Synergistic roles of climate warming and human occupation in Patagonian megafaunal extinctions during the Last Deglaciation

52,000 years of woolly rhinoceros population dynamics reveal extinction mechanisms

The extinction of the woolly rhinoceros (Coelodonta antiquitatis) at the onset of the Holocene remains an enigma, with conflicting evidence regarding its cause and spatiotemporal dynamics. This partly reflects challenges in determining demographic responses of late Quaternary megafauna to climatic and anthropogenic causal drivers with available genetic and paleontological techniques. Here, we show that elucidating mechanisms of ancient extinctions can benefit from a detailed understanding of fine-scale metapopulation dynamics, operating over many millennia. Using an abundant fossil record, ancient DNA, and high-resolution simulation models, we untangle the ecological mechanisms and causal drivers that are likely to have been integral in the decline and later extinction of the woolly rhinoceros. Our 52,000-y reconstruction of distribution-wide metapopulation dynamics supports a pathway to extinction that began long before the Holocene, when the combination of cooling temperatures and low but sustained hunting by humans trapped woolly rhinoceroses in suboptimal habitats along the southern edge of their range. Modeling indicates that this ecological trap intensified after the end of the last ice age, preventing colonization of newly formed suitable habitats, weakening stabilizing metapopulation processes, triggering the extinction of the woolly rhinoceros in the early Holocene. Our findings suggest that fragmentation and resultant metapopulation dynamics should be explicitly considered in explanations of late Quaternary megafauna extinctions, sending a clarion call to the fragility of the remaining large-bodied grazers restricted to disjunct fragments of poor-quality habitat due to anthropogenic environmental change.

A neotropical perspective on the uniqueness of the Holocene among interglacials

Understanding how tropical systems have responded to large-scale climate change, such as glacial-interglacial oscillations, and how human impacts have altered those responses is key to current and future ecology. A sedimentary record recovered from Lake Junín, in the Peruvian Andes (4085 m elevation) spans the last 670,000 years and represents the longest continuous and empirically-dated record of tropical vegetation change to date. Spanning seven glacial-interglacial oscillations, fossil pollen and charcoal recovered from the core showed the general dominance of grasslands, although during the warmest times some Andean forest trees grew above their modern limits near the lake. Fire was very rare until the last 12,000 years, when humans were in the landscape. Here we show that, due to human activity, our present interglacial, the Holocene, has a distinctive vegetation composition and ecological trajectory compared with six previous interglacials. Our data reinforce the view that modern vegetation assemblages of high Andean grasslands and the presence of a defined tree line are aspects of a human-modified landscape.

Pampean megamammals in Europe: the fossil collections from Santiago Roth

Santiago Roth was a Swiss fossil finder, naturalist, and paleontologist that emigrated to Argentina in 1866. His work largely influenced the discipline in the country at the end of the twentieth century, particularly the stratigraphy of the Pampean region. Some of his collections of Pampean fossils were sold to museums and private collectors in Europe and were accompanied by elaborated catalogues. Fossils in the Roth's catalogues N° 2 and 3 are housed today in the Natural History Museum of Denmark, fossils from catalogues N° 4 to 6, were sold to Swiss museums, with Catalogue N° 5 currently housed at the Department of Paleontology, Universität Zürich. Here, we provide a general framework on the stratigraphy from the Roth's Pampean fossil sites, summarize the history of the Pampean fossils in Europe originally collected by Roth, and provide historical and curatorial details of the Roth's collection at the Department of Paleontology, Universität Zürich.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13358-023-00283-5.

Changes in projectile design and size of prey reveal the central role of Fishtail points in megafauna hunting in South America

Fishtail projectile points are the earliest widespread projectile type in South America, and share chronology and techno-morphology with Clovis, the oldest North American projectile type. Both were temporally associated with late Pleistocene megafaunal extinctions. Although the elusive direct evidence of human exploitation of megafauna in South America had kept Fishtails out of the extinction debate, a recent paper showed a strong relationship between the temporal density and spatial distribution of megafauna and Fishtail projectile points, and proposed that this weapon was designed and used for megafauna hunting, contributing to their extinction. If so, this technology must be distinctly different from post-FPP technologies (i.e., early Holocene projectile points), used for hunting smaller prey, in terms of distribution and functional properties. In this paper, we explore the changes in projectile point technology, as well as the body mass of potential megafaunal prey, and show that Fishtails were strongly related to the largest extinct megafaunal species.

