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Most researchers assume minimal impact of pretreatment on strontium isotope ratios ( 87 Sr/ 86 Sr) for bones and teeth, and methods vary tremendously. We compared 14 pretreatment methods, including no prep other than powdering enamel, ashing, soaking in water, an oxidizing agent (bleach or hydrogen peroxide) or acetic acid (0.1 M, 1.0 M, and 1.0 M buffered with calcium acetate), and a combination of these steps. We prepared and analyzed aliquots of powdered molar enamel from three proboscideans (one modern captive Indian elephant, Elephas maximus indicus ; one Pleistocene mastodon, Mammut americanum ; and one Miocene gomphothere, Afrochoerodon kisumuensis ). Each pretreatment was performed in triplicate and we measured 87 Sr/ 86 Sr, Sr concentration, and uranium (U) concentration, using the same lab space and instrumentation for all samples. Variability in 87 Sr/ 86 Sr and Sr and U concentrations was considerable across pretreatments. Mean 87 Sr/ 86 Sr across methods ranged from 0.70999 to 0.71029 for the modern tooth, 0.71458 to 0.71502 for the Pleistocene tooth, and 0.70804 to 0.70817 for the Miocene tooth. The modern tooth contained the least Sr and negligible U. The Pleistocene tooth contained slightly more Sr and measurable amounts of U, and the Miocene tooth had approximately 5x more Sr and U than the Pleistocene tooth. For all three teeth, variance in 87 Sr/ 86 Sr, Sr concentrations, and U concentrations among replicates was statistically indistinguishable across pretreatments, but there were apparent differences among pretreatments for the modern and Pleistocene teeth. Both contained relatively little Sr, and it is possible that small amounts of exogenous Sr from reagents, building materials or dust affected some replicates for some pretreatments. For the modern tooth, median 87 Sr/ 86 Sr varied considerably (but statistically insignificantly) across pretreatments. For the Pleistocene tooth, variability in median 87 Sr/ 86 Sr was also considerable; some pretreatments were statistically distinct but there were no obvious patterns among methods. For the Miocene tooth, variability in median 87 Sr/ 86 Sr was much smaller, but there were significant differences among pretreatments. Most pretreatments yielded 87 Sr/ 86 Sr and Sr concentrations comparable to, or lower than, untreated powder, suggesting selective removal of exogenous material with high 87 Sr/ 86 Sr. Further evaluation of the mechanisms driving isotopic variability both within and among pretreatment methods is warranted. Researchers should clearly report their methods and avoid combining data obtained using different methods. Small differences in 87 Sr/ 86 Sr could impact data interpretations, especially in areas where isotopic variability is low. 

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. 

Recently expanded estimates for when humans arrived on Madagascar (up to approximately 10 000 years ago) highlight questions about the causes of the island's relatively late megafaunal extinctions (approximately 2000–500 years ago). Introduced domesticated animals could have contributed to extinctions, but the arrival times and past diets of exotic animals are poorly known. To conduct the first explicit test of the potential for competition between introduced livestock and extinct endemic megafauna in southern and western Madagascar, we generated new radiocarbon and stable carbon and nitrogen isotope data from the bone collagen of introduced ungulates (zebu cattle, ovicaprids and bushpigs, n = 66) and endemic megafauna (pygmy hippopotamuses, giant tortoises and elephant birds, n = 68), and combined these data with existing data from endemic megafauna (n = 282, including giant lemurs). Radiocarbon dates confirm that introduced and endemic herbivores briefly overlapped chronologically in this region between 1000 and 800 calibrated years before present (cal BP). Moreover, stable isotope data suggest that goats, tortoises and hippos had broadly similar diets or exploited similar habitats. These data support the potential for both direct and indirect forms of competition between introduced and endemic herbivores. We argue that competition with introduced herbivores, mediated by opportunistic hunting by humans and exacerbated by environmental change, contributed to the late extinction of endemic megafauna on Madagascar. 

Introduced predators currently threaten endemic animals on Madagascar through predation, facilitation of human-led hunts, competition, and disease transmission, but the antiquity and past consequences of these introductions are poorly known. We use directly radiocarbon dated bones of introduced dogs ( Canis familiaris ) to test whether dogs could have aided human-led hunts of the island’s extinct megafauna. We compare carbon and nitrogen isotope data from the bone collagen of dogs and endemic “fosa” ( Cryptoprocta spp.) in central and southwestern Madagascar to test for competition between introduced and endemic predators. The distinct isotopic niches of dogs and fosa suggest that any past antagonistic relationship between these predators did not follow from predation or competition for shared prey. Radiocarbon dates confirm that dogs have been present on Madagascar for over a millennium and suggest that they at least briefly co-occurred with the island’s extinct megafauna, which included giant lemurs, elephant birds, and pygmy hippopotamuses. Today, dogs share a mutualism with pastoralists who also occasionally hunt endemic vertebrates, and similar behavior is reflected in deposits at several Malagasy paleontological sites that contain dog and livestock bones along with butchered bones of extinct megafauna and extant lemurs. Dogs on Madagascar have had a wide range of diets during the past millennium, but relatively high stable carbon isotope values suggest few individuals relied primarily on forest bushmeat. Our newly generated data suggest that dogs were part of a suite of animal introductions beginning over a millennium ago that coincided with widespread landscape transformation and megafaunal extinction. 

