The exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by Homo sapiens. A crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets. Such data suggest that, by the Late Pleistocene, humans had begun to engage in activities that have led to alterations in the distributions of a vast array of species across most, if not all, taxonomic groups. Changes to biodiversity have included extinctions, extirpations, and shifts in species composition, diversity, and community structure. We outline key examples of these changes, highlighting findings from the study of new datasets, like ancient DNA (aDNA), stable isotopes, and microfossils, as well as the application of new statistical and computational methods to datasets that have accumulated significantly in recent decades. We focus on four major phases that witnessed broad anthropogenic alterations to biodiversity—the Late Pleistocene global human expansion, the Neolithic spread of agriculture, the era of island colonization, and the emergence of early urbanized societies and commercial networks. Archaeological evidence documents millennia of anthropogenic transformations that have created novel ecosystems around the world. This record has implications for ecological and evolutionary research, conservation strategies, and the maintenance of ecosystem services, pointing to a significant need for broader cross-disciplinary engagement between archaeology and the biological and environmental sciences.

The reshaping of global biodiversity is one of the most significant impacts humans have had on Earth’s ecosystems. As our planet experiences its sixth “mass extinction event” (1), the effect of anthropogenic landscape modification, habitat fragmentation, overexploitation, and species invasions could not be more apparent (2, 3). These transformations are linked largely to the industrial economies, burgeoning populations, and dense transport networks of contemporary human societies. Accordingly, the human-mediated alteration of species distributions has been characterized as a modern phenomenon with limited, and largely insignificant, historical antecedents. This conventional understanding fails to account for several decades of archaeological, paleoecological, and genetic research that reveal a long and widespread history of human transformation of global biodiversity (4⇓–6). The evolutionary trajectory of Homo sapiens has seen growing capacities for advanced cognition and demographic and geographic expansion, along with an exponential increase in the scope and impact of human niche constructing activities (7) that have culminated in fundamental changes to planetary ecosystems.

Drawing upon findings from a range of new methods and datasets, including new cross-disciplinary research programs, we explore this uniquely human trajectory and reveal a pattern of significant long-term, anthropogenic shaping of species distributions on all of the earth’s major occupied continents and islands. We show that, even before the Age of Discovery, cumulative human activities over millennia resulted in dramatic changes to the abundance and geographic range of a diverse array of organisms across taxonomic groups. Few, if any, regions can be characterized as pristine. Extinction has been the starkest of these anthropogenic impacts, but widespread changes to species abundance, composition, community structure, richness, and genetic diversity as a result of human niche construction are also increasingly demonstrable and of equally lasting impact.

We highlight the role of new classes of data, such as ancient DNA (aDNA), stable isotopes, and microfossils, as well as new approaches, including powerful morphometric, chronometric, computational, and statistical methods, for understanding changes to species distributions at various scales (Fig. 1). The increasingly systematic application of traditional environmental archaeology methods in the last few decades is also yielding new insights. While acknowledging that human engagement in niche construction has very early origins, we focus on examples from four key phases of more recent and wide-reaching anthropogenic change: the Late Pleistocene near-global dispersal of H. sapiens; the emergence and spread of agriculture beginning in the Early Holocene; the colonization of the world’s islands; and the premodern expansion of urbanization and trade beginning in the Bronze Age. Although not exhaustive, our review highlights key trends, including the significant prehistoric and historic reorganization of species distributions at local, regional, and intercontinental scales; a broadly accelerating but uneven rate of alien species introductions across multiple geographical regions; and the involvement of a wide range of species, including plant and animal domesticates, as well as a diverse array of wild, commensal, invasive, and pathogenic species. We emphasize the role of these cumulative changes in contributing to the creation of novel ecosystems over the long term. We conclude by considering the implications of an archaeologically informed perspective on contemporary biodiversity for how we understand, study, and conserve the earth’s biomes, as well as how we comprehend the evolutionary pressures exerted by human ecosystem engineering.