A palaeoecological perspective on the transformation of the tropical Andes by early human activity

Palaeoecological records suggest that humans have been in the Andes since at least 14 000 years ago. Early human impacts on Andean ecosystems included an increase in fire activity and the extinction of the Pleistocene megafauna. These changes in Andean ecosystems coincided with rapid climate change as species were migrating upslope in response to deglacial warming. Microrefugia probably played a vital role in the speed and genetic composition of that migration. The period from ca 14 500 to 12 500 years ago was when novel combinations of plant species appeared to form no-analogue assemblages in the Andes. By 12 000 years ago most areas in what are today the Andean grasslands were being burned and modified by human activity. As the vegetation of these highland settings has been modified by human activity for the entirety of the Holocene, they should be regarded as long-term manufactutred landscapes. The sharp tree lines separating Andean forests from grasslands that we see today were probably also created by repeated burning and owe their position more to human-induced fire than climatic constraints. In areas that were readly penetrated by humans on the forested slopes of the Andes, substantial modification and settlement had occurred by the mid-Holocene. In hard-to-reach areas, however, the amount of human modification may always have been minimal, and these slopes can be considered as being close to natural in their vegetation. This article is part of the theme issue 'Tropical forests in the deep human past'.

A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives

Background: The evolutionary relationships of Felidae during their Early-Middle Miocene radiation is contentious. Although the early common ancestors have been subsumed under the grade-group Pseudaelurus, this group is thought to be paraphyletic, including the early ancestors of both modern cats and extinct sabretooths. Methods: Here, we sequenced a draft nuclear genome of Smilodon populator, dated to 13,182 ± 90 cal BP, making this the oldest palaeogenome from South America to date, a region known to be problematic for ancient DNA preservation. We analysed this genome, together with genomes from other extinct and extant cats to investigate their phylogenetic relationships. Results: We confirm a deep divergence (~20.65 Ma) within sabre-toothed cats. Through the analysis of both simulated and empirical data, we show a lack of gene flow between Smilodon and contemporary Felidae. Conclusions: Given that some species traditionally assigned to Pseudaelurus originated in the Early Miocene ~20 Ma, this indicates that some species of Pseudaelurus may be younger than the lineages they purportedly gave rise to, further supporting the hypothesis that Pseudaelurus was paraphyletic.

Equids engineer desert water availability

Megafauna play important roles in the biosphere, yet little is known about how they shape dryland ecosystems. We report on an overlooked form of ecosystem engineering by donkeys and horses. In the deserts of North America, digging of ≤2-meter wells to groundwater by feral equids increased the density of water features, reduced distances between waters, and, at times, provided the only water present. Vertebrate richness and activity were higher at equid wells than at adjacent dry sites, and, by mimicking flood disturbance, equid wells became nurseries for riparian trees. Our results suggest that equids, even those that are introduced or feral, are able to buffer water availability, which may increase resilience to ongoing human-caused aridification.

Late Pleistocene South American megafaunal extinctions associated with rise of Fishtail points and human population

In the 1970s, Paul Martin proposed that big game hunters armed with fluted projectile points colonized the Americas and drove the extinction of megafauna. Around fifty years later, the central role of humans in the extinctions is still strongly debated in North American archaeology, but little considered in South America. Here we analyze the temporal dynamic and spatial distribution of South American megafauna and fluted (Fishtail) projectile points to evaluate the role of humans in Pleistocene extinctions. We observe a strong relationship between the temporal density and spatial distribution of megafaunal species stratigraphically associated with humans and Fishtail projectile points, as well as with the fluctuations in human demography. On this basis we propose that the direct effect of human predation was the main factor driving the megafaunal decline, with other secondary, but necessary, co-occurring factors for the collapse of the megafaunal community.

Relative demographic susceptibility does not explain the extinction chronology of Sahul's megafauna

The causes of Sahul’s megafauna extinctions remain uncertain, although several interacting factors were likely responsible. To examine the relative support for hypotheses regarding plausible ecological mechanisms underlying these extinctions, we constructed the first stochastic, age-structured models for 13 extinct megafauna species from five functional/taxonomic groups, as well as 8 extant species within these groups for comparison. Perturbing specific demographic rates individually, we tested which species were more demographically susceptible to extinction, and then compared these relative sensitivities to the fossil-derived extinction chronology. Our models show that the macropodiformes were the least demographically susceptible to extinction, followed by carnivores, monotremes, vombatiform herbivores, and large birds. Five of the eight extant species were as or more susceptible than the extinct species. There was no clear relationship between extinction susceptibility and the extinction chronology for any perturbation scenario, while body mass and generation length explained much of the variation in relative risk. Our results reveal that the actual mechanisms leading to the observed extinction chronology were unlikely related to variation in demographic susceptibility per se, but were possibly driven instead by finer-scale variation in climate change and/or human prey choice and relative hunting success.

