A warrant for applied palaeozoology

The human side of biodiversity: coevolution of the human niche, palaeo-synanthropy and ecosystem complexity in the deep human past

Today's biodiversity crisis fundamentally threatens the habitability of the planet, thus ranking among the primary human challenges of our time. Much emphasis is currently placed on the loss of biodiversity in the Anthropocene, yet these debates often portray biodiversity as a purely natural phenomenon without much consideration of its human dimensions and frequently lack long-term vistas. This paper offers a deep-time perspective on the key role of the evolving human niche in ecosystem functioning and biodiversity dynamics. We summarize research on past hunter-gatherer ecosystem contributions and argue that human-environment feedback systems with important biodiversity consequences are probably a recurrent feature of the Late Pleistocene, perhaps with even deeper roots. We update current understandings of the human niche in this light and suggest that the formation of palaeo-synanthropic niches in other animals proffers a powerful model system to investigate recursive interactions of foragers and ecosystems. Archaeology holds important knowledge here and shows that ecosystem contributions vary greatly in relation to different human lifeways, some of which are lost today. We therefore recommend paying more attention to the intricate relationship between biodiversity and cultural diversity, contending that promotion of the former depends on fostering the latter. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Spatiotemporal impacts of the Anthropocene on small mammal communities, and the role of small biological preserves in maintaining biodiversity

The multi-faceted impacts of the Anthropocene are increasingly modifying natural ecosystems and threatening biodiversity. Can small protected spaces conserve small mammal diversity across spatial and temporal scales of human impact? We identified small mammal remains from modern raptor pellets and Holocene archeological sites along a human modification gradient in the San Francisco Bay Area, CA and evaluated alpha and beta diversity across sites and time periods. We found that Shannon diversity, standardized species richness, and evenness decrease across modern sites based on level of human modification, with no corresponding change between Holocene sites. Additionally, the alpha diversity of modern sites with moderate and high levels of human modification was significantly lower than the diversity of modern sites with low levels of human modification as well as all Holocene sites. On the other hand, the small mammal communities from Jasper Ridge Biological Preserve, a small protected area, retain Holocene levels of alpha diversity. Jasper Ridge has also changed less over time in terms of overall community composition (beta diversity) than more modified sites. Despite this, Holocene and Anthropocene communities are distinct regardless of study area. Our results suggest that small mammal communities today are fundamentally different from even a few centuries ago, but that even relatively small protected spaces can partially conserve native faunal communities, highlighting their important role in urban conservation.

Leveraging palaeoproteomics to address conservation and restoration agendas

Archaeological and paleontological records offer tremendous yet often untapped potential for examining long-term biodiversity trends and the impact of climate change and human activity on ecosystems. Yet, zooarchaeological and fossil remains suffer various limitations, including that they are often highly fragmented and morphologically unidentifiable, preventing them from being optimally leveraged for addressing fundamental research questions in archaeology, paleontology, and conservation paleobiology. Here, we explore the potential of palaeoproteomics—the study of ancient proteins—to serve as a critical tool for creating richer, more informative datasets about biodiversity change that can be leveraged to generate more realistic, constructive, and effective conservation and restoration strategies into the future.

Mobilizing the past to shape a better Anthropocene

As our planet emerges into a new epoch in which humans dominate the Earth system, it is imperative that societies initiate a new phase of responsible environmental stewardship. Here we argue that information from the past has a valuable role to play in enhancing the sustainability and resilience of our societies. We highlight the ways that past data can be mobilized for a variety of efforts, from supporting conservation to increasing agricultural sustainability and food security. At a practical level, solutions from the past often do not require fossil fuels, can be locally run and managed, and have been tested over the long term. Past failures reveal non-viable solutions and expose vulnerabilities. To more effectively leverage increasing knowledge about the past, we advocate greater cross-disciplinary collaboration, systematic engagement with stakeholders and policymakers, and approaches that bring together the best of the past with the cutting-edge technologies and solutions of tomorrow.

