Madagascar’s biota underwent substantial change following human colonization of the island in the Late Holocene. The timing of human arrival and its role in the extinction of megafauna have received considerable attention. However, the impacts of human activities on regional ecosystems remain poorly studied. Here, we focus on reconstructing changes in the composition of terrestrial and aquatic ecosystems to evaluate the impact of human land use and climate variability. We conducted a paleoenvironmental study, using a sediment record that spans the last ∼1,145 years, collected from a lakebed in the Namonte Basin of southwest Madagascar. We examined physical (X-ray fluorescence and stratigraphy) and biotic indicators (pollen, diatoms and micro- and macro-charcoal particles) to infer terrestrial and aquatic ecosystem change. The fossil pollen data indicate that composition of grasslands and dry deciduous forest in the region remained relatively stable during an arid event associated with northward displacement of the Intertropical Convergence Zone (ITCZ) between ∼1,145 and 555 calibrated calendar years before present (cal yr BP). Charcoal particles indicate that widespread fires occurred in the region, resulting from a combination of climate drivers and human agency during the entire span covered by the paleorecord. Following settlement by pastoral communities and the disappearance of endemic megafauna ∼1,000 cal yr BP, grasslands expanded and the abundance of trees that rely on large animals for seed dispersal gradually declined. A reduction in the abundance of pollen taxa characteristic of dry forest coincided with an abrupt increase in charcoal particles between ∼230 and 35 cal yr BP, when agro-pastoral communities immigrated into the region. Deforestation and soil erosion, indicated by a relatively rapid sedimentation rate and high K/Zr and Fe/Zr, intensified between 180 and 70 cal yr BP and caused a consequent increase in lake turbidity, resulting in more rapid turnover of the aquatic diatom community. Land use and ongoing climate change have continued to transform local terrestrial and freshwater ecosystems during the last ∼70 years. The current composition of terrestrial and aquatic ecosystems reflects the legacy of extinction of native biota, invasion of exotic species, and diminished use of traditional land management practices.

Madagascar experienced a major faunal turnover near the end of the first millenium CE that particularly affected terrestrial, large-bodied vertebrate species. Teasing apart the relative impacts of people and climate on this event requires a focus on regional records with good chronological control. These records may document coeval changes in rainfall, faunal composition, and human activities. Here we present new paleontological and paleoclimatological data from southwestern Madagascar, the driest part of the island today. We collected over 1500 subfossil bones from deposits at a coastal site called Antsirafaly and from both flooded and dry cave deposits at Tsimanampesotse National Park. We built a chronology of Late Holocene changes in faunal assemblages based on 65 radiocarbon-dated specimens and subfossil associations. We collected stalagmites primarily within Tsimanampesotse but also at two additional locations in southern Madagascar. These provided information regarding hydroclimate variability over the past 120,000 years. Prior research has supported a primary role for drought (rather than humans) in triggering faunal turnover at Tsimanampesotse. This is based on evidence of: (1) a large freshwater ecosystem west of what is now the hypersaline Lake Tsimanampesotse, which supported freshwater mollusks and waterfowl (including animals that could not survive on resources offered by the hypersaline lake today); (2) abundant now-extinct terrestrial vertebrates; (3) regional decline or disappearance of certain tree species; and (4) scant local human presence. Our new data allow us to document the hydroclimate of the subarid southwest during the Holocene, as well as shifts in faunal composition (including local extirpations, large-vertebrate population collapse, and the appearance of introduced species). These records affirm that climate alone cannot have produced the observed vertebrate turnover in the southwest. Human activity, including the introduction of cattle, as well as associated changes in habitat exploitation, also played an important role.