24.0 kyr cal BP stone artefact from Vale da Pedra Furada, Piauí, Brazil: Techno-functional analysis

Current archaeological paradigm proposes that the first peopling of the Americas does not exceed the Last Glacial Maximum period. In this context, the acceptance of the anthropogenic character of the earliest stone artefacts generally rests on the presence of projectile points considered no more as typocentric but as typognomonic, since it allows, by itself, to certify the human character of the other associated artefacts. In other words, without this presence, nothing is certain. Archaeological research at Piauí (Brazil) attests to a Pleistocene human presence between 41 and 14 cal kyr BP, without any record of lithic projectile points. Here, we report the discovery and interpretation of an unusual stone artefact in the Vale da Pedra Furada site, in a context dating back to 24 cal kyr BP. The knapping stigmata and macroscopic use-wear traces reveal a conception centred on the configuration of double bevels and the production in the same specimen of at least two successive artefacts with probably different functions. This piece unambiguously presents an anthropic character and reveals a technical novelty during the Pleistocene occupation of South America.

Climate change, not human population growth, correlates with Late Quaternary megafauna declines in North America

The disappearance of many North American megafauna at the end of the Pleistocene is a contentious topic. While the proposed causes for megafaunal extinction are varied, most researchers fall into three broad camps emphasizing human overhunting, climate change, or some combination of the two. Understanding the cause of megafaunal extinctions requires the analysis of through-time relationships between climate change and megafauna and human population dynamics. To do so, many researchers have used summed probability density functions (SPDFs) as a proxy for through-time fluctuations in human and megafauna population sizes. SPDFs, however, conflate process variation with the chronological uncertainty inherent in radiocarbon dates. Recently, a new Bayesian regression technique was developed that overcomes this problem-Radiocarbon-dated Event-Count (REC) Modelling. Here we employ REC models to test whether declines in North American megafauna species could be best explained by climate changes, increases in human population densities, or both, using the largest available database of megafauna and human radiocarbon dates. Our results suggest that there is currently no evidence for a persistent through-time relationship between human and megafauna population levels in North America. There is, however, evidence that decreases in global temperature correlated with megafauna population declines.

Ancient DNA from the Asiatic Wild Dog (Cuon alpinus) from Europe

The Asiatic wild dog (Cuon alpinus), restricted today largely to South and Southeast Asia, was widespread throughout Eurasia and even reached North America during the Pleistocene. Like many other species, it suffered from a huge range loss towards the end of the Pleistocene and went extinct in most of its former distribution. The fossil record of the dhole is scattered and the identification of fossils can be complicated by an overlap in size and a high morphological similarity between dholes and other canid species. We generated almost complete mitochondrial genomes for six putative dhole fossils from Europe. By using three lines of evidence, i.e., the number of reads mapping to various canid mitochondrial genomes, the evaluation and quantification of the mapping evenness along the reference genomes and phylogenetic analysis, we were able to identify two out of six samples as dhole, whereas four samples represent wolf fossils. This highlights the contribution genetic data can make when trying to identify the species affiliation of fossil specimens. The ancient dhole sequences are highly divergent when compared to modern dhole sequences, but the scarcity of dhole data for comparison impedes a more extensive analysis.

Functional traits of the world's late Quaternary large-bodied avian and mammalian herbivores

Prehistoric and recent extinctions of large-bodied terrestrial herbivores had significant and lasting impacts on Earth's ecosystems due to the loss of their distinct trait combinations. The world's surviving large-bodied avian and mammalian herbivores remain among the most threatened taxa. As such, a greater understanding of the ecological impacts of large herbivore losses is increasingly important. However, comprehensive and ecologically-relevant trait datasets for extinct and extant herbivores are lacking. Here, we present HerbiTraits, a comprehensive functional trait dataset for all late Quaternary terrestrial avian and mammalian herbivores ≥10 kg (545 species). HerbiTraits includes key traits that influence how herbivores interact with ecosystems, namely body mass, diet, fermentation type, habitat use, and limb morphology. Trait data were compiled from 557 sources and comprise the best available knowledge on late Quaternary large-bodied herbivores. HerbiTraits provides a tool for the analysis of herbivore functional diversity both past and present and its effects on Earth's ecosystems.