Integrating fish scale and bone isotopic compositions for 'deep time' retrospective studies

Isotopic studies of archived fish scales have tremendous potential to develop long-term retrospectives that provide important insights into how humans have altered aquatic ecosystems. However, fish specimens in museum archives and other repositories typically date to time periods when the impacts of industrial societies may have already caused profound environmental changes. Archaeological fish bones offer an opportunity to bridge this key temporal gap by providing samples spanning from the recent past to as far back as the Pleistocene. Collagen is the primary protein component of both fish scale and bone, but the comparability of isotopic compositions from these tissues has not been established experimentally. To lay the framework for integrating isotopic datasets from these tissues, we compare δ¹³C and δ¹⁵N of bone and scale collagen, as well as other tissues, from fish with life-time controlled diets. Results show that while there is no difference in δ¹³C between scale and bone collagen, there may be a very slight but meaningful inter-tissue offset in δ¹⁵N (<0.3‰). We discuss potential sources of δ¹⁵N variation in scale and bone collagen measurements. Because there is no difference in scale and bone δ¹³C, and the observed offset in δ¹⁵N is very small (less than analytical uncertainty in many studies), our findings demonstrate that collagen isotopic compositions from these tissues should be directly comparable when integrating datasets from modern and ancient samples to build more powerful, millennium-scale isotopic times series. In linking isotopic compositions of collagen from modern, historical (scales), and archaeological (bones) fish, our findings open the way for more nuanced contextualization of how ecosystems functioned prior to large-scale exploitation and how they have responded to mounting anthropogenic pressures in the intervening centuries.

ZooArchNet: Connecting zooarchaeological specimens to the biodiversity and archaeology data networks

Interdisciplinary collaborations and data sharing are essential to addressing the long history of human-environmental interactions underlying the modern biodiversity crisis. Such collaborations are increasingly facilitated by, and dependent upon, sharing open access data from a variety of disciplinary communities and data sources, including those within biology, paleontology, and archaeology. Significant advances in biodiversity open data sharing have focused on neontological and paleontological specimen records, making available over a billion records through the Global Biodiversity Information Facility. But to date, less effort has been placed on the integration of important archaeological sources of biodiversity, such as zooarchaeological specimens. Zooarchaeological specimens are rich with both biological and cultural heritage data documenting nearly all phases of human interaction with animals and the surrounding environment through time, filling a critical gap between paleontological and neontological sources of data within biodiversity networks. Here we describe technical advances for mobilizing zooarchaeological specimen-specific biological and cultural data. In particular, we demonstrate adaptations in the workflow used by biodiversity publisher VertNet to mobilize Darwin Core formatted zooarchaeological data to the GBIF network. We also show how a linked open data approach can be used to connect existing biodiversity publishing mechanisms with archaeoinformatics publishing mechanisms through collaboration with the Open Context platform. Examples of ZooArchNet published datasets are used to show the efficacy of creating this critically needed bridge between biological and archaeological sources of open access data. These technical advances and efforts to support data publication are placed in the larger context of ZooarchNet, a new project meant to build community around new approaches to interconnect zoorchaeological data and knowledge across disciplines.

An 11 000-year-old giant muntjac subfossil from Northern Vietnam: implications for past and present populations

Described at the end of the twentieth century, the large-antlered or giant muntjac, Muntiacus gigas (syn. vuquangensis), is a Critically Endangered species currently restricted to the Annamite region in Southeast Asia. Here we report subfossil evidence of giant muntjac, a mandible fragment dated between 11.1 and 11.4 thousand years before present, from northern Vietnam. We describe morphological and metric criteria for diagnosis and consider the specimen in the context of regional archaeological and palaeontological records of Muntiacus. We then consider the palaeoenvironmental context of the specimen and the implications for habitat requirements for extant populations. The new specimen extends the known spatial and temporal range of giant muntjacs in Vietnam and is further evidence that this species was more widely distributed in the Holocene than current records indicate. While regional proxy evidence indicates a drier climate and more open woodland habitats at the onset of the Holocene, contextual evidence indicates that the specimen derived from an animal inhabiting limestone karst forest. This record also supports the assertion that remnant populations are in a refugial state, as a result of anthropogenic pressures, rather than representing a centre of endemism. These facts underscore the urgent need for the conservation of remaining populations.

