Search

Past and ongoing human activities have shaped the geographical ranges and diversity of species. New genomic techniques applied to degraded samples, such as those from natural history collections, can uncover the complex evolutionary consequences of human pressures and generate baselines for interpreting magnitudes of species loss or persistence relevant to conservation. Here we integrate mitogenomic data with historical records from a recently rediscovered Bahamian hutia ( Geocapromys ingrahami ; (FMP Z02816)) specimen at the Fairbanks Museum & Planetarium (Vermont, USA) to determine when and where the specimen was collected and to place it in a phylogenetic context with specimens that both predate (palaeontological) and postdate (archaeological) human arrival in The Bahamas. We determined that this specimen was part of the same population as the named holotype specimen in 1891 on East Plana Cay (EPC). Bahamian hutia populations were widely extirpated following European colonization. Today, EPC hosts the last remaining natural Bahamian hutia population. Mitogenomic data places the focal specimen within the southern Bahamian hutia population, which is now largely restricted to EPC. The results reveal previously undocumented genetic continuity among the EPC population for at least the past 500 years, highlighting how ‘dark’ museum specimens inform new conservation-relevant understandings of diversity.

Species reintroductions involve considerable uncertainty, especially in highly altered landscapes. Historical, geographic, and taxonomic analogies can help reduce this uncertainty by enabling conservationists to better assess habitat suitability in proposed reintroduction sites. We illustrate this approach using the example of the California grizzly, an iconic species proposed for reintroduction.

Ancient biomolecule analyses are proving increasingly useful in the study of evolutionary patterns, including extinct organisms. Proteomic sequencing techniques complement genomic approaches, having the potential to examine lineages further back in time than achievable using ancient DNA, given the less stringent preservation requirements. In this study, we demonstrate the ability to use collagen sequence analyses via proteomics to assist species delimitation as a foundation for informing evolutionary patterns. We uncover biogeographic information of an enigmatic and recently extinct lineage of Nesophontes across their range on the Caribbean islands. First, evolutionary relationships reconstructed from collagen sequences reaffirm the affinity of Nesophontes and Solenodon as sister taxa within Solenodonota. This relationship helps lay the foundation for testing geographical isolation hypotheses across islands within the Greater Antilles, including movement from Cuba toward Hispaniola. Second, our results are consistent with Cuba having just two species of Nesophontes (N. micrus and N. major) that exhibit intrapopulation morphological variation. Finally, analysis of the recently described species from the Cayman Islands (N. hemicingulus) indicates that it is a closer relative to N. major rather than N. micrus as previously speculated. This proteomic sequencing improves our understanding of the origin, evolution, and distribution of this extinct mammal lineage, particularly with respect to the approximate timing of speciation. Such knowledge is vital for this biodiversity hotspot, where the magnitude of recent extinctions may obscure true estimates of species richness in the past.

Conservation paleobiology has coalesced over the last two decades since its formal coining, united by the goal of applying geohistorical records to inform the conservation, management, and restoration of biodiversity and ecosystem services. Yet, the field is still attempting to form an identity distinct from its academic roots. Here, we ask a deceptively simple question: What is conservation paleobiology? To track its development as a field, we synthesize complementary perspectives from a survey of the scientific community that is familiar with conservation paleobiology and a systematic literature review of publications that use the term. We present an overview of conservation paleobiology’s research scope and compare survey participants’ perceptions of what it is and what it should be as a field. We find that conservation paleobiologists use a variety of geohistorical data in their work, although research is typified by near-time records of marine molluscs and terrestrial mammals collected over local to regional spatial scales. Our results also confirm the field’s broad disciplinary basis: survey participants indicated that conservation paleobiology can incorporate information from a wide range of disciplines spanning conservation biology, ecology, historical ecology, paleontology, and archaeology. Finally, we show that conservation paleobiologists have yet to reach a consensus on how applied the field should be in practice. The survey revealed that many participants thought the field should be more applied but that most do not currently engage with conservation practice. Reflecting on how conservation paleobiology has developed over the last two decades, we discuss opportunities to promote community cohesion, strengthen collaborations within conservation science, and align training priorities with the field’s identity as it continues to crystallize.

