Across the last ~50,000 years (the late Quaternary) terrestrial vertebrate faunas have experienced severe losses of large species (megafauna), with most extinctions occurring in the Late Pleistocene and Early to Middle Holocene. Debate on the causes has been ongoing for over 200 years, intensifying from the 1960s onward. Here, we outline criteria that any causal hypothesis needs to account for. Importantly, this extinction event is unique relative to other Cenozoic (the last 66 million years) extinctions in its strong size bias. For example, only 11 out of 57 species of megaherbivores (body mass ≥1,000 kg) survived to the present. In addition to mammalian megafauna, certain other groups also experienced substantial extinctions, mainly large non-mammalian vertebrates and smaller but megafauna-associated taxa. Further, extinction severity and dates varied among continents, but severely affected all biomes, from the Arctic to the tropics. We synthesise the evidence for and against climatic or modern human (Homo sapiens) causation, the only existing tenable hypotheses. Our review shows that there is little support for any major influence of climate, neither in global extinction patterns nor in fine-scale spatiotemporal and mechanistic evidence. Conversely, there is strong and increasing support for human pressures as the key driver of these extinctions, with emerging evidence for an initial onset linked to pre-sapiens hominins prior to the Late Pleistocene. Subsequently, we synthesize the evidence for ecosystem consequences of megafauna extinctions and discuss the implications for conservation and restoration. A broad range of evidence indicates that the megafauna extinctions have elicited profound changes to ecosystem structure and functioning. The late-Quaternary megafauna extinctions thereby represent an early, large-scale human-driven environmental transformation, constituting a progenitor of the Anthropocene, where humans are now a major player in planetary functioning. Finally, we conclude that megafauna restoration via trophic rewilding can be expected to have positive effects on biodiversity across varied Anthropocene settings.

Mammal populations are declining in biodiverse tropical regions. Global analyses have identified Indonesia as a hotspot of vertebrate decline, although relatively few data are available to substantiate these claims. We reviewed research articles published during 2000–2020 on 104 medium-sized to large terrestrial mammal species found in Indonesia to help inform conservation management and future research. We identified 308 peer-reviewed studies published in English or Bahasa Indonesia, with an increase in publication rate (articles published per year) over time. Studies of species distributions dominated the literature, followed by publications on abundance, species diversity and combinations of these topics. Most publications concerned single-species studies conducted at a single location and a single point in time. We identify four key issues that should be addressed by future research and conservation efforts: (1) disproportionate focus on a small number of species; (2) geographical bias towards west Indonesia (Sumatra, Kalimantan and Java–Bali), with few published studies from central (Sulawesi, Nusa Tenggara and Maluku) and east (Papua) Indonesia; (3) limitations to survey design, sampling effort and data analysis; and (4) lack of long-term wildlife population studies. We also note challenges local researchers face in publishing their studies in international journals because of language barriers and costs. Greater use of existing biodiversity data and continued capacity building for local researchers, particularly those in central and east Indonesia, are critical to effectively guide future wildlife monitoring and improve the conservation status of Indonesian mammals.

Large frugivores provide critical seed dispersal services for many plant species and their extirpation from forested ecosystems can cause compositional shifts in regenerating plant cohorts. Yet, we still poorly understand whether large seed-dispersers have complementary or redundant roles for forest regeneration. Here, to assess the functional complementarity of large-bodied frugivores in forest regeneration, we quantified the effects of varying abundance of hornbills, primates and the forest elephant on the density, species richness and the mean weighted seed length of animal-dispersed tree species among seedlings in five sites in a forest–savanna mosaic in D. R. Congo, while accounting for percentage forest cover and the local presence of fruiting trees. We found that the abundance of primates was positively associated with species richness of seedlings, while percentage forest cover was negatively associated (R2 = 0.19). The abundance of hornbills, the presence of elephants and percentage forest cover were positively associated with mean seed length of the regenerating cohort (R2 = 0.13). Spatially explicit analysis indicated that some additional processes have an important influence on these response indices. Primates would seem to have a preponderant role for maintaining relatively high species richness, while hornbills and elephant would seem to be predominantly responsible for the recruitment of large-seeded trees. Our results could indicate that these taxa of frugivores play complementary functional roles for forest regeneration. This suggests that the extirpation of one or more of these dispersers would likely not be functionally compensated for by the remaining taxa, hence possibly cascading into compositional shifts.