Prioritizing sites for conservation based on similarity to historical baselines and feasibility of protection

The concept of shifting baselines in conservation science implies advocacy for the use of historical knowledge to inform these baselines but does not address the feasibility of restoring sites to those baselines. In many regions, conservation feasibility varies among sites due to differences in resource availability, statutory power, and land-owner participation. We used zooarchaeological records to identify a historical baseline of the freshwater mussel community's composition before Euro-American influence at a river-reach scale (i.e., a kilometer stretch of river that is abiotically similar) in the Leon River of central Texas (U.S.A.). We evaluated how the community reference position and the feasibility of conservation might enable identification of sites where conservation actions would preserve historically representative communities and be likely to succeed. We devised a conceptual model that incorporated community information and landscape factors to link the best conservation areas to potential cost and conservation benefits. Using fuzzy ordination, we identified modern mussel beds that were most like the historical baseline. We then quantified housing density and land use near each river reach identified to estimate feasibility of habitat restoration. Using our conceptual framework, we identified reaches of high conservation value (i.e., contain the best mussel beds) and where restoration actions would be most likely to succeed. Reaches above Lake Belton were most similar in species composition and relative abundance to zooarchaeological sites. A subset of these mussel beds occurred in locations where conservation actions appeared most feasible. Our results show how to use zooarchaeological data (biodiversity data often readily available) and estimates of conservation feasibility to inform conservation priorities at a local spatial scale.

The overkill model and its impact on environmental research

Research on human-environment interactions that informs ecological practices and guides conservation and restoration has become increasingly interdisciplinary over the last few decades. Fueled in part by the debate over defining a start date for the Anthropocene, historical disciplines like archeology, paleontology, geology, and history are playing an important role in understanding long-term anthropogenic impacts on the planet. Pleistocene overkill, the notion that humans overhunted megafauna near the end of the Pleistocene in the Americas, Australia, and beyond, is used as prime example of the impact that humans can have on the planet. However, the importance of the overkill model for explaining human-environment interactions and anthropogenic impacts appears to differ across disciplines. There is still considerable debate, particularly within archeology, about the extent to which people may have been the cause of these extinctions. To evaluate how different disciplines interpret and use the overkill model, we conducted a citation analysis of selected works of the main proponent of the overkill model, Paul Martin. We examined the ideas and arguments for which Martin's overkill publications were cited and how they differed between archeologists and ecologists. Archeologists cite overkill as one in a combination of causal mechanisms for the extinctions. In contrast, ecologists are more likely to accept that humans caused the extinctions. Aspects of the overkill argument are also treated as established ecological processes. For some ecologists, overkill provides an analog for modern-day human impacts and supports the argument that humans have "always" been somewhat selfish overconsumers. The Pleistocene rewilding and de-extinction movements are built upon these perspectives. The use of overkill in ecological publications suggests that despite increasing interdisciplinarity, communication with disciplines outside of ecology is not always reciprocal or even.

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.

Insights into the pre-European mammalian fauna of the southern Flinders Ranges, South Australia

Many Australian mammal species have suffered significant declines since European colonisation. During the first century of settlement, information on species distribution was rarely recorded. However, fossil accumulations can assist the reconstruction of historical distributions. We examine a fossil vertebrate assemblage from Mair’s Cave, one of few known from the southern Flinders Ranges, South Australia. The Mair’s Cave assemblage was dominated by mammals but also included birds and reptiles. Of the 18 mammals recovered, two have not previously been recorded from the southern Flinders Ranges, at least one is extinct and seven are recognised as threatened nationally. Characteristics of the assemblage suggest that it was accumulated by a Tyto owl species. Remains of Tyto delicatula and a larger unidentified owl were recovered from the assemblage. Most mammals identified from the assemblage presently occupy Australia’s semiarid zone, but a single specimen of the broad-toothed rat (Mastacomys fuscus), which primarily occurs in high-moisture, low-temperature environments was also recovered. This suggests either that the southern Flinders Ranges once experienced higher past precipitation, or that M. fuscus can tolerate a broader climatic range than its current distribution suggests. Our study contributes new knowledge on the biogeography and ecology of several mammal species, data useful for helping to refine restoration targets.

