Philippa Kaur

Zala, S. M., Potts, W. K. & Penn, D. J. Scent-marking displays provide honest signals of health and infection. Behav. Ecol. 15, 338–344 (2004).Article 

Google Scholar 
Allen, M. L., Wallace, C. F. & Wilmers, C. C. Patterns in bobcat (Lynx rufus) scent marking and communication behaviors. J. Ethol. 33, 9–14 (2014).Article 

Google Scholar 
White, A. M., Swaisgood, R. R. & Zhang, H. The highs and lows of chemical communication in giant pandas (Ailuropoda melanoleuca): Effect of scent deposition height on signal discrimination. Behav. Ecol. Sociobiol. 51, 519–529 (2002).Article 

Google Scholar 
Scordato, E. S., Dubay, G. & Drea, C. M. Chemical composition of scent marks in the ringtailed lemur (Lemur catta): Glandular differences, seasonal variation, and individual signatures. Chem. Senses 32, 493–504 (2007).Article 
CAS 
PubMed 

Google Scholar 
Maynard Smith, J. & Harper, D. Animal Signals (Oxford University Press, 2003).
Google Scholar 
Stockley, P., Bottell, L. & Hurst, J. L. Wake up and smell the conflict: Odour signals in female competition. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 368, 20130082 https://doi.org/10.1098/rstb.2013.0082 (2013).Article 
PubMed 
PubMed Central 

Google Scholar 
Petrulis, A. Chemosignals, hormones and mammalian reproduction. Horm. Behav. 63, 723–741 (2013).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Coombes, H. A., Stockley, P. & Hurst, J. L. Female chemical signalling underlying reproduction in mammals. J. Chem. Ecol. 44, 851–873 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Harmsen, B. J., Foster, R. J., Gutierrez, S. M., Marin, S. Y. & Patrick, C. Scrape-marking behavior of jaguars (Panthera onca) and pumas (Puma concolor). J. Mammal. 91, 1225–1234 (2010).Article 

Google Scholar 
Lamb, C. T. et al. Density-dependent signaling: An alternative hypothesis on the function of chemical signaling in a non-territorial solitary carnivore. PLoS ONE 12, e0184176 https://doi.org/10.1371/journal.pone.0184176 (2017).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Woodmansee, K. B., Zabel, C. J., Glickman, S. E., Frank, L. G. & Keppel, G. Scent marking (pasting) in a colony of immature spotted hyenas (Crocuta crocuta): A developmental study. J. Comp. Psychol. 105, 10–14 (1991).Article 
CAS 
PubMed 

Google Scholar 
Rasmussen, L. E. L., Riddle, H. S. & Krishnamurthy, V. Mellifluous matures to malodorous in musth. Nature 415, 975–976 (2002).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Surov, A. V. & Maltsev, A. N. Analysis of chemical communication in mammals: Zoological and ecological aspects. Biol. Bull. 43, 1175–1183 (2016).Article 

Google Scholar 
Hurst, J. L. Female recognition and assessment of males through scent. Behav. Brain Res. 200, 295–303 (2009).Article 
CAS 
PubMed 

Google Scholar 
Mills, M. G. L. & Gorman, M. L. The scent-marking behaviour of the spotted hyaena Crocuta crocuta in the southern Kalahari. J. Zool. 212, 483–497 (1987).Article 

Google Scholar 
Gassett, J. W. et al. Volatile compounds from interdigital gland of male white-tailed deer (Odocoileus virginianus). J. Chem. Ecol. 22, 1689–1696 (1996).Article 
CAS 
PubMed 

Google Scholar 
Stoeckelhuber, M., Sliwa, A. & Welsch, U. Histo-physiology of the scent-marking glands of the penile pad, anal Pouch, and the forefoot in the aardwolf (Proteles cristatus). Anat. Rec. 259, 312–326 (2000).Article 
CAS 

Google Scholar 
Begg, C. M., Begg, K. S., Du Toit, J. T. & Mills, M. G. L. Scent-marking behaviour of the honey badger, Mellivora capensis (Mustelidae), in the southern Kalahari. Anim. Behav. 66, 917–929 (2003).Article 

Google Scholar 
Yasui, T., Tsukise, A. & Meyer, W. Histochemical analysis of glycoconjugates in the eccrine glands of the raccoon digital pads. Eur. J. Histochem. 48, 393–402 (2004).CAS 
PubMed 

Google Scholar 
Johnston, R. E. Scent marking by male golden hamsters (Mesocricetus aurutus) I. Effects of odors and social encounters. Z. Tierpsychol. 37, 75–98 (1975).Article 
CAS 
PubMed 

Google Scholar 
Caspers, B., Wibbelt, G. & Voigt, C. C. Histological examinations of facial glands in Saccopteryx bilineata (Chiroptera, Emballonuridae), and their potential use in territorial marking. Zoomorphology 128, 37–43 (2008).Article 

Google Scholar 
Lawson, R. E., Putnam, R. J. & Fielding, A. H. Individual signatures in scent gland secretions of Eurasian deer. J. Zool. 251, 399–410 (2000).Article 

Google Scholar 
Smith, T. E., Tomlinson, A. J., Mlotkiewicz, J. A. & Abbott, D. H. Female marmoset monkeys (Callithrix jacchus) can be identified from the chemical composition of their scent marks. Chem. Senses 26, 449–458 (2001).Article 
CAS 
PubMed 

Google Scholar 
del Barco-Trillo, J., LaVenture, A. B. & Johnston, R. E. Male hamsters discriminate estrous state from vaginal secretions and individuals from flank marks. Behav. Process. 82, 18–24 (2009).Article 

Google Scholar 
Sun, L. & Müller-Schwarze, D. Anal gland secretion codes for family membership in the beaver. Behav. Ecol. Sociobiol. 44, 199–208 (1998).Article 

Google Scholar 
Zhang, J. X. et al. Possible coding for recognition of sexes, individuals and species in anal gland volatiles of Mustela eversmanni and M. sibirica. Chem. Senses 28, 381–388 (2003).Article 
PubMed 