No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal “subfossil” remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ∼160 kg) and other extraordinary Malagasy megafauna that survived into the past millennium. Yet, much about the evolutionary biology of these now-extinct species remains unknown, along with persistent phylogenetic uncertainty in some cases. Thankfully, despite the challenges of DNA preservation in tropical and subtropical environments, technical advances have enabled the recovery of ancient DNA from some Malagasy subfossil specimens. Here, we present a nuclear genome sequence (∼2× coverage) for one of the largest extinct lemurs, the koala lemur Megaladapis edwardsi (∼85 kg). To support the testing of key phylogenetic and evolutionary hypotheses, we also generated high-coverage nuclear genomes for two extant lemurs, Eulemur rufifrons and Lepilemur mustelinus , and we aligned these sequences with previously published genomes for three other extant lemurs and 47 nonlemur vertebrates. Our phylogenetic results confirm that Megaladapis is most closely related to the extant Lemuridae (typified in our analysis by E. rufifrons ) to the exclusion of L. mustelinus , which contradicts morphology-based phylogenies. Our evolutionary analyses identified significant convergent evolution between M. edwardsi and an extant folivore (a colobine monkey) and an herbivore (horse) in genes encoding proteins that function in plant toxin biodegradation and nutrient absorption. These results suggest that koala lemurs were highly adapted to a leaf-based diet, which may also explain their convergent craniodental morphology with the small-bodied folivore Lepilemur . 

The relative importance of climate and humans in the disappearance of the Malagasy megafauna remains under debate. Data from southwestern Madagascar imply aridification contributed substantially to the late Holocene decline of the megafauna (the Aridification Hypothesis). Evidence for aridification includes carbon isotopes from tree rings, lacustrine charcoal concentrations and pollen assemblages, and changes in fossil vertebrate assemblages indicative of a local loss of pluvial conditions. In contrast, speleothem records from northwestern Madagascar suggest that megafaunal decline and habitat change resulted primarily from human activity including agropastoralism (the Subsistence Shift Hypothesis). Could there have been contrasting mechanisms of decline in different parts of Madagascar? Or are we lacking the precisely dated, high resolution records needed to fully understand the complex processes behind megafaunal decline? Reconciling these contrasting hypotheses requires additional climate records from southwestern Madagascar. We recovered a stalagmite (AF2) from Asafora Cave in the spiny thicket ecoregion, ~10 km from the southwest coast and just southeast of the Velondriake Marine Reserve. U-series and 14C dating of samples taken from the core of this stalagmite provide a highly precise chronology of the changes in hydroclimate and vegetation in this region over the past 3000 years. Speleothem stable oxygen and carbon isotope analyses provide insight into past rainfall variability and vegetation changes respectively. We compare these records with those for a stalagmite (AB2) from Anjohibe Cave in northwestern Madagascar. Lastly, odds ratio analyses of radiocarbon dates for extinct and extant subfossils allow us to describe and compare the temporal trajectories of megafaunal decline in the southwest and the northwest. Combined, these analyses allow us to test the Aridification Hypothesis for megafaunal extinction. The trajectories of megafaunal decline differed in northwestern and southwestern Madagascar. In the southwest, unlike the northwest, there is no evidence of decoupling of speleothem stable carbon and oxygen isotopes. Instead, habitat changes in the southwest were largely related to variation in hydroclimate (including a prolonged drought). The megafaunal collapse here occurred in tandem with the drought, and agropastoralism likely contributed to that demise only after the megafauna had already suffered drought-related population reduction. Our results offer some support for the Aridification Hypothesis, but with three caveats: first, that there was no island-wide aridification; second, that aridification likely impacted megafaunal decline only in the driest parts of Madagascar; and third, that aridification was not the sole factor promotingmegafaunal decline even in the dry southwest. A number of megafaunal species survived the prolonged drought of the first millennium, and then likely succumbed to the activities of agropastoralists. 

A new fossil site in a previously unexplored part of western Madagascar (the Beanka Protected Area) has yielded remains of many recently extinct vertebrates, including giant lemurs (Babakotia radofilai, Palaeopropithecus kelyus, Pachylemur sp., and Archaeolemur edwardsi), carnivores (Cryptoprocta spelea), the aardvark-like Plesiorycteropus sp., and giant ground cuckoos (Coua). Many of these represent considerable range extensions. Extant species that were extirpated from the region (e.g., Prolemur simus) are also present. Calibrated radiocarbon ages for 10 bones from extinct primates span the last three millennia. The largely undisturbed taphonomy of bone deposits supports the interpretation that many specimens fell in from a rock ledge above the entrance. Some primates and other mammals may have been prey items of avian predators, but human predation is also evident. Strontium isotope ratios (87Sr/86Sr) suggest that fossils were local to the area. Pottery sherds and bones of extinct and extant vertebrates with cut and chop marks indicate human activity in previous centuries. Scarcity of charcoal and human artifacts suggests only occasional visitation to the site by humans. The fossil assemblage from this site is unusual in that, while it contains many sloth lemurs, it lacks ratites, hippopotami, and crocodiles typical of nearly all other Holocene subfossil sites on Madagascar.