Primates are important seed dispersers in tropical forests, but they are being lost due to forest fragmentation. We compared post-dispersal seed fate and seedling density for the tree Dialium guianense, in forest fragments in which its main seed disperser, the mantled howler monkey (Alouatta palliata) is present, and in fragments in which it is absent. We also carried out a germination experiment to assess gut-passage effect. Seeds extracted from fruits had very low germination (2%) compared with defecated seeds (70%). Seeds in monkey faeces had a lower probability of being attacked by predators, but a higher probability of being attacked by fungus, when compared with seeds inside fruits. Seed fate was similar in fragments with vs. without monkeys, and in sites under parent trees vs. under monkey sleeping sites. Seedling density was highest under sleeping sites in fragments with monkeys, followed by sites under parent trees in fragments with monkeys, and it was lowest in uninhabited fragments, regardless of deposition site. Our study adds to an increasing line of evidence suggesting that loss of frugivores can have strong consequences for plant recruitment.

Contemporary defaunation of fragmented forests potentially alters patterns of seed predation and dispersal. Alternatively, the remaining fauna may compensate for missing animals, resulting in equivalent rates of seed dispersal and predation. In the Los Tuxtlas region of southern Mexico, populations of large terrestrial fruit-eating mammals are diminished or absent from many forest remnants. This study reports fruit removal and seed predation patterns of Poulsenia armata (Moraceae), in forest fragments and a continuous forest (LTBS). Contrary to expectation, we found no differences in seed predation (mean ± SD) between LTBS (7.2 ± 1.8 seeds per station) and forest fragments (5.6 ± 1.1). However more fruits were removed in the LTBS (11.4 ± 0.9 fruits per station) than in forest fragments (8.1 ± 0.8). Animal activity, recorded by camera traps, differed between animal guild with fewer seed dispersers in forest fragments (mean = 0.43 ± 0.02 photos wk−1) than in the LTBS (mean = 0.68 ± 0.05). Fruits and seeds attracted many species of mammal (n = 12) in both habitats, indicating substantial redundancy. Remnant forest patches in the Los Tuxtlas landscape retain great ecological value, both as refuges for mammals and habitats for trees, such as P. armata.

Originally proposed in 2005 as a way to use financial incentives to tackle global climate change, Reducing Emissions from Deforestation and forest Degradation (REDD) has evolved to include conservation, sustainable management of forests and enhancement of forest carbon stocks, in what is now known as REDD+. Biodiversity protection is still viewed principally as a co-benefit of the REDD+ process, with conservation of forest tree cover and carbon stocks providing the main measure of success. However, focusing solely on tree cover and carbon stocks does not always protect other species, which may be threatened by other factors, most notably hunting. We present evidence from the literature that loss of biodiversity can affect forest composition, tree survival and forest resilience and may in some cases ultimately lead to a reduction in carbon storage. We argue that REDD+ projects should specifically mitigate for threats to biodiversity if they are to maximize carbon storage potential in the long term.

This study tested whether the reduction in the number of large-bodied seed dispersers is correlated with shifts in the taxonomic and functional (e.g. dispersal mode and seed size) traits of the seeding communities within small fragments of semi-deciduous forest, southern Mexico. In five fragments (2.3–640 ha) and one continuous forest site we sampled tree and seedling species in 40 (20 × 20 m) and 120 (3 × 3 m) plots respectively, and recorded the incidence (presence/absence) of the disperser fauna (three common large-birds and >500-g mammals). Tree and seedling species were categorized according to dispersal mode, seed size and whether they originated from local (i.e. from dropped) or immigrant (i.e. from actively dispersed) seeds. Fragment size negatively correlated with number of species of medium to large vertebrate seed-dispersers and number of seedlings of large-seeded species, but had no influence on functional traits of the adult-tree community. Between 41% and 61% of all seedlings were considered as immigrants and the proportion of immigrant seedlings of large-seeded tree species was negatively correlated with forest size. The results suggest that biased defaunation in small forest fragments may seriously reduce recruitment of large-seeded tree species (>1.4 cm length) dispersed by vertebrates, negatively affecting successional trajectories of small forest fragments.

