Samuel Melton

Efforts to identify the genetic basis of human adaptations from polymorphism data have sought footprints of "classic selective sweeps" (in which a beneficial mutation arises and rapidly fixes in the population).Yet it remains unknown whether this form of natural selection was common in our evolution. We examined the evidence for classic sweeps in resequencing data from 179 human genomes. As expected under a recurrent-sweep model, we found that diversity levels decrease near exons and conserved noncoding regions. In contrast to expectation, however, the trough in diversity around human-specific amino acid substitutions is no more pronounced than around synonymous substitutions. Moreover, relative to the genome background, amino acid and putative regulatory sites are not significantly enriched in alleles that are highly differentiated between populations. These findings indicate that classic sweeps were not a dominant mode of human adaptation over the past ~250,000 years.

Human intestinal stem cell and crypt dynamics remain poorly characterized because transgenic lineage-tracing methods are impractical in humans. Here, we have circumvented this problem by quantitatively using somatic mtDNA mutations to trace clonal lineages. By analyzing clonal imprints on the walls of colonic crypts, we show that human intestinal stem cells conform to one-dimensional neutral drift dynamics with a "functional" stem cell number of five to six in both normal patients and individuals with familial adenomatous polyposis (germline APC(-/+)). Furthermore, we show that, in adenomatous crypts (APC(-/-)), there is a proportionate increase in both functional stem cell number and the loss/replacement rate. Finally, by analyzing fields of mtDNA mutant crypts, we show that a normal colon crypt divides around once every 30-40 years, and the division rate is increased in adenomas by at least an order of magnitude. These data provide in vivo quantification of human intestinal stem cell and crypt dynamics.

Computational analysis of gene expression to determine both the sequence of lineage choices made by multipotent cells and to identify the genes influencing these decisions is challenging. Here we discover a pattern in the expression levels of a sparse subset of genes among cell types in B- and T-cell developmental lineages that correlates with developmental topologies. We develop a statistical framework using this pattern to simultaneously infer lineage transitions and the genes that determine these relationships. We use this technique to reconstruct the early hematopoietic and intestinal developmental trees. We extend this framework to analyze single-cell RNA-seq data from early human cortical development, inferring a neocortical-hindbrain split in early progenitor cells and the key genes that could control this lineage decision. Our work allows us to simultaneously infer both the identity and lineage of cell types as well as a small set of key genes whose expression patterns reflect these relationships.

(Cell Reports 8, 940–947; August 21, 2014) In the originally published version of this article, we discovered several errors relating to the analysis of the crypt fission rate. (1) In fresh-frozen (FF) tissue samples, enzymatic deficiency of CCO can be measured using a cytochrome C oxidation assay (two-color enzyme histochemistry). In formalin-fixed paraffin-embedded (FFPE) samples, since the CCO enzyme is no longer active, immunohistochemistry (IHC) for CCO protein is required. Deficiency of enzymatic activity, as measured in FF samples, can be caused by mutations that alter either enzyme function or cause loss of expression, whereas only loss-of-expression mutations are detectable in FFPE samples. Consequently, the rate of detection of CCO- patches is expected to differ between the two methods. Although we intended to analyze exclusively enzyme histochemistry of fresh-frozen samples, it has come to our attention that IHC data from 6 FFPE samples was mistakenly included in the analysis of crypt fission rate. To examine the consequence of this, we removed the FFPE samples from our original dataset and re-fitted the mathematical model to the remaining FF data. The mean fission rate was not altered significantly (κoriginal=0.028 divisions/crypt/year versus κFF−only=0.027 divisions/crypt/year). (2) An error was found in the line of code that was used to perform a correction to account for the probability of two independent CCO- events occurring by chance in adjacent crypts. This mistake means that the number of doublets was underestimated by 6.7%. This had a minimal effect on our estimate of the crypt fission rates (κoriginal=0.028 divisions/crypt/year versus κcorrection=0.027 divisions/crypt/year). (3) Finally, in our original study, single isolated CCO- crypts (patches of size 1) were omitted in the mathematical fitting procedure of the crypt fission model. When single CCO- crypts are included, we found that the mean fission rate of the disease-free cohort is lower than our previous estimate (κoriginal=0.028 divisions/crypt/year versus κCCO≥1=0.009 divisions/crypt/year). We note that this revised estimate is similar to the crypt fission rate (0.0068 divisions/crypt/year) recently reported by Nicholson et al., 2018Nicholson A.M. Olpe C. Hoyle A. Thorsen A.-S. Rus T. Colombé M. Brunton-Sim R. Kemp R. Marks K. Quirke P. et al.Fixation and Spread of Somatic Mutations in Adult Human Colonic Epithelium.Cell Stem Cell. 2018; 22: 909-918.e8Abstract Full Text Full Text PDF PubMed Scopus (63) Google Scholar using an alternative marker of clonal lineages. All raw patch size data and the original and a Jupyter notebook detailing the revised calculations of crypt fission rates are available via GitHub: https://github.com/CalumGabbutt/PatchSizeRevisions. We are particularly grateful to Calum Gabbutt for uncovering these errors and preparing the revised estimates and code. The authors regret these errors. Quantification of Crypt and Stem Cell Evolution in the Normal and Neoplastic Human ColonBaker et al.Cell ReportsAugust 7, 2014In BriefBaker et al. examine the in vivo stem cell biology of human colonic crypts. They reveal that each crypt contains a small number of functional stem cells and that stem cell division is predominantly symmetric and also quantify perturbation of stem cell architecture within adenomas. Additionally, they measure the division rate of human colonic crypts as once every 30–40 years in the healthy colon and demonstrate that the crypt division rate is increased 10-fold within small adenomas. Full-Text PDF Open Access