Four Key Phases of Anthropogenic Transformation

Global Colonization. Fossil evidence demonstrates that H. sapiens was present ∼195,000 y ago (195 ka) in East Africa (19) and that, by 12 ka, our species had dispersed to the far corners of Eurasia, Australia, and the Americas (20). Mounting evidence indicates that these Late Pleistocene dispersals, and the increase in global human populations with which they are associated, were linked in complex ways with a variety of species extinctions, extirpations, translocations, and new modes of niche modification. Evaluating Pleistocene anthropogenic impacts remains challenging, but novel methods and approaches are providing solutions to long-standing problems posed by limited preservation and chronological resolution. New data link the geographic and demographic expansion of H. sapiens to fire regime change and transformations to plant community composition. For example, pollen and microcharcoal records indicate that the early colonists of New Guinea deliberately burned and disturbed tropical rainforests to promote the growth of useful plants, especially gap colonizers like yams (Dioscorea spp.), which have been identified from microscopic starch residues extracted from some of the region’s earliest stone tools (21). (For species other than H. sapiens, this manuscript employs common species names, although the scientific name for each species discussed is also provided at first mention. For humans, the scientific name is further specified when it is important to distinguish from other hominid species.) Vegetation burning also enhanced hunting opportunities by drawing game and other faunal resources to new plant growth. A human contribution to the shaping of early fire regimes has been demonstrated for Africa and, after human arrival, in Borneo, Australia, and the Americas (22⇓⇓–25). The human-mediated translocation of species now dates back to the Late Pleistocene. For example, the northern common cuscus (Phalanger orientalis), endemic to New Guinea, was transported to eastern Indonesia, the Solomon Islands, and the Bismarck Archipelago beginning ∼20–23 ka, becoming a key subsistence species (26, 27). Other taxa were also moved; together with a species of bandicoot (Echymipera kalubu) and the Admiralty cuscus (Spilocuscus kraemeri), the Canarium indicum tree was introduced to Manus by ∼13 ka, followed a few millennia later by the rat Rattus praetor (26). Translocation patterns mirror patterns of maritime obsidian exchange in Melanesia in the Late Pleistocene and Early Holocene (26). Evidence of human overexploitation has been suggested for some Late Pleistocene faunal sequences. Diverse archaeological assemblages, from Africa, Europe, and South Asia, for example, document the Late Pleistocene appearance of small, quick, and difficult-to-catch game, such as fish, birds, rabbits, rodents and monkeys, that may signal anthropogenic impacts to resource availability (28, 29). Other studies document decreases in the size of certain species, such as limpets and tortoises, that may also reflect resource overexploitation (e.g., refs. 8 and 30). Some of these changes may result from the expansion of bone, stone, shell, fiber, and other tool repertoires in the Late Pleistocene, enabling new forms of intensive exploitation (e.g., refs. 31 and 32). One of the most significant impacts of the Late Pleistocene expansion of our species may have been on megafauna (Fig. S1). The human role in the Late Quaternary extinction episode, which saw at least 101 of 150 genera of Earth’s megafauna (animals larger than 44 kg) go extinct between 50 and 10 ka (33), has long been contentious (e.g., refs. 34⇓–36). Recent analyses support at least a partial anthropogenic impetus in numerous regions, and a dominant human role in others (37, 38). Of particular importance are new global analyses drawing on higher resolution data and computational modeling approaches. These studies indicate an important role for humans and an inverse relationship between severity of extinction and duration of hominin–megafauna coevolution, with uniformly high extinction rates in areas where H. sapiens was the first hominin to arrive (39, 40) (Fig. S1). Fig. S1. Proportions of megafauna known to be extinct in each region of the globe relative to the length of coevolution and contact with humans (genus Homo) (adapted from figure 1C in ref. 39 and figure 1 in ref. 40). The numbers next to each pie chart indicate the total number of megafauna genera originally present within each region. New regional analyses support these findings. For example, recent high-resolution paleoecological and stable isotope data from Australia, where no hominins existed before ∼55 ka, show that megafaunal collapse occurred during a period of climatic stability and most closely correlates with human arrival (41). Improved chronologies for various Australian and Tasmanian sites (e.g., refs. 42 and 43) support anthropogenic rather than climatic explanations for megafaunal extinctions. Chronometric resolution remains poor for South America, although recent studies support a human role in megafaunal extinction in Patagonia (44), whereas data from aDNA studies suggest that climatic extinction drivers were more influential in northern regions (e.g., ref. 45). Implicating humans in Late Pleistocene megafaunal extinctions suggests an anthropogenic role in subsequent and major biosphere transformations that followed their demise (33, 46, 47). Megafauna were keystone species whose disappearance had dramatic effects on ecosystem structure, fire regimes, seed dispersal, land surface albedo, and nutrient availability (41, 46, 48) (Fig. 2A). Fig. 2. Cascade effects of changes to species, showing long-term transformation of landscapes. (A) Impact of eliminating large herbivores (49). (B) Long-term effects of ancient agriculture on soil geochemistry and plant biodiversity in forests (50⇓–52). (C) Limnological responses to cultural disturbance of lake watershed (53, 54).