Were domestic camelids present on the prehispanic South American agricultural frontier? An ancient DNA study

The southern boundary of prehispanic farming in South America occurs in central Mendoza Province, Argentina at approximately 34 degrees south latitude. Archaeological evidence of farming includes the recovery of macrobotanical remains of cultigens and isotopic chemistry of human bone. Since the 1990s, archaeologists have also hypothesized that the llama (Lama glama), a domesticated South American camelid, was also herded near the southern boundary of prehispanic farming. The remains of a wild congeneric camelid, the guanaco (Lama guanicoe), however, are common in archaeological sites throughout Mendoza Province. It is difficult to distinguish bones of the domestic llama from wild guanaco in terms of osteological morphology, and therefore, claims that llama were in geographic areas where guanaco were also present based on osteometric analysis alone remain equivocal. A recent study, for example, claimed that twenty-five percent of the camelid remains from the high elevation Andes site of Laguna del Diamante S4 were identified based on osteometric evidence as domestic llama, but guanaco are also a likely candidate since the two species overlap in size. We test the hypothesis that domesticated camelids occurred in prehispanic, southern Mendoza through analysis of ancient DNA. We generated whole mitochondrial genome datasets from 41 samples from southern Mendoza late Holocene archaeological sites, located between 450 and 3400 meters above sea level (masl). All camelid samples from those sites were identified as guanaco; thus, we have no evidence to support the hypothesis that the domestic llama occurred in prehispanic southern Mendoza.

Rapid radiation of humans in South America after the last glacial maximum: A radiocarbon-based study

The early peopling of the Americas has been one of the most hotly contested topics in American anthropology and a research issue that draws archaeologists into a multidisciplinary debate. In South America, although the background data on this issue has increased exponentially in recent decades, the core questions related to the temporal and spatial patterns of the colonization process remain open. In this paper we tackle these questions in the light of the quantitative analysis of a screened radiocarbon database of more than 1600 early dates. We explore the frequency of radiocarbon dates as proxies for assessing population growth; and define a reliable and statistically well supported lower chronological bound (not to the exact date) for the earliest human arrival. Our results suggest that the earliest chronological threshold for the peopling of South America should be between 16,600 and 15,100, with a mean estimated date ~ 15,500 cal BP (post Last Glacial Maximum). Population would have grown until the end of Antarctic Cold Reversal stadial ~12,500 cal BP at the time of the main extinctions of megafauna–, when the increase rate slows, probably as a result of the changes that occurred in the trophic niche of humans.

Introduced herbivores restore Late Pleistocene ecological functions

Large-bodied mammalian herbivores dominated Earth's terrestrial ecosystems for several million years before undergoing substantial extinctions and declines during the Late Pleistocene (LP) due to prehistoric human impacts. The decline of large herbivores led to widespread ecological changes due to the loss of their ecological functions, as driven by their unique combinations of traits. However, recently, humans have significantly increased herbivore species richness through introductions in many parts of the world, potentially counteracting LP losses. Here, we assessed the extent to which introduced herbivore species restore lost-or contribute novel-functions relative to preextinction LP assemblages. We constructed multidimensional trait spaces using a trait database for all extant and extinct mammalian herbivores ≥10 kg known from the earliest LP (∼130,000 ybp) to the present day. Extinction-driven contractions of LP trait space have been offset through introductions by ∼39% globally. Analysis of trait space overlap reveals that assemblages with introduced species are overall more similar to those of the LP than native-only assemblages. This is because 64% of introduced species are more similar to extinct rather than extant species within their respective continents. Many introduced herbivores restore trait combinations that have the capacity to influence ecosystem processes, such as wildfire and shrub expansion in drylands. Although introduced species have long been a source of contention, our findings indicate that they may, in part, restore ecological functions reflective of the past several million years before widespread human-driven extinctions.