Significance Multiple representatives of eulipotyphlan mammals (shrews, hedgehogs, moles, and solenodons) are venomous, but little is known about the evolutionary history and composition of their oral venom systems. Herein we characterized venom from the endangered Hispaniolan solenodon (Solenodon paradoxus) and find that it consists of hypotensive proteins likely used to facilitate vertebrate prey capture. We demonstrate that venom has evolved independently on at least 4 occasions in eulipotyphlans, and that molecular components of these venoms have also evolved convergently, with kallikrein-1 proteins coopted as toxins in both solenodons and shrews following their divergence over 70 million years ago. Our findings present an elegant example of convergent molecular evolution and highlight that mammalian venom systems may be subjected to evolutionary constraints., Venom systems are key adaptations that have evolved throughout the tree of life and typically facilitate predation or defense. Despite venoms being model systems for studying a variety of evolutionary and physiological processes, many taxonomic groups remain understudied, including venomous mammals. Within the order Eulipotyphla, multiple shrew species and solenodons have oral venom systems. Despite morphological variation of their delivery systems, it remains unclear whether venom represents the ancestral state in this group or is the result of multiple independent origins. We investigated the origin and evolution of venom in eulipotyphlans by characterizing the venom system of the endangered Hispaniolan solenodon (Solenodon paradoxus). We constructed a genome to underpin proteomic identifications of solenodon venom toxins, before undertaking evolutionary analyses of those constituents, and functional assessments of the secreted venom. Our findings show that solenodon venom consists of multiple paralogous kallikrein 1 (KLK1) serine proteases, which cause hypotensive effects in vivo, and seem likely to have evolved to facilitate vertebrate prey capture. Comparative analyses provide convincing evidence that the oral venom systems of solenodons and shrews have evolved convergently, with the 4 independent origins of venom in eulipotyphlans outnumbering all other venom origins in mammals. We find that KLK1s have been independently coopted into the venom of shrews and solenodons following their divergence during the late Cretaceous, suggesting that evolutionary constraints may be acting on these genes. Consequently, our findings represent a striking example of convergent molecular evolution and demonstrate that distinct structural backgrounds can yield equivalent functions.

While trends in tropical deforestation are alarming, conservation biologists are increasingly recognizing the potential for species survival in human-modified landscapes. Identifying the factors underlying such persistence, however, requires basic ecological knowledge of a species' resource use. Here, we generate such data to guide conservation of an understudied venomous mammal, the Hispaniolan solenodon (

An accurate understanding of biodiversity of the past is critical for contextualizing biodiversity patterns and trends in the present. Emerging techniques are refining our ability to decipher otherwise cryptic human-mediated species translocations across the Quaternary, yet these techniques are often used in isolation, rather than part of an interdisciplinary hypothesis-testing toolkit, limiting their scope and application. Here we illustrate the use of such an integrative approach and report the occurrence of North America’s largest terrestrial mammalian carnivore, the short-faced bear, Arctodus simus, from Daisy Cave (CA-SMI-261), an important early human occupation site on the California Channel Islands. We identified the specimen by corroborating morphological, protein, and mitogenomic lines of evidence, and evaluated the potential natural and anthropogenic mechanisms of its transport and deposition. While representing just a single specimen, our combination of techniques opened a window into the behavior of an enigmatic species, suggesting that A. simus was a wide-ranging scavenger utilizing terrestrial and marine carcasses. This discovery highlights the utility of bridging archaeological and paleontological datasets to disentangle complex biogeographic scenarios and reveal unexpected biodiversity for island systems worldwide.

The developmental transition to motherhood requires gene expression changes that alter the brain to drive the female to perform maternal behaviors. We broadly examined the global transcriptional response in the mouse maternal brain, by examining four brain regions: hypothalamus, hippocampus, neocortex, and cerebellum, in virgin females, two pregnancy time points, and three postpartum time points. We find that overall there are hundreds of differentially expressed genes, but each brain region and time point shows a unique molecular signature, with only 49 genes differentially expressed in all four regions. Interestingly, a set of “early-response genes” is repressed in all brain regions during pregnancy and postpartum stages. Several genes previously implicated in underlying postpartum depression change expression. This study serves as an atlas of gene expression changes in the maternal brain, with the results demonstrating that pregnancy, parturition, and postpartum maternal experience substantially impact diverse brain regions.