Lake Ontario salmon (Salmo salar) were not migratory: A long-standing historical debate solved through stable isotope analysis

Lake Ontario once supported a large complex of Atlantic Salmon (Salmo salar) populations that became extinct prior to scientific study. Since the 1860s, research efforts to conserve and reintroduce a sustainable population of Atlantic Salmon have focused on determining whether Lake Ontario's original salmon populations had migrated to the Atlantic Ocean as part of their lifecycle (anadromy), stayed in the lake year-round (potamodromy), or both. We used stable carbon, nitrogen, and sulfur isotope analyses of archaeological bones and historical museum-archived salmon scales to show that the original salmon populations from Lake Ontario completed their entire lifecycle without migrating to the Atlantic Ocean. With a time depth of more than 500 years, our findings provide a unique baseline with significant potential for informing modern restocking and conservation efforts.

Implications of Time-Averaged Death Assemblages for Ecology and Conservation Biology

Biologists increasingly appreciate the importance of community-level attributes in the functioning and temporal turnover of ecosystems, but data other than species richness are difficult to acquire over the habitat-to-regional and decadal-to-millennial scales needed to recognize biodiversity change, discriminate between natural and anthropogenic drivers, and inform theoretical and applied ecology. Death assemblages (DAs)—the actively accumulating organic remains encountered in present-day seabeds and landscapes, as distinct from permanently buried fossil assemblages—are an underexploited source of historical information at precisely these scales. Meta-analyses, dynamic modeling, and individual case studies, particularly of mollusks and mammals, reveal that DAs differ from censused living assemblages (LAs) primarily because they are temporally coarse, time-averaged samples, contrary to concerns that postmortem bias dominates. Temporal pooling predictably damps the ability of DAs to detect small-scale variation, but promotes their ability to inventory rare species; estimate the abundance structure of the metacommunity; document range changes; evaluate historic habitat use; and identify now-absent species, community states, and anthropogenically shifted baselines.

Integrating paleobiology, archeology, and history to inform biological conservation

The search for novel approaches to establishing ecological baselines (reference conditions) is constrained by the fact that most ecological studies span the past few decades, at most, and investigate ecosystems that have been substantially altered by human activities for decades, centuries, or more. Paleobiology, archeology, and history provide historical ecological context for biological conservation, remediation, and restoration. We argue that linking historical ecology explicitly with conservation can help unify related disciplines of conservation paleobiology, conservation archeobiology, and environmental history. Differences in the spatial and temporal resolution and extent (scale) of prehistoric, historic, and modern ecological data remain obstacles to integrating historical ecology and conservation biology, but the prolonged temporal extents of historical ecological data can help establish more complete baselines for restoration, document a historical range of ecological variability, and assist in determining desired future conditions. We used the eastern oyster (Crassostrea virginica) fishery of the Chesapeake Bay (U.S.A.) to demonstrate the utility of historical ecological data for elucidating oyster conservation and the need for an approach to conservation that transcends disciplinary boundaries. Historical ecological studies from the Chesapeake have documented dramatic declines (as much as 99%) in oyster abundance since the early to mid-1800 s, changes in oyster size in response to different nutrient levels from the sixteenth to nineteenth centuries, and substantial reductions in oyster accretion rates (from 10 mm/year to effectively 0 mm/year) from the Late Holocene to modern times. Better integration of different historical ecological data sets and increased collaboration between paleobiologists, geologists, archeologists, environmental historians, and ecologists to create standardized research designs and methodologies will help unify prehistoric, historic, and modern time perspectives on biological conservation.