Google Scholar 
Kean, E. F., Müller, C. T. & Chadwick, E. A. Otter scent signals age, sex, and reproductive status. Chem. Senses 36, 555–564 (2011).Article 
CAS 
PubMed 

Google Scholar 
Rosell, F. et al. Brown bears possess anal sacs and secretions may code for sex. J. Zool. 283, 143–152 (2011).Article 

Google Scholar 
Buesching, C. D., Waterhouse, J. S. & Macdonald, D. W. Gas-chromatographic analyses of the subcaudal gland secretion of the European badger (Meles meles) part I: Chemical differences related to individual parameters. J. Chem. Ecol. 28, 41–56 (2002).Article 
CAS 
PubMed 

Google Scholar 
Yuan, H. et al. Anogenital gland secretions code for sex and age in the giant panda, Ailuropoda melanoleuca. Can. J. Zool. 82, 1596–1604 (2004).Article 

Google Scholar 
Kent, L. & Tang-Martínez, Z. Evidence of individual odors and individual discrimination in the raccoon, Procyon lotor. J. Mammal. 95, 1254–1262 (2014).Article 

Google Scholar 
Woodley, S. K. & Baum, M. J. Differential activation of glomeruli in the ferret’s main olfactory bulb by anal scent gland odours from males and females: An early step in mate identification. Eur. J. Neurosci. 20, 1025–1032 (2004).Article 
PubMed 
PubMed Central 

Google Scholar 
Allen, M. L. et al. The role of scent marking in mate selection by female pumas (Puma concolor). PLoS ONE 10, e0139087 https://doi.org/10.1371/journal.pone.0139087 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Latour, P. Interactions between free-ranging, adult male polar bears (Ursus maritimus Phipps): A case of adult social play. Can. J. Zool. 59, 1775–1783 (1981).Article 

Google Scholar 
Nie, Y., Swaisgood, R. R., Zhang, Z., Liu, X. & Wei, F. Reproductive competition and fecal testosterone in wild male giant pandas (Ailuropoda melanoleuca). Behav. Ecol. Sociobiol. 66, 721–730 (2012).Article 

Google Scholar 
Clapham, M. & Kitchin, J. Social play in wild brown bears of varying age-sex class. Acta Ethol. 19, 181–188 (2016).Article 

Google Scholar 
Stonorov, D. & Stokes, A. W. Social behavior of the Alaska brown bear. Int. Conf. Bear Res. Manag. 2, 232–242 (1972).
Google Scholar 
Clapham, M., Nevin, O. T., Ramsey, A. D. & Rosell, F. A hypothetico-deductive approach to assessing the social function of chemical signalling in a non-territorial solitary carnivore. PLoS ONE 7, e35404 https://doi.org/10.1371/journal.pone.0035404 (2012).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Clapham, M., Nevin, O. T., Ramsey, A. D. & Rosell, F. The function of strategic tree selectivity in the chemical signalling of brown bears. Anim. Behav. 85, 1351–1357 (2013).Article 

Google Scholar 
Owen, M. A. et al. An experimental investigation of chemical communication in the polar bear. J. Zool. 295, 36–43 (2015).Article 

Google Scholar 
Sergiel, A. et al. Histological, chemical and behavioural evidence of pedal communication in brown bears. Sci. Rep. 7, 1052 https://doi.org/10.1038/s41598-017-01136-1 (2017).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Tomiyasu, J. et al. Morphological and histological features of the vomeronasal organ in the brown bear. J. Anat. 231, 749–757 (2017).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Tomiyasu, J. et al. Testicular regulation of seasonal change in apocrine glands in the back skin of the brown bear (Ursus arctos). J. Vet. Med. Sci. 80, 1034–1040 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Tomiyasu, J. et al. Testosterone-related and seasonal changes in sebaceous glands in the back skin of adult male brown bears (Ursus arctos). Can. J. Zool. 96, 205–211 (2018).Article 
CAS 

Google Scholar 
Burst, T. L. & Pelton, M. R. Black bear mark trees in the Smoky mountains. Int. Conf. Bear Res. Manag. 5, 45–53 (1983).
Google Scholar 
Mattson, D. J. & Greene, G. I. Tree rubbing by Yellowstone grizzly bears Ursus arctos. Wildl. Biol. 1, 1–9 (2003).
Google Scholar 
Nie, Y. et al. Giant panda scent-marking strategies in the wild: Role of season, sex and marking surface. Anim. Behav. 84, 39–44 (2012).Article 

Google Scholar 
Revilla, E. et al. Brown bear communication hubs: Patterns and correlates of tree rubbing and pedal marking at a long-term marking site. PeerJ 9, 10447 https://doi.org/10.7717/peerj.10447 (2021).Article 

Google Scholar 
Clapham, M., Nevin, O. T., Ramsey, A. D. & Rosell, F. Scent-marking investment and motor patterns are affected by the age and sex of wild brown bears. Anim. Behav. 94, 107–116 (2014).Article 

Google Scholar 
Taylor, A. P., Gunther, M. S. & Allen, M. L. Black bear marking behaviour at rub trees during the breeding season in northern California. Behaviour 152, 1097–1111 (2015).Article 

Google Scholar 
Filipczyková, E., Heitkönig, I., Castellanos, A., Hantson, W. & Steyaert, S. Marking behavior of Andean bears in an Ecuadorian cloud forest: A pilot study. Ursus 27, 122–128 (2017).Article 

Google Scholar 
Stringham, S. F. Aggressive body language of bears and wildlife viewing: A response to Geist (2011). Hum.-Wildl. Interact. 5, 4 (2011).
Google Scholar 
Swaisgood, R. R., Lindburg, D. G. & Zhang, H. Discrimination of oestrous status in giant pandas (Ailuropoda melanoleuca) via chemical cues in urine. J. Zool. 257, 381–386 (2002).Article 

Google Scholar 
Wilson, A. E. et al. Behavioral, semiochemical and androgen responses by male giant pandas to the olfactory sexual receptivity cues of females. Theriogenology 114, 330–337 (2018).Article 
CAS 
PubMed 