Climate-human interaction associated with southeast Australian megafauna extinction patterns

The mechanisms leading to megafauna (>44 kg) extinctions in Late Pleistocene (126,000—12,000 years ago) Australia are highly contested because standard chronological analyses rely on scarce data of varying quality and ignore spatial complexity. Relevant archaeological and palaeontological records are most often also biased by differential preservation resulting in under-representated older events. Chronological analyses have attributed megafaunal extinctions to climate change, humans, or a combination of the two, but rarely consider spatial variation in extinction patterns, initial human appearance trajectories, and palaeoclimate change together. Here we develop a statistical approach to infer spatio-temporal trajectories of megafauna extirpations (local extinctions) and initial human appearance in south-eastern Australia. We identify a combined climate-human effect on regional extirpation patterns suggesting that small, mobile Aboriginal populations potentially needed access to drinkable water to survive arid ecosystems, but were simultaneously constrained by climate-dependent net landscape primary productivity. Thus, the co-drivers of megafauna extirpations were themselves constrained by the spatial distribution of climate-dependent water sources.

Whether Australia’s Pleistocene megafauna extinctions were caused by climate change, humans, or both is debated. Here, the authors infer the spatio-temporal trajectories of regional extinctions and find that water availability mediates the relationship among climate, human migration and megafauna extinctions.

Paleoamerican Occupation, Stone Tools from the Cueva del Medio, and Considerations for the Late Pleistocene Archaeology in Southern South America

Archaeological excavations at the Cueva del Medio performed during the 1980s and 1990s yielded an important record of both faunal and stone tool remains, as well as data, to discuss issues that occurred during the Terminal Pleistocene. Due to that, the shaped Paleoamerican artifacts collected in the author’s excavations were partially informed. The present article provides unpublished data on the field-work, the results of a techno-morphological analysis of the stone tools, and considerations about early hunter-gatherer societies along with their regional paleo-environmental interactions, as well other topics regarding the regional archaeological process during the last millennium of the Pleistocene. Findings from there have been extremely useful for discussing diverse paleo-ecological and archaeological topics and have extended the knowledge and discussions about different Pleistocene scientific issues, mainly related with flora, fauna, and the colonization of southern Patagonia.

Demography of avian scavengers after Pleistocene megafaunal extinction

The late Quaternary megafauna extinctions reshaped species assemblages, yet we know little about how extant obligate scavengers responded to this abrupt ecological change. To explore whether obligate scavengers persisted by depending on contemporary community linkages or via foraging flexibility, we tested the importance of the trophic interaction between pumas (Puma concolor) and native camelids (Vicugna vicugna and Lama guanicoe) for the persistence of Andean condors (Vultur gryphus) in southern South America, and compared the demographic history of three vultures in different continents. We sequenced and compiled mtDNA to reconstruct past population dynamics. Our results suggest that Andean condors increased in population size >10 KYA, whereas vicuñas and pumas showed stable populations and guanacos a recent (<10 KYA) demographic expansion, suggesting independent trajectories between species. Further, vultures showed positive demographic trends: white-backed vultures (Gyps africanus) increased in population size, matching attenuated community changes in Africa, and California condors (Gymnogyps californianus) exhibited a steep demographic expansion ~20 KYA largely concurrent with North American megafaunal extinctions. Our results suggest that dietary plasticity of extant vulture lineages allowed them to thrive despite historical environmental changes. This dietary flexibility, however, is now detrimental as it enhances risk to toxicological compounds harbored by modern carrion resources.

A late Pleistocene human footprint from the Pilauco archaeological site, northern Patagonia, Chile

The present study describes the discovery of a singular sedimentary structure corresponding to an ichnite that was excavated at the paleo-archaeological site Pilauco (Osorno, Chile). The trace fossil is associated with megafauna bones, plant material and unifacial lithic tools. Here we present a detailed analysis of the Pilauco ichnite and associated sedimentary structures, as well as new radiocarbon data. The ichnological analysis confidently assigns the trace to the ichnospecies Hominipes modernus—a hominoid footprint usually related to Homo sapiens. Some particular characteristics of the Pilauco trace include an elongated distal hallux, lateral digit impressions obliterated by the collapsed sediment, and sediment lumps inside and around the trace. In order to evaluate the origin of the ichnite, trackmaking experiments are performed on re-hydrated fossil bed sediments. The results demonstrate that a human agent could easily generate a footprint morphology equivalent to the sedimentary structure when walking on a saturated substrate. Based on the evidence, we conclude that the trackmaker might well have been a bare-footed adult human. This finding, along with the presence of lithic artifacts in the same sedimentary levels, might represent further evidence for a pre-Clovis South American colonization of northern Patagonia, as originally proposed for the nearby Monte Verde site.