The human-mediated movement of species across biogeographic boundaries—whether intentional or accidental—is dramatically reshaping the modern world. Yet humans have been reshaping ecosystems and translocating species for millennia, and acknowledging the deeper roots of these phenomena is important for contextualizing present-day biodiversity loss, ecosystem functioning and management needs. Here, we present the first database of terrestrial vertebrate species introductions spanning the entire anthropogenic history of a system: the Caribbean. We employ this approximately 7000-year dataset to assess the roles of historical contingency and priority effects in shaping present-day community structure and conservation outcomes, finding that serial human colonization events contributed to habitat modifications and species extinctions that shaped the trajectories of subsequent species introductions by other human groups. We contextualized spatial and temporal patterns of species introductions within cultural practices and population histories of Indigenous, colonial and modern human societies, and show that the taxonomic and biogeographic diversity of introduced species reflects diversifying reasons for species introductions through time. Recognition of the complex social and economic structures across the 7000-year human history of the Caribbean provides the necessary context for interpreting the formation of an Anthropocene biota.

As fossilized feces, coprolites represent direct evidence of animal behavior captured in the fossil record. They encapsulate past ecological interactions between a consumer and its prey and, when they contain plant material, can also guide paleoenvironmental reconstructions. Here we describe the first coprolites from the lagerstätte Rancho La Brea (RLB) in Los Angeles, California, which also represent the first confirmed coprolites from an asphaltic (“tar pit”) context globally. Combining multiple lines of evidence, including radiocarbon dating, body size reconstructions, stable isotope analysis, scanning electron microscopy, and sediment analyses, we document hundreds of rodent coprolites found in association with plant material, and tentatively assign them to the woodrat genus Neotoma. Neotoma nests (i.e., middens) and their associated coprolites inform paleoclimatic reconstructions for the arid southwestern US but are not typically preserved in coastal areas due to environmental and physiological characteristics. The serendipitous activity of an asphalt seep preserved coprolites and their original cellulosic material for 50,000 years at RLB, yielding a snapshot of coastal California during Marine Isotope Stage 3. This discovery augments the proxies available at an already critical fossil locality and highlights the potential for more comprehensive paleoenvironmental analyses at other asphaltic localities globally.

The extensive postglacial mammal losses in the West Indies provide an opportunity to evaluate extinction dynamics, but limited data have hindered our ability to test hypotheses. Here, we analyze the tempo and dynamics of extinction using a novel data set of faunal last-appearance dates and human first-appearance dates, demonstrating widespread overlap between humans and now-extinct native mammals. Humans arrived in four waves (Lithic, Archaic, Ceramic, and European), each associated with increased environmental impact. Large-bodied mammals and several bats were extinct by the Archaic, following protracted extinction dynamics perhaps reflecting habitat loss. Most small-bodied rodents and lipotyphlan insectivores survived the Ceramic, but extensive landscape transformation and the introduction of invasive mammals following European colonization caused further extinctions, leaving a threatened remnant fauna. Both large- and small-bodied nonvolant mammals disappeared, reflecting complex relationships between body size, ecology, and anthropogenic change. Extinct bats were generally larger species, paralleling declines from natural catastrophes.

The Jamaican primate, Xenothrix mcgregori, regarded variously as either a pitheciid or a stem platyrrhine, was the terminal branch of a clade that likely entered the West Indies at least as early as the Early Miocene, although its lineage is represented by fossils of Quaternary age only. We present a new direct radiocarbon-based date of 1,477 ± 34 calibrated years before present (cal BP) for the last documented appearance of this species in the fossil record. We employed the Gaussian-resampled, inverse-weighted McInerny et al. (GRIWM) method to estimate the extinction date of X. mcgregori, based on the data presented here as well as 6 other dates derived from X. mcgregori sites. On this basis, we estimated a last occurrence ∼900 BP. The cause or causes of this extinction, as well as the many others that occurred in late Quaternary of the Greater Antilles, remain a matter of debate. The likeliest inference is that these losses were largely if not completely anthropogenically driven. Although many species and populations of primates are critically threatened today, the loss of X. mcgregori stands as the most recent species-level extinction within Anthropoidea corroborated by radiometric evidence.

The Caribbean archipelago is a hotspot of biodiversity characterized by a high rate of extinction. Recent studies have examined these losses, but the causes of the Antillean Late Quaternary vertebrate extinctions, and especially the role of humans, are still unclear. Current results provide support for climate-related and human-induced extinctions, but often downplaying other complex bio-ecological factors that are difficult to model or to detect from the fossil and archaeological record. Here, we discuss Caribbean vertebrate extinctions and the potential role of humans derived from new and existing fossil and archaeological data from Cuba. Our results indicate that losses of Cuba’s native fauna occurred in three waves: one during the late Pleistocene and early Holocene, a second during the middle Holocene, and a third one during the last 2 ka, coinciding with the arrival of agroceramists and the early Europeans. The coexistence of now-extinct species with multiple cultural groups in Cuba for over 4 ka implies that Cuban indigenous non-ceramic cultures exerted far fewer extinction pressures to native fauna than the later agroceramists and Europeans that followed. This suggests a determinant value to increased technological sophistication and demographics as the most plausible effective extinction drivers.