Google Scholar 
Sillero-Zubiri, C. & Macdonald, D. W. Scent-marking and territorial behaviour of Ethiopian wolves Canis simensis. J. Zool. 245, 351–361 (1998).Article 

Google Scholar 
Stępniak, K. M., Niedźwiecka, N., Szewczyk, M. & Mysłajek, R. W. Scent marking in wolves Canis lupus inhabiting managed lowland forests in Poland. Mammal Res. 65, 629–638 (2020).Article 

Google Scholar 
Liu, D. et al. Do anogenital gland secretions of giant panda code for their sexual ability? Chin. Sci. Bull. 51, 1986–1995 (2006).Article 
CAS 

Google Scholar 
Tattoni, C., Bragalanti, N., Groff, C. & Rovero, F. Patterns in the use of rub trees by the Eurasian brown bear. Hystrix 26, 118 (2015).
Google Scholar 
Zhang, J. X. et al. Potential chemosignals in the anogenital gland secretion of giant pandas, Ailuropoda melanoleuca, associated with sex and individual identity. J. Chem. Ecol. 34, 398–407 (2008).Article 
CAS 
PubMed 

Google Scholar 
Swaisgood, R. R., Lindburg, D. G., Zhou, X. & Owen, M. A. The effects of sex, reproductive condition and context on discrimination of conspecific odours by giant pandas. Anim. Behav. 60, 227–237 (2000).Article 
CAS 
PubMed 

Google Scholar 
Swaisgood, R., Lindburg, D. & Zhou, X. Giant pandas discriminate individual differences in conspecific scent. Anim. Behav. 57, 1045–1053 (1999).Article 
CAS 
PubMed 

Google Scholar 
Liu, D. et al. Do urinary chemosignals code for sex, age, and season in the giant panda, Ailuropoda melanoleuca? in Chemical Signals in Vertebrates. Vol. 12. 207–222 (eds. East, M. L. & Dehnhard, M.). https://doi.org/10.1007/978-1-4614-5927-9_16 (Springer, 2013).Hagey, L. & MacDonald, E. Chemical cues identify gender and individuality in giant pandas (Ailuropoda melanoleuca). J. Chem. Ecol. 29, 1479–1488 (2003).Article 
CAS 
PubMed 

Google Scholar 
Wilson, A. E., Sparks, D. L., Knott, K. K., Willard, S. & Brown, A. Implementing solid phase microextraction (SPME) as a tool to detect volatile compounds produced by giant pandas in the environment. PLoS ONE 13, e0208618 https://doi.org/10.1371/journal.pone.0208618 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wilson, A. E. et al. Field air analysis of volatile compounds from free-ranging giant pandas. Ursus 29, 75–81 (2019).Article 

Google Scholar 
Crupi, A. P., Waite, J. N., Flynn, R. W. & Beier, L. Brown bear population estimation in Yakutat, Southeast Alaska. Alaska Department of Fish and Game https://doi.org/10.13140/RG.2.2.35947.54568 (2017).Article 

Google Scholar 
Sikes, R. S., Gannon, W. L. & The Animal Care and Use Committee of the American Society of Mammalogists. Guidelines of the American Society of Mammalogists for the use of wild mammals in research. J. Mammal. 92, 235–253 (2011).Matson, G. et al. A Laboratory Manual for Cementum Age Determination of Alaska Brown Bear First Premolar Teeth. Alaska Department of Fish and Game, Division of Wildlife Conservation https://www.adfg.alaska.gov/index.cfm?adfg=librarypublications.wildlifepublicationsdetails&pubidentifier=3374 (1993).Seryodkin, I. V. Marking activity of the Kamchatka brown bear (Ursus arctos piscator). Achiev. Life Sci. 8, 153–161 (2014).
Google Scholar 
Peralbo-Molina, A., Calderón-Santiago, M., Jurado-Gámez, B., Luque De Castro, M. D. & Priego-Capote, F. Exhaled breath condensate to discriminate individuals with different smoking habits by GC-TOF/MS. Sci. Rep. 7, 1421 https://doi.org/10.1038/s41598-017-01564-z (2017).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Liu, D. et al. Male panda (Ailuropoda melanoleuca) urine contains kinship information. Chin. Sci. Bull. 53, 2793–2800 (2008).CAS 

Google Scholar 
Kean, E. F., Chadwick, E. A. & Müller, C. T. Scent signals individual identity and country of origin in otters. Mamm. Biol. Z. Säugetierkd. 80, 99–105 (2015).Article 

Google Scholar 
R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.r-project.org/ (2020).Harris, R. L., Holland, B. R., Cameron, E. Z., Davies, N. W. & Nicol, S. C. Chemical signals in the echidna: Differences between seasons, sexes, individuals and gland types. J. Zool. 293, 171–180 (2014).Article 

Google Scholar 
Vaglio, S. et al. Sternal gland scent-marking signals sex, age, rank, and group identity in captive mandrills. Chem. Senses 41, 177–186 (2016).PubMed 

Google Scholar 
Knott, K. K. et al. Blood-based biomarkers of selenium and thyroid status indicate possible adverse biological effects of mercury and polychlorinated biphenyls in Southern Beaufort Sea polar bears. Environ. Res. 111, 1124–1136 (2011).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wilson, A. E. et al. Development and validation of protein biomarkers of health in grizzly bears. Conserv. Physiol. 8, coaa056 https://doi.org/10.1093/conphys/coaa056 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Oksanen, J. et al. Vegan: community ecology package. R package version 2.6-4. https://CRAN.R-project.org/package=vegan (2020).Williams, C. L., Ybarra, A. R., Meredith, A. N., Durrant, B. S. & Tubbs, C. W. Gut microbiota and phytoestrogen-associated infertility in Southern White Rhinoceros. MBio 10, e00311-19 https://doi.org/10.1128/mBio.00311-19 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Dill-McFarland, K. A., Breaker, J. D. & Suen, G. Microbial succession in the gastrointestinal tract of dairy cows from 2 weeks to first lactation. Sci. Rep. 7, 40864 https://doi.org/10.1038/srep40864 (2017).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Williams, C. L. et al. Dietary changes during weaning shape the gut microbiota of red pandas (Ailurus fulgens). Conserv. Physiol. 6, cox075 https://doi.org/10.1093/conphys/cox075 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bolar, K. STAT: interactive document for working with basic statistical analysis. R package version 0.1.0. https://CRAN.R-project.org/package=STAT (2019).Gese, E. & Ruff, R. Scent-marking by coyotes, Canis latrans: The influence of social and ecological factors. Anim. Behav. 54, 1155–1166 (1997).Article 
CAS 
PubMed 

