The research, led by Kim Dianne Ligue-Sabio and colleagues at the University of the Philippines Mindanao, is notable not just for what it found but for how it found it. Over three fieldwork sessions conducted between May 2021 and May 2022, the team logged 270.5 hours of direct observation across 29 days, recording the behavior of visible troop members in 1,082 scan samples. Each scan lasted five minutes and was followed by a ten-minute pause, creating a fifteen-minute sampling cycle that ran from 6:00 AM to 6:00 PM. At every scan, the observers noted the primary behavior of each visible animal and recorded the GPS coordinates of the troop’s approximate center, generating a rich spatiotemporal dataset that could be interrogated with formal spatial statistics.

The five most frequently observed behaviors were moving, recorded in 99.26 percent of scans, resting at 92.42 percent, grooming at 68.48 percent, feeding at 67.74 percent, and foraging at 57.12 percent. To analyze these, the researchers turned to the Getis-Ord Gi* statistic, a hotspot detection method that identifies statistically significant clusters of activity, and to a more sophisticated technique called Emerging Hotspot Analysis. The latter builds a space-time cube, aggregating the fifteen-minute scans into hourly bins across a fishnet grid, then applies both the Getis-Ord statistic and the Mann-Kendall trend test to classify each bin as a new, consecutive, intensifying, persistent, diminishing, sporadic, oscillating, or historical hotspot or coldspot. The result is a map that shows not just where behaviors cluster, but how those clusters rise and fall through the day.

The temporal findings were strikingly clean. Foraging peaked between 8:00 and 9:00 in the morning and then declined steadily, a trend confirmed by the Mann-Kendall statistic. Grooming showed the opposite trajectory, climbing through the afternoon to peak between 4:00 and 5:00 PM. Feeding, resting, and moving showed no significant monotonic trends across the day. Read together, the data describe a troop that prioritizes energy acquisition early, exploiting both provisioned food and wild resources, and then shifts its attention to social bonding and rest as the day winds down. It is a familiar structure of primate time budgets, but here it plays out across a landscape divided between houses and forest.

The spatial analysis added a second layer of insight. Feeding, grooming, and resting clustered tightly, with significant spatial autocorrelation emerging at distance bands as short as two meters and never exceeding seventeen meters. This tight clustering suggests repeated use of specific, localized spots for social and resting activities, likely anchored to the fixed provisioning site and a consistent sleeping area within the village. Foraging, by contrast, only clustered at a thirty-meter bandwidth, and its hotspots extended deep into the forest-agricultural mosaic, well beyond the built-up zone. The researchers interpret this broader dispersion as a strategy for locating diverse food resources and reducing within-group competition by avoiding the repeated exploitation of the same patches.

Perhaps the most consequential finding concerns diet. Despite being fed regularly by the Moncadista community, a local religious sect that regards the macaques as spiritually connected to their ancestors and strictly prohibits hunting them, the animals continued to forage intensively for natural foods. Observers recorded them eating Chinese bamboo leaves, fruits, grass, and insects in the forest, alongside provisioned bananas, eggs, peanuts, and even junk food in the village. The persistence of foraging hotspots in the forest suggests that human provisioning alone does not meet the troop’s nutritional needs, particularly for a group of at least fifty individuals. Primates actively forage to maintain an optimal nutritional balance, and insects in particular provide protein that cultivated crops may lack. The implication for conservation is direct: even provisioned macaque populations depend on intact forest habitat.

The study also offers a window into why the macaques prefer the village for their downtime. Although there is no hunting pressure anywhere in the troop’s range, grooming and resting hotspots were concentrated in built-up areas while coldspots for these behaviors appeared throughout the forest. The researchers observed a telling incident in the forest: the appearance of a large red-tailed green rat snake triggered synchronized alarm calls and mobbing behavior by more than twenty macaques, a response never seen in the village. Farm deterrents such as dogs and slingshots are present in agricultural areas, while the macaques appear habituated to the domestic dogs within the settlement. This pattern fits the predator avoidance and human-shield hypotheses, in which prey animals use proximity to humans as a buffer against predators, combined with the proximity-to-food-resource hypothesis that favors resting sites near reliable food.

Methodologically, the paper makes a case for pairing static and dynamic spatial tools. The conventional hotspot analysis pinpointed key areas of activity that could serve as targets for management interventions, such as preserving foraging zones or timing tourism activities. The emerging hotspot analysis then revealed how those areas function differently across the day: feeding and foraging in the village produced oscillating hotspots, meaning the animals engaged in those behaviors elsewhere earlier, while grooming and resting produced consecutive hotspots that only intensified toward the end of the day. The two approaches validated each other where patterns agreed and exposed new structure where they diverged, though the researchers caution that aggregating scans into hourly bins may have smoothed away finer behavioral fluctuations.