Sedimentary record from Patagonia, southern Chile supports cosmic-impact triggering of biomass burning, climate change, and megafaunal extinctions at 12.8 ka

The Younger Dryas (YD) impact hypothesis posits that fragments of a large, disintegrating asteroid/comet struck North America, South America, Europe, and western Asia ~12,800 years ago. Multiple airbursts/impacts produced the YD boundary layer (YDB), depositing peak concentrations of platinum, high-temperature spherules, meltglass, and nanodiamonds, forming an isochronous datum at >50 sites across ~50 million km² of Earth's surface. This proposed event triggered extensive biomass burning, brief impact winter, YD climate change, and contributed to extinctions of late Pleistocene megafauna. In the most extensive investigation south of the equator, we report on a ~12,800-year-old sequence at Pilauco, Chile (~40°S), that exhibits peak YD boundary concentrations of platinum, gold, high-temperature iron- and chromium-rich spherules, and native iron particles rarely found in nature. A major peak in charcoal abundance marks an intense biomass-burning episode, synchronous with dramatic changes in vegetation, including a high-disturbance regime, seasonality in precipitation, and warmer conditions. This is anti-phased with northern-hemispheric cooling at the YD onset, whose rapidity suggests atmospheric linkage. The sudden disappearance of megafaunal remains and dung fungi in the YDB layer at Pilauco correlates with megafaunal extinctions across the Americas. The Pilauco record appears consistent with YDB impact evidence found at sites on four continents.

Campo Laborde: A Late Pleistocene giant ground sloth kill and butchering site in the Pampas

The extinction of Pleistocene megafauna and the role played by humans have been subjects of constant debate in American archeology. Previous evidence from the Pampas region of Argentina suggested that this environment might have provided a refugium for the Holocene survival of several megamammals. However, recent excavations and more advanced accelerator mass spectrometry radiocarbon dating at Campo Laborde site in the Argentinian Pampas challenge the Holocene survival of Pleistocene megamammals and provide original and high-quality information documenting direct human impact on the Pleistocene fauna. The new data offer definitive evidence for hunting and butchering of Megatherium americanum (giant ground sloth) at 12,600 cal years BP and dispute previous interpretations that Pleistocene megamammals survived into the Holocene in the Pampas.

Palaeogenomics of the Hydrocarbon Producing Microalga Botryococcus braunii

Botryococcus braunii is a colonial microalga that appears early in the fossil record and is a sensitive proxy of environmental and hydroclimatic conditions. Palaeozoic Botryococcus fossils which contribute up to 90% of oil shales and approximately 1% of crude oil, co-localise with diagnostic geolipids from the degradation of source-signature hydrocarbons. However more recent Holocene sediments demonstrate no such association. Consequently, Botryococcus are identified in younger sediments by morphology alone, where potential misclassifications could lead to inaccurate paleoenvironmental reconstructions. Here we show that a combination of flow cytometry and ancient DNA (aDNA) sequencing can unambiguously identify Botryococcus microfossils in Holocene sediments with hitherto unparalleled accuracy and rapidity. The application of aDNA sequencing to microfossils offers a far-reaching opportunity for understanding environmental change in the recent geological record. When allied with other high-resolution palaeoenvironmental information such as aDNA sequencing of humans and megafauna, aDNA from microfossils may allow a deeper and more precise understanding of past environments, ecologies and migrations.

High-quality fossil dates support a synchronous, Late Holocene extinction of devils and thylacines in mainland Australia

The last large marsupial carnivores-the Tasmanian devil (Sarcophilis harrisii) and thylacine (Thylacinus cynocephalus)-went extinct on mainland Australia during the mid-Holocene. Based on the youngest fossil dates (approx. 3500 years before present, BP), these extinctions are often considered synchronous and driven by a common cause. However, many published devil dates have recently been rejected as unreliable, shifting the youngest mainland fossil age to 25 500 years BP and challenging the synchronous-extinction hypothesis. Here we provide 24 and 20 new ages for devils and thylacines, respectively, and collate existing, reliable radiocarbon dates by quality-filtering available records. We use this new dataset to estimate an extinction time for both species by applying the Gaussian-resampled, inverse-weighted McInerney (GRIWM) method. Our new data and analysis definitively support the synchronous-extinction hypothesis, estimating that the mainland devil and thylacine extinctions occurred between 3179 and 3227 years BP.