Emergence and Spread of Agriculture and Pastoralism. The beginning of the Holocene (<11.7 ka) witnessed fundamental shifts in climatic and geological regimes globally, as well as in human societies. The Early to Middle Holocene in many regions worldwide saw the beginning of agricultural economies, placing new evolutionary pressures on plants, animals, and microbes, and resulting in major demographic expansions for humans (55). This Neolithic period opened the way for a radical transformation in the human capacity for niche construction, increasingly demonstrated through the accumulation of zooarchaeological and archaeobotanical data, as well as the application of biomolecular techniques. One of the major outcomes of the Neolithic was the inexorable spread of agriculture from ∼14–20 centers of early domestication (56) to encompass large swaths of the Old and New Worlds. This expansion had unprecedented and enduring impacts on species distributions. Key among these transformations was the promotion and expansion of a range of human-favored taxa, including newly created species (and subspecies) of domesticated crops and animals. Cumulative archaeological data show that crops and animals saw significant prehistoric and historic range expansion (Fig. 3). The scale of agriculture and land use in some regions was significant; for example, expansion of land area used for livestock and rice (Oryza sativa) paddy agriculture was sufficient to increase atmospheric methane emissions between 4,000 and 1,000 y B.P. (57) whereas deforestation and tillage are suggested to have contributed to increasing CO 2 over the past 8,000 y (58). Fig. 3. Global spread of selected food crops (red) and domesticated and commensal animals (blue) through time. (A) Wheat (Triticum spp.). (B) Sorghum (Sorghum bicolor). (C) Rice (Oryza sativa, Oryza glaberrima). (D) Cattle (Bos taurus, Bos indicus). (E) Dog (Canis familiaris). (F) Rat (Rattus rattus, Rattus tanezumi, Rattus norvegicus, Rattus exulans). The major spread of rats to global islands beginning by 3 ka is not apparent at the scale shown. (Note that maps use different temporal scales, appropriate to individual species and their temporality of spread; hatching indicates natural distribution.) Modern and aDNA studies are shedding light on patterns of genetic adaptation and hybridization that shaped crop dispersal (e.g., ref. 59) whereas plant microfossil and genetic studies are beginning to clarify the spread of tropical species (e.g., refs. 60 and 61). The geographic expansion of agricultural crops was a complex process that carried along other species and transformed local ecosystems in diverse ways (Fig. 3 A–C). Crops often moved as part of ecological packages that included nondomesticated or weed species. In the European Neolithic, for example, some crop weeds derived ultimately from the Near East whereas others were European plants promoted by anthropogenic disturbance and the novel ecologies of cultivated plots (e.g., ref. 62). Such weeds came to be important components of regional wild vegetation, in some cases becoming more common in regions where they were introduced than in their zones of origin. This naturalization occurred to such a degree that, for many of the most widespread weeds, it is unclear where in the world they originated (63). Domesticated animals also dispersed across the world’s landmasses. New high resolution aDNA, protein, isotope, and geometric-morphometric techniques join standard archaeobiological methods to reveal the expansion of different livestock species across the globe (Fig. 3 D and E). Sheep (Ovis aries), goat (Capra hircus), and cattle (Bos taurus) were domesticated in the Near East ∼10.5 ka and arrived in Europe, Africa, and South Asia within a few millennia (57, 64). Chickens (Gallus gallus) were domesticated in East Asia (although the specific timing and location remains contentious), reached Britain by the second half of the last millennium before the common era (B.C.E.), and now outnumber people by more than three to one (65). Wild boar (Sus spp.) populations in East Asia and Anatolia were domesticated independently, and, like all major animal domesticates, pigs (Sus scrofa) are now associated with humans well outside their natural Old World distribution (66). Dogs (Canis familiaris), the only animal domesticated before the emergence of agricultural societies, are now the most abundant and ubiquitous carnivore, with an estimated 700 million to 1 billion dogs worldwide (67). The biomass of wild vertebrates is now vanishingly small compared with that of domestic animals (68). Neolithic dispersals also featured pathogens. Ancient DNA, stable isotope, and other studies are clarifying the spread of pathogens favored by shifts in diet, lifestyle, mobility, and human–animal relationships with the onset of agriculture. Ancient DNA from Yersinia pestis and Mycobacterium tuberculosis has been identified from Neolithic human skeletons (e.g., refs. 69 and 70) and linked to large-scale population movements (69, 71). Plant and animal pathogens also spread in the Neolithic. The northwest European elm decline (3700–3600 B.C.E.) may have been caused in part by the spread of a pathogen, such as the fungal disease Ophiostoma, carried by the elm bark beetle (Scolytus scolytus), which saw habitat expansion with clearance for agriculture (72). The spread of human populations and the species they favored altered the distributions of existing species, sometimes in synergy with Holocene climatic changes. Numerous regional studies demonstrate the link between Neolithic agriculture and the creation of more open landscapes, facilitated through various means from fire to the cutting and coppicing of trees (73, 74). For example, the early Neolithic corresponded with shifts away from deciduous tree cover in various regions of central and northern Europe (e.g., ref. 74). The spread of farmers into central Africa caused an encroachment on rainforest by some expanded savannah species (75). Early rice cultivation in the coastal wetlands of eastern China was linked to clearance of alder-dominated wetland scrub (76). Early to Middle Holocene forest clearance correlates with a variety of broader species and habitat impacts. The transformation of forests and tall grassland into pastures that began 7–8 ka in central and northern Eurasia is linked to radically increased herbivore load due to the grazing of introduced species (77, 78). Together with forest burning, this activity significantly accentuated climate-induced vegetation change, with resultant changes in albedo in Tibet suggested to have impacted the monsoon system (78). Forest removal and agricultural activities increased erosion and impacted lake biota, including lacustrine microfloras and microfaunas (e.g., diatoms, macrophytes, and foraminifera) (Fig. 2C). Paleolimnological studies in lowland Europe, for example, suggest human-mediated increases in mesotrophic–eutrophic planktonic diatoms, including Asterionella formosa and Fragilaria crotonensis, by 5,000 y B.P. (79).

Island Colonization. The colonization of islands was a feature of H. sapiens expansion from the Late Pleistocene onwards but accelerated significantly in the Holocene as maritime technological advances enabled humans to reach increasingly remote oceanic islands (80). Evidence from global island-focused research programs suggests that ancient humans had major impacts on island ecosystems that often lacked the resilience of continental biomes (81, 82). Island ecologies are often characterized by high endemism, naive and/or disharmonic fauna, and low functional redundancy (83). Thus, the overall impact on islands of human-transported species, anthropogenic fire, deforestation, and predation was often the radical restructuring of island ecosystems. Species translocations to islands were so common in the past that archaeologists often speak of “transported landscapes” (84). These new landscapes included a broad range of domesticated animals, commensals, crops, weeds, microbes, and other species carried by humans. For example, Neolithic colonizers who arrived on Cyprus brought domestic cereals, pulses, sheep, goat, cattle, pigs, domestic dogs, and cats (Felis catus), as well as mainland game animals such as fallow deer (Dama dama), fox (Vulpes vulpes), and wild boar beginning 10.6 ka (64, 85). Polynesian people, expanding across the Pacific after ∼3,500 y B.P. (84), introduced a broad range of domesticated species, including the crops taro (Colocasia esculenta), yam (Dioscorea spp.), and banana (Musa spp.), and such animals as the domestic pig, chicken, dog, and Pacific rat (Rattus exulans). In the Caribbean, Archaic and Ceramic period peoples introduced a variety of species, including wild avocado (Persea americana), manioc/cassava (Manihot esculenta), maize (Zea mays), tobacco (Nicotiana rustica), and various trees, as well as dogs, opossums (Didelphis sp.), guinea pigs (Cavia porcellus), and shrews (Nesophontes