The effects of defaunation on growth and digestion were measured in sheep fed fresh Digitaria decumbens grass cut at four stages of regrowth 14, 28, 42, and 56 days, and with different protein to energy (P/E) ratios. Two completely randomized designs trials (growth and digestion) were conducted using faunated animals, defaunated rams and protozoa free lambs. The digestion trial: eight faunated and eight defaunated rams fitted with ruminal and duodenal cannulas were fed 4 diets (diets D1 to D4) to measure digestion parameters. The dietary P/E ratios were 120 (D1), 130 (D2), 130 (D3), and 140 (D4) g PDIN/UFL (Protein Digested in the small Intestine supplied by microbial protein from rumen-degraded protein/Feed Unit for Lactation) and the grass stages of regrowth were 56, 42, 28, and 14 days, respectively. Increasing the dietary P/E ratios increased dry matter intake (DMI) and the total tract digestibility of organic matter (OM), NDF and CP. Defaunation decreased DMI, except for rams fed D4 diet. Defaunation also decreased total tract digestibility of OM except for rams fed D1 diet and that of NDF except for rams fed D1 and D4 diets. Increasing the dietary P/E ratios also increased nitrogen intake and ammonia (NH3) concentration in the rumen, whereas defaunation decreased them. The dietary P/E ratio increased non-NH3 nitrogen and microbial nitrogen duodenal flows and microbial efficiency. Defaunation did not affect duodenal flows of neither non-NH3 nitrogen and microbial nitrogen or microbial efficiency. The growth trial: 20 faunated and 20 protozoa free lambs were fed four diets (diets D5 to D8) to measure their average daily gain (ADG). The dietary P/E ratios were 60 (D5), 70 (D6), 80 (D7) and 100 (D8) g PDIN/UFL and the stages of regrowth were 56, 42, 28, and 14 days, respectively. DMI of lambs increased with P/E ratio. Protozoa free lambs had greater DMI than faunated ones when fed D7 diet (80.8 v. 74.9 g/kg LW0.75, respectively). The ADG of the lambs increased with P/E ratio. Fed on the same D5 diet, protozoa free lambs had greater ADG than faunated lambs (29.8 v. 11.6 g/day, respectively). In conclusion, animal response to defaunation was modulated by the P/E ratio of the D. decumbens grass diets. Defaunation increased ADG of lambs fed forage with the lowest P/E ratio, while digestion and nitrogen duodenal flows of rams fed the lowest P/E ratio were not affected.

Inadequate nutrition is the main cause of low productivity by ruminants in sub-Saharan Africa. The primary feed resources in the region include natural pasture and crop residues that have tough texture, poor digestibility and are deficient in nutrients. These deficiencies can be corrected by supplementation with high-density feeds such as oilseed cakes and proteins of animal origin. However, protein sources such as oilseed cakes are beyond the economic reach of most farmers, while the incidence of bovine spongiform encephalopathy in Western intensive animal production may be thought to argue against the use of animal proteins. Local tree legumes have been investigated as potential supplements for ruminants because of their beneficial effect of increasing metabolizable energy intake, N intake and feed efficiency, and improving animal performance. However, our work has suggested that some plant materials may have a nutritional value beyond simply their nutrient content, i.e. as rumen-manipulating agents. The foliage of some tree legumes has been shown to be selectively toxic to rumen protozoa. Rumen protozoa ingest and digest bacteria and fungi, degrading their cellular protein to NH3. Microbial protein turnover due to protozoal predation in the rumen may result in the net microbial protein outflow being less than half the total protein synthesized. Results from in vivo experiments have clearly shown that duodenal flow of both undegraded dietary and bacterial protein is generally increased by defaunation. However, no practical method has been developed to date to eliminate protozoa. Anti-protozoal plants may be promising, safe, natural defaunating agents.

Samples and extracts of foliage from African multipurpose trees were screened for their effects on rumen protozoa and bacteria with a view to predicting their safety as feed supplements and for identifying species with potential antiprotozoal activity. The species tested were Acacia aneura, Charnaecytisus palmensis, Brachychiton populneum, Flindersia maculosa, Sesbania sesban, Leucaena leucocephala and Vernonia amyedalina. Antimicrobial effects were mild except for S. sesban, which was highly toxic to rumen protozoa in vitro, and A. aneura, which was toxic to rumen bacteria. The antiprotozoal factor in S. sesban was apparently associated with the fraction of the plant containing saponins. When S. sesban was fed to sheep, protozoal numbers fell by 60 % after 4 d, but the population recovered after a further 10 d. In vitro experiments demonstrated that washed protozoa from later times were no more resistant to S. sesban than on initial exposure, suggesting that other micro-organisms, probably the bacteria, adapted to detoxify the antiprotozoal agent. Thus S. sesban may be useful in suppressing protozoa and thereby improving protein flow from the rumen, but only if the bacterial metabolism of the antiprotozoal factor can be avoided.