Evolution and extinction of the giant rhinoceros Elasmotherium sibiricum sheds light on late Quaternary megafaunal extinctions

Understanding extinction events requires an unbiased record of the chronology and ecology of victims and survivors. The rhinoceros Elasmotherium sibiricum, known as the 'Siberian unicorn', was believed to have gone extinct around 200,000 years ago-well before the late Quaternary megafaunal extinction event. However, no absolute dating, genetic analysis or quantitative ecological assessment of this species has been undertaken. Here, we show, by accelerator mass spectrometry radiocarbon dating of 23 individuals, including cross-validation by compound-specific analysis, that E. sibiricum survived in Eastern Europe and Central Asia until at least 39,000 years ago, corroborating a wave of megafaunal turnover before the Last Glacial Maximum in Eurasia, in addition to the better-known late-glacial event. Stable isotope data indicate a dry steppe niche for E. sibiricum and, together with morphology, a highly specialized diet that probably contributed to its extinction. We further demonstrate, with DNA sequencing data, a very deep phylogenetic split between the subfamilies Elasmotheriinae and Rhinocerotinae that includes all the living rhinoceroses, settling a debate based on fossil evidence and confirming that the two lineages had diverged by the Eocene. As the last surviving member of the Elasmotheriinae, the demise of the 'Siberian unicorn' marked the extinction of this subfamily.

Co-extinctions annihilate planetary life during extreme environmental change

Climate change and human activity are dooming species at an unprecedented rate via a plethora of direct and indirect, often synergic, mechanisms. Among these, primary extinctions driven by environmental change could be just the tip of an enormous extinction iceberg. As our understanding of the importance of ecological interactions in shaping ecosystem identity advances, it is becoming clearer how the disappearance of consumers following the depletion of their resources — a process known as ‘co-extinction’ — is more likely the major driver of biodiversity loss. Although the general relevance of co-extinctions is supported by a sound and robust theoretical background, the challenges in obtaining empirical information about ongoing (and past) co-extinction events complicate the assessment of their relative contributions to the rapid decline of species diversity even in well-known systems, let alone at the global scale. By subjecting a large set of virtual Earths to different trajectories of extreme environmental change (global heating and cooling), and by tracking species loss up to the complete annihilation of all life either accounting or not for co-extinction processes, we show how ecological dependencies amplify the direct effects of environmental change on the collapse of planetary diversity by up to ten times.

Comparing genetic diversity and demographic history in co-distributed wild South American camelids

Vicuñas and guanacos are two species of wild South American camelids that are key ruminants in the ecosystems where they occur. Although closely related, these species feature differing ecologies and life history characters, which are expected to influence both their genetic diversity and population differentiation at different spatial scales. Here, using mitochondrial and microsatellite genetic markers, we show that vicuña display lower genetic diversity within populations than guanaco but exhibit more structure across their Peruvian range, which may reflect a combination of natural genetic differentiation linked to geographic isolation and recent anthropogenic population declines. Coalescent-based demographic analyses indicate that both species have passed through a strong bottleneck, reducing their effective population sizes from over 20,000 to less than 1000 individuals. For vicuña, this bottleneck is inferred to have taken place ~3300 years ago, but to have occurred more recently for guanaco at ~2000 years ago. These inferred dates are considerably later than the onset of domestication (when the alpaca was domesticated from the vicuña while the llama was domesticated from the guanaco), coinciding instead with a major human population expansion following the mid-Holocene cold period. As importantly, they imply earlier declines than the well-documented Spanish conquest, where major mass mortality events were recorded for Andean human and camelid populations. We argue that underlying species' differences and recent demographic perturbations have influenced genetic diversity in modern vicuña and guanaco populations, and these processes should be carefully evaluated in the development and implementation of management strategies for these important genetic resources.