The setting itself is unusual and worth savoring. New Israel sits within Mount Apo Natural Park, a protected area whose original tropical lowland dipterocarp forest has been transformed into a patchwork of residences, secondary forest, and small farms growing taro, cassava, sweet potato, and fruit trees. The community has built a small tourism industry around the macaques, complete with parks and ziplines. During the first fieldwork session, conducted amid COVID-19 pandemic restrictions when tourist visits were limited, the troop’s ranging area in the forest was markedly larger, at roughly 184,000 square meters, than in the later sessions, which shrank to under 95,000 square meters. The authors suggest that reduced tourist provisioning may have pushed the macaques to forage more widely, though visitor data were not systematically collected.

For a species whose fortunes have turned grim, the study carries real weight. In 2024, the International Union for Conservation of Nature reclassified the long-tailed macaque as Endangered, citing a 50 to 70 percent decline in global populations over three decades driven by hunting, biomedical exploitation, the pet trade, and habitat loss. Understanding how the species navigates human-modified landscapes is therefore no longer academic. The New Israel macaques demonstrate remarkable behavioral plasticity, running a daily circuit that treats village and forest as complementary resources rather than alternatives. The authors argue that conservation planning must account for both, protecting forest foraging grounds while managing the built-up areas where interactions occur. Future work, they note, should quantify provisioning rates, predator presence, and food distribution to build fuller models of what draws these adaptable primates back and forth across the boundary between two worlds.

Subject of Research: Spatiotemporal behavioral patterns of long-tailed macaques in a human-modified Philippine landscape

Article Title: Spatiotemporal patterns of behavior by long-tailed macaques Macaca fascicularis (Raffles 1821) in a human-modified environment

Article References: Ligue-Sabio, K. D., Plaza, A. R., Sabanal, B., Oguis, G. F., Torrefiel, J., & Gamalo, L. E. (2026). Spatiotemporal patterns of behavior by long-tailed macaques Macaca fascicularis (Raffles 1821) in a human-modified environment. Discover Conservation, 3(1), Article 3. https://doi.org/10.1007/s44353-025-00071-x

Image Credits: AI Generated

DOI: 10.1007/s44353-025-00071-x

Keywords: long-tailed macaques, Macaca fascicularis, hotspot analysis, emerging hotspot analysis, human-wildlife coexistence, behavioral ecology, foraging behavior, food provisioning, Mount Apo, conservation planning, primates, Philippines

Endogenous retroviruses, or ERVs, are the fossilized remnants of retroviruses that once infected the germ-line cells of ancestral hosts. When a retrovirus inserts its provirus into the DNA of a sperm or egg cell that goes on to contribute to the next generation, the insertion can be inherited vertically, copying itself into every cell of every descendant. Over millions of years these elements accumulate mutations, deletions and recombination events, but their diagnostic architecture, including long terminal repeats flanking the core retroviral genes gag, pol and env, often remains recognizable. Because integration events are effectively permanent and their ages can be estimated, ERVs function as paleontological records of the viruses that circulated in host populations deep in evolutionary time.

To recover these viral fossils from the macaque genome, the researchers employed a homology-based, genome-wide screen designed to detect relatively intact proviruses rather than the far more numerous degraded fragments and solo long terminal repeats that litter mammalian genomes. The survey exploited the current highest-quality chromosome-level assembly available for M. fascicularis, an important practical consideration because fragmented assemblies can obscure proviral structure and misplace insertions. Candidate elements were then subjected to structural annotation and phylogenetic classification, anchoring the new macaque sequences within the broader landscape of vertebrate retroviral diversity.

Classification relied on one of the most conserved regions of the retroviral toolkit: the reverse transcriptase domain of the pol gene. Because this enzyme performs the essential step of copying viral RNA into DNA, its sequence is under strong functional constraint and retains enough phylogenetic signal to place divergent elements into their correct lineages. Building multiple alignments of the recovered reverse transcriptase domains and reconstructing their evolutionary relationships, the team found that the macaque proviruses fall into betaretroviral, gammaretroviral and unclassified lineages, with the beta and gamma groups clearly predominating. This pattern mirrors what has been observed in many other mammalian genomes, where betaretroviruses and gammaretroviruses have historically been prolific colonizers of germ lines.