edithae) (86). Such introductions played a role in making islands more habitable for humans. Before human habitation, Cyprus had a low density of food animals (85), and the islands of the Pacific often lacked edible plants and possessed limited nonmarine fauna (87). In island Southeast Asia, humans transported a range of domesticates, as well as various species of deer, primate, civet, cuscus, wallaby, bird, shrew, rat, and lizard to generate habitats more favorable to human sustenance (27). Anthropogenic landscapes were created through species introductions, as well as habitat modification, including fire and other means, which reshaped the composition and abundance of native species. On the Pacific island of Tonga, Polynesians introduced at least 40 plant species, mostly trees, shrubs, and herbaceous cultigens (88). They burned and cleared indigenous rainforests, altering the abundance and distribution of species to favor useful native plants such as Canarium harveyi, Casuarina equisetifolia, Erythrina variegata, and Pandanus tectorius (88). Not all translocated plants were introduced for subsistence; paper mulberry (Broussonetia papyrifera), for example, is a fiber crop introduced across the Pacific in prehistory for making barkcloth (89). Numerous species were unintentionally introduced to islands, including commensal and parasitic species adapted to the human niche. Although a variety of plants were deliberately carried to the subtropical islands of Polynesia in the pre-European era, at least 17 were unintentionally introduced weed species (90). Pacific rats and black rats (Rattus rattus) were widely introduced to global islands as accidental stowaways on boats beginning in the Middle Holocene (Fig. 3C), as were house mice (Mus musculus), various commensal shrews and lizards, and numerous insects and land snails, with the movements of many now clarified through genetic and aDNA studies. Genetic data demonstrate that Helicobacter pylori, a human pathogen, moved with prehistoric populations expanding through Melanesia and into the Pacific (91). Extinctions and extirpations were a common consequence of island colonization in prehistory. Thousands of bird populations in the Pacific went extinct after Polynesian colonization (92). One recent study of nonpasserine birds on 41 Pacific islands shows that two-thirds went extinct between initial prehistoric colonization and European contact (93). Bird species extinctions impact important ecosystem processes like decomposition, pollination, and seed dispersal, leading to trophic cascades (94). Human impacts have been primarily responsible for the extinction of four genera of giant sloths in the Caribbean, as well as nine taxa of snakes, lizards, bats, birds, and rodents on Antigua between 2350 and 550 B.C.E. (82, 95). Floral extinctions have not been as well-studied, but a range of island plant species went extinct on islands in prehistoric times. Pollen and wood charcoal analyses demonstrate at least 18 plant extinctions on Rapanui (Easter Island), for example, and show dense palm forest disappearing within 200 y of human settlement (96). New chronometric data are revealing the rapidity with which prehistoric extinctions sometimes unfolded (80). New Zealand saw numerous vertebrate extinctions after Polynesian arrival (e.g., refs. 80 and 92), including the elimination of various species of moa (Dinornis) within two centuries of human colonization (97). Recent studies of sea lion and penguin aDNA show that several New Zealand species once thought to have survived early human impacts were extirpated soon after human arrival and replaced within a few centuries by nonindigenous lineages from the subantarctic region (98). Extinction and extirpation rates underestimate human impacts because not all species under pressure went extinct. Although Hawaiian geese (Branta sandvicensis), unlike other species, survived the prehistoric colonization of Hawaii by humans, aDNA research points to a drastic reduction in their genetic diversity after human arrival (99). Zooarchaeological data from the Caribbean point to the overharvesting and decline of a variety of island marine species beginning ∼2,000 y ago, with biomass, mean trophic level, and average size all radically altered (86). Research on California’s Channel Islands points to similar impacts on a broad range of marine animals as a result of overexploitation by prehistoric hunter-gatherers (81, 82), patterns increasingly recognized on islands around the world.