Google Scholar 
Thompson, C. L. et al. What smells? Developing in-field methods to characterize the chemical composition of wild mammalian scent cues. Ecol. Evol. 10, 4691–4701 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Charpentier, M. J. E., Barthes, N., Proffit, M., Bessière, J.-M. & Grison, C. Critical thinking in the chemical ecology of mammalian communication: Roadmap for future studies. Funct. Ecol. 26, 769–774 (2012).Article 

Google Scholar 
Martín, J., Carranza, J., López, P., Alarcos, S. & Pérez-González, J. A new sexual signal in rutting male red deer: Age related chemical scent constituents in the belly black spot. Mamm. Biol. 79, 362–368 (2014).Article 

Google Scholar 
Carranza, J. et al. The dark ventral patch: A bimodal flexible trait related to male competition in red deer. PLoS ONE 15, 0241374 https://doi.org/10.1371/journal.pone.0241374 (2020).Article 
CAS 

Google Scholar 
Kean, E. F., Bruford, M. W., Russo, I. R. M., Müller, C. T. & Chadwick, E. A. Odour dialects among wild mammals. Sci. Rep. 7, 13593 https://doi.org/10.1038/s41598-017-12706-8 (2017).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Marneweck, C., Jürgens, A. & Shrader, A. M. The role of middens in white rhino olfactory communication. Anim. Behav. 140, 7–18 (2018).Article 

Google Scholar 
Linklater, W. L., Mayer, K. & Swaisgood, R. R. Chemical signals of age, sex and identity in black rhinoceros. Anim. Behav. 85, 671–677 (2013).Article 

Google Scholar 
White, A. M., Swaisgood, R. R. & Zhang, H. Chemical communication in the giant panda (Ailuropoda melanoleuca): The role of age in the signaller and assessor. J. Zool. 259, 171–178 (2003).Article 

Google Scholar 
Steiger, S., Schmitt, T. & Schaefer, H. M. The origin and dynamic evolution of chemical information transfer. Proc. R. Soc. B Biol. Sci. 278, 970–979 https://doi.org/10.1098/rspb.2010.2285 (2011).Article 

Google Scholar 
Williams, C. L. et al. Wildlife-microbiome interactions and disease: Exploring opportunities for disease mitigation across ecological scales. Drug Discov. Today Dis. Models 28, 105–115 (2018).Article 

Google Scholar 
Chiang, Y. R., Wei, S. T. S., Wang, P. H., Wu, P. H. & Yu, C. P. Microbial degradation of steroid sex hormones: Implications for environmental and ecological studies. Microb. Biotechnol. 13, 926–949 (2020).Article 
CAS 
PubMed 

Google Scholar 
Williams, C. L., Garcia-Reyero, N., Martyniuk, C. J., Tubbs, C. W. & Bisesi, J. H. Regulation of endocrine systems by the microbiome: Perspectives from comparative animal models. Gen. Comp. Endocrinol. 292, 113437 (2020).Article 
CAS 
PubMed 

Google Scholar 
Theis, K. R., Venkataraman, A., Wagner, A. P., Holekamp, K. E. & Schmidt, T. M. Age-related variation in the scent pouch bacterial communities of striped hyenas (Hyaena hyaena). Chem. Signals Vertebr. 13, 87–103 (2016).Article 

Google Scholar 
Steyaert, S. M. J. G., Endrestøl, A., Hackländer, K., Swenson, J. E. & Zedrosser, A. The mating system of the brown bear Ursus arctos. Mammal Rev. 42, 12–34 (2012).Article 

Google Scholar 
Bellemain, E. et al. The dilemma of female mate selection in the brown bear, a species with sexually selected infanticide. Proc. R. Soc. B Biol. Sci. 273, 283–291 https://doi.org/10.1098/rspb.2005.3331 (2006).Article 

Google Scholar 
Zedrosser, A., Bellemain, E., Taberlet, P. & Swenson, J. E. Genetic estimates of annual reproductive success in male brown bears: The effects of body size, age, internal relatedness and population density. J. Anim. Ecol. 76, 368–375 (2007).Article 
PubMed 

Google Scholar 
Schwartz, C. C. et al. Reproductive maturation and senescence in the female brown bear. Ursus 14, 109–119 (2003).
Google Scholar 
Schulte, B. A., Freeman, E. W., Goodwin, T. E., Hollister-Smith, J. & Rasmussen, L. E. L. Honest signalling through chemicals by elephants with applications for care and conservation. Appl. Anim. Behav. Sci. 102, 344–363 (2007).Article 

Google Scholar 
Støen, O.-G., Bellemain, E., Sæbø, S. & Swenson, J. E. Kin-related spatial structure in brown bears Ursus arctos. Behav. Ecol. Sociobiol. 59, 191–197 (2005).Article 

Google Scholar 
Egbert, A. L. & Stokes, A. W. The social behaviour of brown bears on an Alaskan salmon stream. Int. Conf. Bear Res. Manag. 3, 41–56 (1976).
Google Scholar 
Craighead, J. J., Sumner, J. S. & Mitchell, J. A. The Grizzly Bears of Yellowstone: Their Ecology in the Yellowstone Ecosystem, 1959–1992 (Island Press, 1995).
Google Scholar 
Burgener, N., Dehnhard, M., Hofer, H. & East, M. L. Does anal gland scent signal identity in the spotted hyaena? Anim.
Behav. 77, 707–715 (2009).Article 

Google Scholar 
Noonan, M. J. et al. Knowing me, knowing you: Anal gland secretion of European badgers (Meles meles) codes for individuality, sex and social group membership. J. Chem. Ecol. 45, 823–837 (2019).Article 
CAS 
PubMed 