Drivers of Late Quaternary megafaunal extinctions are relevant to modern conservation policy in a world of growing human population density, climate change, and faunal decline. Traditional debates tend toward global solutions, blaming either dramatic climate change or dispersals of Homo sapiens to new regions. Inherent limitations to archaeological and paleontological data sets often require reliance on scant, poorly resolved lines of evidence. However, recent developments in scientific technologies allow for more local, context-specific approaches. In the present article, we highlight how developments in five such methodologies (radiocarbon approaches, stable isotope analysis, ancient DNA, ancient proteomics, microscopy) have helped drive detailed analysis of specific megafaunal species, their particular ecological settings, and responses to new competitors or predators, climate change, and other external phenomena. The detailed case studies of faunal community composition, extinction chronologies, and demographic trends enabled by these methods examine megafaunal extinctions at scales appropriate for practical understanding of threats against particular species in their habitats today.

As the last habitable continent colonized by humans, the site of multiple domestication hotspots, and the location of the largest Pleistocene megafaunal extinction, South America is central to human prehistory. Yet remarkably little is known about human population dynamics during colonization, subsequent expansions, and domestication. Here we reconstruct the spatiotemporal patterns of human population growth in South America using a newly aggregated database of 1,147 archaeological sites and 5,464 calibrated radiocarbon dates spanning fourteen thousand to two thousand years ago (ka). We demonstrate that, rather than a steady exponential expansion, the demographic history of South Americans is characterized by two distinct phases. First, humans spread rapidly throughout the continent, but remained at low population sizes for 8,000 years, including a 4,000-year period of 'boom-and-bust' oscillations with no net growth. Supplementation of hunting with domesticated crops and animals had a minimal impact on population carrying capacity. Only with widespread sedentism, beginning ~5 ka, did a second demographic phase begin, with evidence for exponential population growth in cultural hotspots, characteristic of the Neolithic transition worldwide. The unique extent of humanity's ability to modify its environment to markedly increase carrying capacity in South America is therefore an unexpectedly recent phenomenon.

Island species are difficult to conserve because they face the synergy of climate change, invasive species, deforestation, and increasing human population densities in areas where land mass is shrinking. The Caribbean island of Hispaniola presents particular challenges because of geopolitical complexities that span 2 countries and hinder coordinated management of species across the island. We employed species distribution modeling to evaluate the impacts of climatic change and anthropogenic activities on the distribution of an endemic mammal of conservation concern, the Hispaniolan solenodon (Solenodon paradoxus). We aggregated occurrence points for this poorly known species for the Last Glacial Maximum (LGM) and the present (1975-2016) based on museum collections, online biodiversity databases, and new field surveys. We quantified degree of overlap between periods and scenarios with Schoener's D. Through a conservation paleobiology lens, we found that over time humans played an increasing role in shaping the distribution of S. paradoxus, thus, providing a foundation for developing conservation strategies on appropriate spatiotemporal scales. Human population density was the single most important predictor of S. paradoxus occurrence. Densities166 people/kmUso del Pasado para Contextualizar los Impactos Antropogénicos en la Distribución Presente y Futura de un Mamífero Endémico del Caribe Resumen Las especies insulares son difíciles de conservar ya que enfrentan la sinergia del cambio climático, las especies invasoras, la deforestación y la densidad creciente de la población humana en áreas en donde la masa de tierra se está encogiendo. La isla caribeña de La Española representa un reto particular debido a las complejidades geopolíticas que abarcan a dos países y obstaculizan el manejo coordinado de las especies en toda la isla. Empleamos el modelado de distribución de especies para evaluar los impactos del cambio climático y las actividades antropogénicas sobre la distribución de un mamífero endémico de importancia para la conservación: el solenodonte de La Española (Solenodon paradoxus). Agregamos puntos de presencia para esta especie muy poco conocida durante el Último Máximo Glacial (LGM, en inglés) y durante el presente (1975-2016) con base en colecciones de museos, bases de datos de biodiversidad en línea y nuevos censos de campo. A través de este lente de paleobiología de la conservación encontramos que con el tiempo los humanos tuvieron un papel cada vez mayor en la distribución de S. paradoxus, proporcionando así los cimientos para el desarrollo de estrategias de conservación a escalas espacio-temporales adecuadas. La densidad de la población humana fue el pronosticador más importante de la presencia de S. paradoxus. Las densidades mayores a 166 personas/km

