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The spread of early herders across Africa is a pivotal event in prehistory, but the context of this event remains poorly understood due to a lack of paleoenvironmental data. We present new radiocarbon dates and multi-proxy Holocene paleoecological records for two distinct settings on the pathways through which livestock herding spread across eastern Africa: the Lake Turkana Basin, which has the earliest record of livestock in eastern Africa, and the Lake Victoria Basin, located farther south. Herbivore diet as inferred from tooth enamel carbon isotopes (n = 368), and pollen and leaf wax biomarker data, do not support a uniform ecological response to increased aridity at the end of the African Humid Period similar to 5 kya, as had been previously thought. Rather, climate change had basin-specific ecological effects, and these in turn met differing human responses. Rather than extrapolating local ecological effects from regional climate records, archaeologists require basin-specific paleoecological data, deeply integrated with archaeological findings. This paper provides such integration for the first time in eastern Africa. Our results highlight the climatologically and ecologically distinctive areas around lake margins, necessitating future paleoenvironmental and archaeological research in inland areas. (C) 2018 Elsevier Ltd. All rights reserved.