integrated brain organoid cell atlas, which provides insights into how well organoids capture aspects of the developing brain. In a fifth paper, Amanda Oliver and colleagues map the gastrointestinal tract to create an atlas and uncover disease-related cellular changes in conditions such as Crohn’s disease and ulcerative colitis. Finally, a detailed thymus map from Nadav Yayon and co-workers tracks the development of immune cells. The cover images captures the breadth of the HCA initiative, overlaying a subway-style network of biological systems on a detailed cellular map.

The cover shows an artist’s impression of the archaic bird Navaornis hestiae, which lived around 80 million years ago. The species is described in a paper by Luis Chiappe, Guillermo Navalón and colleagues in this week’s issue. Newly identified from fossil remains found in what is now Brazil, Navaornis represents a link between Archaeopteryx, one of the earliest birds, and modern species. The skull of the fossil was so well preserved, the researchers were able to reconstruct the brain of Navaornis, which revealed both archaic traits and modern features. The team notes that Navaornis helps to clarify the timing and order certain features appeared in the neuroanatomy of birds.

The cover shows circular extrachromosomal DNA (ecDNA) sitting next to a chromosome. ecDNA has a significant effect on the outcome of cancer treatment — it can render tumours resistant to therapies and so contributes to poor outcomes for patients. Several papers in this issue probe the relationship between ecDNA and cancer. In the first, Charles Swanton, Mariam Jamal-Hanjani, Paul Mischel and colleagues present a comprehensive atlas of ecDNA in cancer, mapping its frequency, origin and associations with outcome. In the second paper, Howard Chang, Paul Mischel and co-workers reveal how different ecDNAs in cancer cells can be inherited during cell division and how that can drive cancer. A third paper, by Paul Mischel, Howard Chang, Christian Hassig and colleagues, identifies a potential vulnerability in cancers containing ecDNA that could open the way for treatment. And a fourth paper by Bishoy Faltas and co-workers examines how ecDNA contributes to tumour evolution and therapy resistance in urothelial carcinoma.