Understanding extinction drivers in a human-dominated world is necessary to preserve biodiversity. We provide an overview of Quaternary extinctions and compare mammalian extinction events on continents and islands after human arrival in system-specific prehistoric and historic contexts. We highlight the role of body size and life-history traits in these extinctions. We find a significant size-bias except for extinctions on small islands in historic times. Using phylogenetic regression and classification trees, we find that while life-history traits are poor predictors of historic extinctions, those associated with difficulty in responding quickly to perturbations, such as small litter size, are good predictors of prehistoric extinctions. Our results are consistent with the idea that prehistoric and historic extinctions form a single continuing event with the same likely primary driver, humans, but the diversity of impacts and affected faunas is much greater in historic extinctions.

BACKGROUND The pace and magnitude of human-caused global change has accelerated dramatically over the past 50 years, overwhelming the capacity of many ecosystems and species to maintain themselves as they have under the more stable conditions that prevailed for at least 11,000 years. The next few decades threaten even more rapid transformations because by 2050, the human population is projected to grow by 3 billion while simultaneously increasing per capita consumption. Thus, to avoid losing many species and the crucial aspects of ecosystems that we need—for both our physical and emotional well-being—new conservation paradigms and integration of information from conservation biology, paleobiology, and the Earth sciences are required. ADVANCES Rather than attempting to hold ecosystems to an idealized conception of the past, as has been the prevailing conservation paradigm until recently, maintaining vibrant ecosystems for the future now requires new approaches that use both historical and novel conservation landscapes, enhance adaptive capacity for ecosystems and organisms, facilitate connectedness, and manage ecosystems for functional integrity rather than focusing entirely on particular species. Scientific breakthroughs needed to underpin such a paradigm shift are emerging at the intersection of ecology and paleobiology, revealing (i) which species and ecosystems will need human intervention to persist; (ii) how to foster population connectivity that anticipates rapidly changing climate and land use; (iii) functional attributes that characterize ecosystems through thousands to millions of years, irrespective of the species that are involved; and (iv) the range of compositional and functional variation that ecosystems have exhibited over their long histories. Such information is necessary for recognizing which current changes foretell transitions to less robust ecological states and which changes may signal benign ecosystem shifts that will cause no substantial loss of ecosystem function or services. Conservation success will also increasingly hinge on choosing among different, sometimes mutually exclusive approaches to best achieve three conceptually distinct goals: maximizing biodiversity, maximizing ecosystem services, and preserving wilderness. These goals vary in applicability depending on whether historical or novel ecosystems are the conservation target. Tradeoffs already occur—for example, managing to maximize certain ecosystem services upon which people depend (such as food production on farm or rangelands) versus maintaining healthy populations of vulnerable species (such as wolves, lions, or elephants). In the future, the choices will be starker, likely involving decisions such as which species are candidates for managed relocation and to which areas, and whether certain areas should be off limits for intensive management, even if it means losing some species that now live there. Developing the capacity to make those choices will require conservation in both historical and novel ecosystems and effective collaboration of scientists, governmental officials, nongovernmental organizations, the legal community, and other stakeholders. OUTLOOK Conservation efforts are currently in a state of transition, with active debate about the relative importance of preserving historical landscapes with minimal human impact on one end of the ideological spectrum versus manipulating novel ecosystems that result from human activities on the other. Although the two approaches are often presented as dichotomous, in fact they are connected by a continuum of practices, and both are needed. In most landscapes, maximizing conservation success will require more integration of paleobiology and conservation biology because in a rapidly changing world, a long-term perspective (encompassing at least millennia) is necessary to specify and select appropriate conservation targets and plans. Although adding this long-term perspective will be essential to sustain biodiversity and all of the facets of nature that humans need as we continue to rapidly change the world over the next few decades, maximizing the chances of success will also require dealing with the root causes of the conservation crisis: rapid growth of the human population, increasing per capita consumption especially in developed countries, and anthropogenic climate change that is rapidly pushing habitats outside the bounds experienced by today’s species.