Google Scholar 
Sun, L. & Müller-Schwarze, D. Sibling recognition in the beaver: A field test for phenotype matching. Anim. Behav. 54, 493–502 (1997).Article 
CAS 
PubMed 

Google Scholar 
Thom, M. D. & Hurst, J. L. Individual recognition by scent. Ann. Zool. Fenn. 41, 765–787 (2004).
Google Scholar 
Roberts, S. A. et al. Individual odour signatures that mice learn are shaped by involatile major urinary proteins (MUPs). BMC Biol. 16, 1–19 https://doi.org/10.1186/s12915-018-0512-9 (2018).Article 
CAS 

Google Scholar 
Henkel, S. & Setchell, J. M. Group and kin recognition via olfactory cues in chimpanzees (Pan troglodytes). Proc. R. Soc. B Biol. Sci. 285, 20181527 https://doi.org/10.1098/rspb.2018.1527 (2018).Article 

Google Scholar 
Vogt, K., Boos, S., Breitenmoser, U. & Kölliker, M. Chemical composition of Eurasian lynx urine conveys information on reproductive state, individual identity, and urine age. Chemoecology 26, 205–217 (2016).Article 
CAS 

Google Scholar 
Wyatt, T. D. Pheromones and signature mixtures: Defining species-wide signals and variable cues for identity in both invertebrates and vertebrates. J. Comp. Physiol. A Neuroethol. Sens. Neural. Behav. Physiol. 196, 685–700 (2010).Article 
CAS 
PubMed 

Google Scholar 
Johnston, R. E. Chemical communication in rodents: From pheromones to individual recognition. J. Mammal. 84, 1141–1162 (2003).Article 

Google Scholar 
Dehnhard, M. Mammal semiochemicals: Understanding pheromones and signature mixtures for better zoo-animal husbandry and conservation. Int. Zoo Yearb. 45, 55–79 (2011).Article 

Google Scholar 
Brennan, P. A. & Kendrick, K. M. Mammalian social odours: Attraction and individual recognition. Philos. Trans. R. Soc. B Biol. Sci. 361, 2061–2078 https://doi.org/10.1098/rstb.2006.1931 (2006).Article 
CAS 

Google Scholar 
Bellemain, E., Swenson, J. E. & Taberlet, P. Mating strategies in relation to sexually selected infanticide in a non-social carnivore: The brown bear. Ethology 112, 238–246 (2006).Article 

Google Scholar 
Rogers, L. L. Effects of food supply and kinship on social behavior, movements, and population growth of black bears in northeastern Minnesota. Wildl. Monogr. 97, 72 (1987).
Google Scholar 
Noyce, K. V. & Garshelis, D. L. Follow the leader: Social cues help guide landscape-level movements of American black bears (Ursus americanus). Can. J. Zool. 92, 1005–1017 (2014).Article 

Google Scholar 
Hansen, J. E., Hertel, A. G., Frank, S. C., Kindberg, J. & Zedrosser, A. Social environment shapes female settlement decisions in a solitary carnivore. Behav. Ecol. 33, 137–146 (2022).Article 
CAS 
PubMed 

Google Scholar 
Morehouse, A. T., Loosen, A. E., Graves, T. A. & Boyce, M. S. The smell of success: Reproductive success related to rub behavior in brown bears. PLoS ONE 16, 247964 https://doi.org/10.1371/journal.pone.0247964 (2021).Article 
CAS 

Google Scholar 
Tschanz, B., Meyer-Holzapfel, M. & Bachmann, S. Das informationssystem bei Braunbären. Z. Tierpsychol. 27, 47–72 (1970).Article 

Google Scholar 
Tattoni, C., Bragalanti, N., Ciolli, M., Groff, C. & Rovero, F. Behavior of the European brown bear at rub trees. Ursus 32e9, 1–11https://doi.org/10.2192/URSUS-D-20-00022.3 (2021).Article 

Google Scholar 
Alberts, A. C. Constraints on the design of chemical communication systems in terrestrial vertebrates. Am. Nat. 139, S62–S89 (1992).Article 

Google Scholar  More

Robertson, G. P. et al. Cellulosic biofuel contributions to a sustainable energy future: Choices and outcomes. Sci. (80-.) 356, 1–9 (2017).Article 

Google Scholar 
Ma, L. et al. The impact of stand age and fertilization on the soil microbiome of Miscanthus × giganteus. Phytobiomes J. 5, 51–59 (2021).Article 

Google Scholar 
Hestrin, R., Lee, M. R., Whitaker, B. K. & Pett-Ridge, J. The switchgrass microbiome: a review of structure, function, and taxonomic distribution. Phytobiomes J. 5, 14–28 (2021).Article 

Google Scholar 
Heaton, E. A., Dohleman, F. G. & Long, S. P. Meeting US biofuel goals with less land: The potential of Miscanthus. Glob. Chang. Biol. 14, 2000–2014 (2008).Article 
ADS 

Google Scholar 
Langholtz, M., Stokes, B. & Eaton, L. 2016 billion-ton report: Advancing domestic resources for a thriving bioeconomy (Executive Summary). Ind. Biotechnol. 12, 282–289 (2016).Article 

Google Scholar 
Roley, S. S. et al. Associative nitrogen fixation (ANF) across a nitrogen input gradient. PLoS One 13, 1–19 (2018).Article 

Google Scholar 
Toju, H. et al. Core microbiomes for sustainable agroecosystems. Nat. Plants 4, 247–257 (2018).Article 
PubMed 

Google Scholar 
Busby, P. E. et al. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol. 15, 1–14 (2017).Article 

Google Scholar 
Wang, N. R. & Haney, C. H. Harnessing the genetic potential of the plant microbiome. Biochem. (Lond.) 42, 20–25 (2020).Article 
CAS 

Google Scholar 
Haskett, T. L., Tkacz, A. & Poole, P. S. Engineering rhizobacteria for sustainable agriculture. ISME J. 15, 949–964 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Hacquard, S. et al. Microbiota and host nutrition across plant and animal kingdoms. Cell Host Microbe 17, 603–616 (2015).Article 
CAS 
PubMed 