The compositional result carries evolutionary weight. Betaretroviruses, relatives of modern mouse mammary tumor virus and the simian retrovirus SERV, and gammaretroviruses, relatives of murine leukemia virus, differ in their envelope biology, host receptor usage and genomic preferences. A predominance of both classes suggests that the macaque lineage experienced repeated, independent waves of retroviral germline invasion rather than a single dominant radiation. Consistent with that interpretation, dating based on the divergence between the paired long terminal repeats of each provirus, which are identical at the moment of integration and accumulate mutations thereafter, indicated that the 106 loci span a broad range of integration ages, recording multiple distinct epochs of retroviral activity in the species’ ancestry.

The macaque proviruses are also distributed across all chromosomes, a pattern consistent with the idea that integration sites reflect a combination of retroviral target-site preferences and post-insertion forces such as selection, recombination and random genetic drift. Studies in human and mouse have shown that different retroviral genera favor different genomic neighborhoods, with some elements preferentially accumulating in gene-poor regions while others insert near transcription units. The chromosome-wide coverage reported for M. fascicularis means that the new dataset can support analyses of integration preference in a primate genome at a resolution previously unavailable for this species.

The biomedical significance of the work extends beyond evolutionary curiosity. The crab-eating macaque, also known as the cynomolgus macaque, is one of the most widely used primate models in drug development, infectious disease research and transplantation studies, and its endangered status in the wild makes the genomic record it carries all the more valuable to document. ERVs in macaques are directly relevant to laboratory safety as well: previous work has identified and characterized simian endogenous retroviruses in captive macaque populations in Indonesia, raising questions about how these elements behave in breeding colonies. A curated, high-confidence catalog of intact proviral loci gives researchers a framework for tracking ERV expression, recombination and potential co-option in an animal model whose transcriptomes are routinely interrogated.

The broader context of ERV biology reinforces that relevance. In humans, endogenous retroviral sequences have been co-opted for essential functions, most famously the syncytin genes derived from retroviral envelopes that mediate placental cell fusion, and ERV-derived regulatory sequences now contribute to innate immune gene networks. Deregulated ERV expression has also been implicated in a growing list of pathologies, including systemic lupus erythematosus, Parkinson’s disease, neuronal aging and cancer immunotherapy responses, where translated retroviral products can provoke interferon signaling or serve as tumor-associated antigens. Establishing which proviruses are intact in the macaque genome is therefore a prerequisite for asking whether analogous host-virus co-option and immune interactions operate in this model species.

The authors are careful to delineate the scope of their catalog. Because the screen targeted relatively intact proviruses, the dataset deliberately excludes the vastly more abundant degraded ERV fragments and solo long terminal repeats, which form when recombination between the two LTRs of an integrated provirus excises the internal sequence. Those eroded elements represent older and numerically dominant chapters of the retroviral record, and their omission means the 106 loci described here constitute a conservative, high-confidence floor rather than a complete inventory of retroviral genetic material in the macaque genome. Even so, the team notes that the curated set provides a reference resource for investigating the evolutionary history and genomic impact of preserved proviruses in an endangered primate.

The study also joins a rapidly expanding comparative effort. Recent surveys have uncovered endogenous retroviruses in red pandas, ducks and primitive ruminants, and genome-mining approaches have shown that retroviruses have pervasively invaded vertebrate genomes across the tree of life. By adding a systematic account for a close human relative, the macaque analysis helps triangulate which retroviral lineages circulated in the common ancestors of Old World monkeys and apes, and which invasions were lineage-specific. The genome assembly data underlying the work are publicly available through the National Center for Biotechnology Information, and the researchers suggest their dataset will serve as a durable foundation for exploring how viral inheritance has shaped, and continues to shape, the genome of one of biomedical science’s most important animal models.

Subject of Research: Discovery and evolutionary characterization of endogenous retrovirus proviruses in the genome of the crab-eating macaque (Macaca fascicularis)

Article Title: Discovery and evolution of endogenous retroviruses in the genome of crab-eating macaque (Macaca fascicularis)

Article References: Shi, W., Mao, L., Chen, Y., Alfred, N., Fu, Y., Bao, Y., Wang, X., Liu, Y., Yang, S., Ji, L., Zhou, C., Xu, J., Li, W., Shan, T., Wang, J., Zhang, W., & Shen, Q. (2026). Discovery and evolution of endogenous retroviruses in the genome of crab-eating macaque (Macaca fascicularis). Molecular Genetics and Genomics, 301(1), Article 189. https://doi.org/10.1007/s00438-026-02518-9

Image Credits: AI Generated

DOI: 10.1007/s00438-026-02518-9

Keywords: endogenous retroviruses, crab-eating macaque, Macaca fascicularis, retrovirus, genome evolution, provirus, phylogenetic analysis, long terminal repeats, reverse transcriptase, genomics, non-human primate model, viral fossils