Lama guanicoe remains from the Chaco ecoregion (Córdoba, Argentina): An osteological approach to the characterization of a relict wild population

Guanacos (Lama guanicoe) are large ungulates that have been valued by human populations in South America since the Late Pleistocene. Even though they were very abundant until the end of the 19th century (before the high deforestation rate of the last decades), guanacos have nearly disappeared in the Gran Chaco ecoregion, with relicts and isolated populations surviving in some areas, such as the shrubland area near the saline depressions of Córdoba province, Argentina. In this report, we present the first data from a locally endangered guanaco wild population, through the study of skeletal remains recovered in La Providencia ranch. Our results showed that most of the elements belonged to adults aged between 36 and 96 months; sex evaluation showed similar numbers of males and females. Statistical analysis of the body size of modern samples from Córdoba demonstrated that guanacos from the Chaco had large dimensions and presented lower size variability than the modern and archaeological specimens in our database. Moreover, they exhibited dimensions similar to those of modern guanacos from Patagonia and San Juan, and to archaeological specimens from Ongamira and Cerro Colorado, although further genetic studies are needed to corroborate a possible phylogenetic relationship. Finally, we used archaeozoological techniques to provide a first characterization of a relict guanaco population from the Chaco ecoregion, demonstrating its value to the study of modern skeletal remains and species conservation biology.

Ancient DNA from Giant Panda (Ailuropoda melanoleuca) of South-Western China Reveals Genetic Diversity Loss during the Holocene

The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cytb and 12s rRNA, partial 16s rRNA and ND1, and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae). Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential.

Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia

Aboriginal Australians represent one of the longest continuous cultural complexes known. Archaeological evidence indicates that Australia and New Guinea were initially settled approximately 50 thousand years ago (ka); however, little is known about the processes underlying the enormous linguistic and phenotypic diversity within Australia. Here we report 111 mitochondrial genomes (mitogenomes) from historical Aboriginal Australian hair samples, whose origins enable us to reconstruct Australian phylogeographic history before European settlement. Marked geographic patterns and deep splits across the major mitochondrial haplogroups imply that the settlement of Australia comprised a single, rapid migration along the east and west coasts that reached southern Australia by 49-45 ka. After continent-wide colonization, strong regional patterns developed and these have survived despite substantial climatic and cultural change during the late Pleistocene and Holocene epochs. Remarkably, we find evidence for the continuous presence of populations in discrete geographic areas dating back to around 50 ka, in agreement with the notable Aboriginal Australian cultural attachment to their country.

Domestication and human demographic history in South America

OBJECTIVES

The early groups of hunter-gatherers who peopled South America faced significant ecological changes in their trophic niche for a relatively short period after the initial peopling. In particular, the incorporation of cultigens during the Holocene led to a wider trophic niche and probably to an increased carrying capacity of the environment. Here, we study the relationship between the incorporation of domestic resources during the Holocene and the demographic dynamics of human populations at a regional scale in South America.

MATERIAL AND METHODS

We employ mitochondrial DNA (mtDNA), radiocarbon data and Bayesian methods to estimate differences in population size, human occupation and explore the demographic changes of human populations in three regions (i.e., South-Central Andes, Northwest, and South Patagonia). We also use archaeological evidence to infer the main diet changes in these regions.

RESULTS

The absolute population size during the later Late Holocene was fifteen times larger in the South-Central Andes than in Northwest Patagonia, and two times larger in the latter region than in South Patagonia. The South-Central Andes display the earlier and more abrupt population growth, beginning about 9000 years BP, whereas Northwest Patagonia exhibits a more slow growth, beginning about 7000-7500 years BP. South Patagonia represents a later and slower population increase.

DISCUSSION

In this work we uncovered a well-supported pattern of the demographic change in the populations from South-Central Andes and Patagonia, obtained on the basis of different data and quantitative approaches, which suggests that the incorporation of domestic resources was paramount for the demographic expansion of these populations during the Holocene.

Humans rather than climate the primary cause of Pleistocene megafaunal extinction in Australia

Environmental histories that span the last full glacial cycle and are representative of regional change in Australia are scarce, hampering assessment of environmental change preceding and concurrent with human dispersal on the continent ca. 47,000 years ago. Here we present a continuous 150,000-year record offshore south-western Australia and identify the timing of two critical late Pleistocene events: wide-scale ecosystem change and regional megafaunal population collapse. We establish that substantial changes in vegetation and fire regime occurred ∼70,000 years ago under a climate much drier than today. We record high levels of the dung fungus Sporormiella, a proxy for herbivore biomass, from 150,000 to 45,000 years ago, then a marked decline indicating megafaunal population collapse, from 45,000 to 43,100 years ago, placing the extinctions within 4,000 years of human dispersal across Australia. These findings rule out climate change, and implicate humans, as the primary extinction cause.

Megafaunal extinction in Australia has been attributed to both climate change and human causation. Here, van der Kaars et al. present a 150,000 year record offshore southwest Australia in which they refine the timing and nature of regional ecosystem changes and megafaunal population collapse.