Google Scholar 
Gopal, M. & Gupta, A. Microbiome selection could spur next-generation plant breeding strategies. Front. Microbiol. 7, 1971 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Hardoim, P. R. et al. The hidden world within plants: Ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol. Mol. Biol. Rev. 79, 293–320 (2015).Article 
PubMed 
PubMed Central 

Google Scholar 
Andrews, J. H. & Harris, R. F. The ecology and biogeography of microorganisms on plant surfaces. Annu. Rev. Phytopathol. 38, 145–180 (2000).Article 
PubMed 

Google Scholar 
Bulgarelli, D., Schlaeppi, K., Spaepen, S., van Themaat, E. V. L. & Schulze-Lefert, P. Structure and functions of the bacterial microbiota of plants. Annu. Rev. Plant Biol. 64, 807–838 (2013).Article 
CAS 
PubMed 

Google Scholar 
Müller, D. B., Vogel, C., Bai, Y. & Vorholt, J. A. The Plant Microbiota: Systems-Level Insights and Perspectives. Annu. Rev. Genet. 50, 120215–034952 (2016).Article 

Google Scholar 
Kuzyakov, Y. & Razavi, B. S. Rhizosphere size and shape: Temporal dynamics and spatial stationarity. Soil Biol. Biochem. 135, 343–360 (2019).Article 
CAS 

Google Scholar 
Bell, T. H. et al. Manipulating wild and tamed phytobiomes: Challenges and opportunities. Phytobiomes J. 3, 3–21 (2019).Article 

Google Scholar 
Chen, T. et al. A plant genetic network for preventing dysbiosis in the phyllosphere. Nature 580, 653–657 (2020).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Vorholt, J. A. Microbial life in the phyllosphere. Nat. Rev. Microbiol. 10, 828–840 (2012).Article 
CAS 
PubMed 

Google Scholar 
Koskella, B. The phyllosphere. Curr. Biol. 30, R1143–R1146 (2020).Article 
CAS 
PubMed 

Google Scholar 
Lindow, S. E. & Brandl, M. T. Microbiology of the phyllosphere. Appl. Environ. Microbiol. 69, 1875–1883 (2003).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bringel, F. & Couée, I. Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics. Front. Microbiol. 6, 486 (2015).Dorokhov, Y. L., Sheshukova, E. V. & Komarova, T. V. Methanol in plant life. Front. Plant Sci. 871, 1–6 (2018).
Google Scholar 
Cavicchioli, R. et al. Scientists’ warning to humanity: microorganisms and climate change. Nat. Rev. Microbiol. 17, 569–586 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Peñuelas, J. & Terradas, J. The foliar microbiome. Trends Plant Sci. 19, 278–280 (2014).Article 
PubMed 

Google Scholar 
Edwards, J. et al. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc. Natl Acad. Sci. USA. 112, E911–E920 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Zhalnina, K. et al. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat. Microbiol. 3, 470 (2018).Article 
CAS 
PubMed 

Google Scholar 
Xu, L. et al. Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria. Proc. Natl Acad. Sci. 115, E4284–E4293 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Shade, A. & Stopnisek, N. Abundance-occupancy distributions to prioritize plant core microbiome membership. Curr. Opin. Microbiol. 49, 50–58 (2019).Article 
PubMed 

Google Scholar 
Stopnisek, N. & Shade, A. Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype. ISME J. 15, 2708–2722 (2021).Grady, K. L., Sorensen, J. W., Stopnisek, N., Guittar, J. & Shade, A. Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops. Nat. Commun. 10, 4135 (2019).Singer, E., Bonnette, J., Kenaley, S. C., Woyke, T. & Juenger, T. E. Plant compartment and genetic variation drive microbiome composition in switchgrass roots. Environ. Microbiol. Rep. 11, 185–195 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Lundberg, D. S. et al. Defining the core Arabidopsis thaliana root microbiome. Nature 488, 86–90 (2012).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bulgarelli, D. et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488, 91–95 (2012).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Bahulikar, R. A., Torres-Jerez, I., Worley, E., Craven, K. & Udvardi, M. K. Diversity of nitrogen-fixing bacteria associated with switchgrass in the native tallgrass prairie of Northern Oklahoma. Appl. Environ. Microbiol. 80, 5636–5643 (2014).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Roley, S. S., Xue, C., Hamilton, S. K., Tiedje, J. M. & Robertson, G. P. Isotopic evidence for episodic nitrogen fixation in switchgrass (Panicum virgatum L.). Soil Biol. Biochem. 129, 90–98 (2019).Article 
CAS 

Google Scholar 
Bowers, R. M. et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725–731 (2017).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Yoon, S. H., Ha, S. M., Lim, J., Kwon, S. & Chun, J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van. Leeuwenhoek, Int. J. Gen. Mol. Microbiol. 110, 1281–1286 (2017).Article 
CAS 

Google Scholar 
Julsing, M. K., Rijpkema, M., Woerdenbag, H. J., Quax, W. J. & Kayser, O. Functional analysis of genes involved in the biosynthesis of isoprene in Bacillus subtilis. Appl. Microbiol. Biotechnol. 75, 1377–1384 (2007).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Carlström, C. I. et al. Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere. Nat. Ecol. Evol. 3, 1445–1454 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Laskowska, E. & Kuczyńska-Wiśnik, D. New insight into the mechanisms protecting bacteria during desiccation. Curr. Genet. 66, 313–318 (2020).Article 
CAS 
PubMed 

Google Scholar 
Zou, H. et al. The metabolism and biotechnological application of betaine in microorganism. Appl. Microbiol. Biotechnol. 100, 3865–3876 (2016).Article 
CAS 
PubMed 

Google Scholar 
Rastogi, G., Coaker, G. L. & Leveau, J. H. J. New insights into the structure and function of phyllosphere microbiota through high-throughput molecular approaches. FEMS Microbiol. Lett. 348, 1–10 (2013).Article 
CAS 
PubMed 

