We report an experimental and computational study of the Hall effect in Mn1−xFexSi, as complemented by measurements in Mn1−xCoxSi, when helimagnetic order is suppressed under substitutional doping. For small x the anomalous Hall effect (AHE) and the topological Hall effect (THE) change sign. Under larger doping the AHE remains small and consistent with the magnetization, while the THE grows by over a factor of ten. Both the sign and the magnitude of the AHE and the THE are in excellent agreement with calculations based on density functional theory. Our study provides the long-sought material-specific microscopic justification, that while the AHE is due to the reciprocal-space Berry curvature, the THE originates in real-space Berry phases.PACS numbers: 71.15.Mb, 71.20.Be Measurements of the Hall effect in chiral magnets with B20 crystal structure have recently attracted great interest [1][2][3][4][5][6][7]. Due to a hierarchy of energy scales [8], comprising in decreasing strength ferromagnetic exchange, Dzyaloshinsky-Moriya (DM) spin-orbit interactions, and higher order spin-orbit coupling terms, magnetic order in these systems displays generically long-wavelength helical modulations. Under a small applied magnetic field this hierarchy of energy scales stabilizes a skyrmion lattice phase (SLP) in the vicinity of the magnetic transition temperature, i.e., a lattice composed of topologically non-trivial whirls of the magnetization [9-16]. The Hall effect, which has been studied most extensively in MnSi [1][2][3][17][18][19], displays thereby three contributions, notably an ordinary Hall effect (OHE), an anomalous Hall effect (AHE) related to the uniform magnetization, and an additional topological Hall effect (THE) in the SLP due to the non-trivial topology of the spin order.It was only recently noticed that the THE and AHE represent the real-and reciprocal-space limits of generalised phase-space Berry phases of the conduction electrons, respectively. First principles calculations in MnSi suggest that these phase-space Berry phases account quantitatively for the DM interaction and may even give rise to an electric charge of the skyrmions [20,21]. However, so far perhaps most spectacular because of the experimental evidence is the notion that the non-trivial topological winding of skyrmions gives rise to Berry phases in real space that may be viewed as an emergent magnetic field B eff = Φ 0 Φ of one flux quantum (Φ 0 = h/e) times the winding number Φ = −1 per skyrmion [1]. The same mechanism also leads to large spin transfer torques in MnSi [22,23] and FeGe at ultralow current densities. In turn, a very large THE in MnGe [4] and SrFeO 3 [5] has fuelled speculations that the emergent fields may even approach the quantum limit.Despite this wide range of interest, the account of Berry phases in the Hall effect has been essentially phenomenological, in particular for the THE, while a material-specific microscopic justification has been missing. This situation is aggravated by the microscopic sensitivity of the TH...