Google Scholar 
Urrejola, C. et al. Genomic features for desiccation tolerance and sugar biosynthesis in the extremophile gloeocapsopsis sp. UTEX B3054. Front. Microbiol. 10, 1–11 (2019).Article 

Google Scholar 
Lacerda-Júnior, G. V. et al. Land use and seasonal effects on the soil microbiome of a Brazilian dry forest. Front. Microbiol. 10, 1–14 (2019).Article 

Google Scholar 
Dai, J. et al. Unraveling adaptation of Pontibacter korlensis to radiation and infertility in desert through complete genome and comparative transcriptomic analysis. Sci. Rep. 5, 1–9 (2015).Article 

Google Scholar 
Harty, C. E. et al. Ethanol stimulates trehalose production through a SpoT-DksA-AlgU-dependent pathway in Pseudomonas aeruginosa. J. Bacteriol. 201, 1–21 (2019).Kimmerer, T. W. & MacDonald, R. C. Acetaldehyde and ethanol biosynthesis in leaves of plants. Plant Physiol. 84, 1204–1209 (1987).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Ferner, E., Rennenberg, H. & Kreuzwieser, J. Effect of flooding on C metabolism of flood-tolerant (Quercus robur) and non-tolerant (Fagus sylvatica) tree species. Tree Physiol. 32, 135–145 (2012).Article 
CAS 
PubMed 

Google Scholar 
Kimmerer, T. W. & Kozlowski, T. T. Ethylene, ethane, acetaldehyde, and ethanol production by plants under stress. Plant Physiol. 69, 840–847 (1982).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Liu, Y. et al. Assessment of drought tolerance of 49 switchgrass (Panicum virgatum) genotypes using physiological and morphological parameters. Biotechnol. Biofuels 8, 1–18 (2015).Article 

Google Scholar 
Wingler, A. et al. Trehalose 6-phosphate is required for the onset of leaf senescence associated with high carbon availability. Plant Physiol. 158, 1241–1251 (2012).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Gottschlich, L., Geiser, P., Bortfeld-Miller, M., Field, C. M. & Vorholt, J. A. Complex general stress response regulation in Sphingomonas melonis Fr1 revealed by transcriptional analyses. Sci. Rep. 9, 1–13 (2019).Article 
CAS 

Google Scholar 
Chen, C., Li, S., McKeever, D. R. & Beattie, G. A. The widespread plant-colonizing bacterial species Pseudomonas syringae detects and exploits an extracellular pool of choline in hosts. Plant J. 75, 891–902 (2013).Article 
CAS 
PubMed 

Google Scholar 
Valenzuela-Soto, E. M. & Figueroa-Soto, C. G. Biosynthesis and degradation of glycine betaine and its potential to control plant growth and development. in Osmoprotectant-Mediated Abiotic Stress Tolerance in Plants (eds. Anwar Hossain, M., Kumar, V., Burritt, D. J., Fujita, M. & Makela, P. S. A.) 241–256 (Springer, 2019). https://doi.org/10.1007/978-3-030-27423-8_5.Kerchev, P., De Smet, B., Waszczak, C., Messens, J. & Van Breusegem, F. Redox strategies for crop improvement. Antioxid. Redox Signal 23, 1186–1205 (2015).Article 
CAS 
PubMed 

Google Scholar 
Considine, M. J. & Foyer, C. H. Redox regulation of plant development. Antioxid. Redox Signal. 21, 1305–1326 (2014).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Spaepen, S., Vanderleyden, J. & Remans, R. Indole-3-acetic acid in microbial and microorganism-plant signaling. FEMS Microbiol. Rev. 31, 425–448 (2007).Article 
CAS 
PubMed 

Google Scholar 
Egamberdieva, D., Wirth, S. J., Alqarawi, A. A., Abd-Allah, E. F. & Hashem, A. Phytohormones and beneficial microbes: Essential components for plants to balance stress and fitness. Front. Microbiol. 8, 1–14 (2017).Article 

Google Scholar 
Lajoie, G., Maglione, R. & Kembel, S. W. Adaptive matching between phyllosphere bacteria and their tree hosts in a neotropical forest. Microbiome 8, 1–10 (2020).Article 

Google Scholar 
McGenity, T. J., Crombie, A. T. & Murrell, J. C. Microbial cycling of isoprene, the most abundantly produced biological volatile organic compound on Earth. ISME J. 12, 931–941 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Sharkey, T. D., Wiberley, A. E. & Donohue, A. R. Isoprene emission from plants: Why and how. Ann. Bot. 101, 5–18 (2008).Article 
CAS 
PubMed 

Google Scholar 
Zuo, Z. et al. Isoprene acts as a signaling molecule in gene networks important for stress responses and plant growth. Plant Physiol. 180, 124–152 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Sharkey, T. D. & Yeh, S. Isoprene emission from plants. Plant Mol. Biol. 52, 407–436 (2001).CAS 

Google Scholar 
Sharkey, T. D., Loreto, F. & Delwiche, C. High carbon dioxide and sun/shade effects on isoprene emission from oak and aspen tree leaves. Plant, Cell Environ. 14, 333–338 (1991).Article 
CAS 

Google Scholar 
Eller, A. S. D. et al. Volatile organic compound emissions from switchgrass cultivars used as biofuel crops. Atmos. Environ. 45, 3333–3337 (2011).Article 
ADS 
CAS 

Google Scholar 
Morrison, E. C., Drewer, J. & Heal, M. R. A comparison of isoprene and monoterpene emission rates from the perennial bioenergy crops short-rotation coppice willow and Miscanthus and the annual arable crops wheat and oilseed rape. GCB Bioenergy 8, 211–225 (2016).Article 
CAS 

Google Scholar 
Sivy, T. L., Shirk, M. C. & Fall, R. Isoprene synthase activity parallels fluctuations of isoprene release during growth of Bacillus subtilis. Biochem. Biophys. Res. Commun. 294, 71–75 (2002).Article 
CAS 
PubMed 

Google Scholar 
Crombie, A. T. et al. Poplar phyllosphere harbors disparate isoprene-degrading bacteria. Proc. Natl Acad. Sci. USA. 115, 13081–13086 (2018).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
El Khawand, M. et al. Isolation of isoprene degrading bacteria from soils, development of isoA gene probes and identification of the active isoprene-degrading soil community using DNA-stable isotope probing. Environ. Microbiol. 18, 2743–2753 (2016).Article 
CAS 
PubMed 

Google Scholar 
Nowicka, B. & Kruk, J. Occurrence, biosynthesis and function of isoprenoid quinones. Biochim. Biophys. Acta – Bioenerg. 1797, 1587–1605 (2010).Article 
CAS 

Google Scholar 
Kałużna, M. et al. Pseudomonas cerasi sp. nov. (non Griffin, 1911) isolated from diseased tissue of cherry. Syst. Appl. Microbiol. 39, 370–377 (2016).Article 
PubMed 

Google Scholar 
El-Tarabily, K. A., Nassar, A. H., Hardy, G. E. S. J. & Sivasithamparam, K. Plant growth promotion and biological control of Pythium aphanidermatum, a pathogen of cucumber, by endophytic actinomycetes. J. Appl. Microbiol 106, 13–26 (2009).Article 
CAS 
PubMed 

Google Scholar 
Javed, Z., Tripathi, G. D., Mishra, M. & Dashora, K. Actinomycetes – the microbial machinery for the organic-cycling, plant growth, and sustainable soil health. Biocatal. Agric. Biotechnol. 31, 101893 (2021).Article 
CAS 

Google Scholar 
Anwar, S., Ali, B. & Sajid, I. Screening of rhizospheric actinomycetes for various in-vitro and in-vivo plant growth promoting (PGP) traits and for agroactive compounds. Front. Microbiol. 7, 1–11 (2016).Article 

Google Scholar 
Bao, L. et al. Microbial community overlap between the phyllosphere and rhizosphere of three plants from Yongxing Island, South China Sea. Microbiologyopen 9, 1–18 (2020).Article 

Google Scholar 
Remus-Emsermann, M. N. P. & Schlechter, R. O. Phyllosphere microbiology: at the interface between microbial individuals and the plant host. N. Phytol. 218, 1327–1333 (2018).Article 

Google Scholar 
Beilsmith, K. et al. Genome-wide association studies on the phyllosphere microbiome: embracing complexity in host–microbe interactions. Plant J. 97, 164–181 (2019).Article 
CAS 
PubMed 

Google Scholar 
Levy, A., Conway, J. M., Dangl, J. L. & Woyke, T. Elucidating bacterial gene functions in the plant microbiome. Cell Host Microbe 24, 475–485 (2018).Article 
CAS 
PubMed 

Google Scholar 
Trivedi, P., Leach, J. E., Tringe, S. G., Sa, T. & Singh, B. K. Plant–microbiome interactions: from community assembly to plant health. Nat. Rev. Microbiol. 18, 607–621 (2020).Article 
CAS 
PubMed 

Google Scholar 
Choi, H. et al. Identification of viruses and viroids infecting tomato and pepper plants in vietnam by metatranscriptomics. Int. J. Mol. Sci. 21, 1–16 (2020).Article 
ADS 

Google Scholar 
Marzano, S. Y. L. & Domier, L. L. Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes. Virus Res 213, 332–342 (2016).Article 
CAS 
PubMed 

Google Scholar 
Chao S, et al. Metatranscriptomic sequencing suggests the presence of novel RNA viruses in rice rransmitted by brown planthopper. Viruses. 13, 2464 (2021).Delmotte, N. et al. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc. Natl Acad. Sci. 106, 16428–16433 (2009).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Suzuki, Y., Makino, A. & Mae, T. An efficient method for extraction of RNA from rice leaves at different ages using benzyl chloride. J. Exp. Bot. 52, 1575–1579 (2001).Article 
CAS 
PubMed 

Google Scholar 
Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl Acad. Sci. 108, 4516–4522 (2011).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).Article 
PubMed 
PubMed Central 

Google Scholar 
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Druzhinina, I. S. et al. Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts. PLoS Genet. 14, e1007322 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Haridas, S. et al. 101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens. Stud. Mycol. 96, 141–153 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Gostinčar, C. et al. Genome sequencing of four Aureobasidium pullulans varieties: Biotechnological potential, stress tolerance, and description of new species. BMC Genomics 15, 549 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Gill, U. S. et al. Draft genome sequence resource of switchgrass rust pathogen, puccinia novopanici isolate ard-01. Phytopathology 109, 1513–1515 (2019).Article 
CAS 
PubMed 

Google Scholar 
Bowsher, A. W., Benucci, G. M. N., Bonito, G. & Shade, A. Seasonal dynamics of core fungi in the switchgrass phyllosphere, and co-occurrence with leaf bacteria. Phytobiomes J. 5, 60–68 (2021).Li, D., Liu, C. M., Luo, R., Sadakane, K. & Lam, T. W. MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015).Article 
CAS 
PubMed 

Google Scholar 
Kang, D. D. et al. MetaBAT 2: An adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 2019, 1–13 (2019).
Google Scholar 
Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S. & Kyrpides, N. C. New insights from uncultivated genomes of the global human gut microbiome. Nature 568, 505–510 (2019).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Swan, B. K. et al. Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proc. Natl Acad. Sci. USA. 110, 11463–11468 (2013).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Eren, A. M. et al. Anvi’o: an advanced analysis and visualization platform for’omics data. PeerJ. 2015, 1–29 (2015).
Google Scholar 
Lee, M. D. GToTree: a user-friendly workflow for phylogenomics. Bioinformatics 35, 4162–4164 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Shaffer, M. et al. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res. 48, 8883–8900 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 36, 996 (2018).Article 
CAS 
PubMed 

Google Scholar 
Suzuki, R. & Shimodaira, H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22, 1540–1542 (2006).Article 
CAS 
PubMed 

Google Scholar 
Blin, K. et al. AntiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res. 49, W29–W35 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Navarro-Muñoz, J. C. et al. A computational framework to explore large-scale biosynthetic diversity. Nat. Chem. Biol. 16, 60–68 (2020).Article 
PubMed 

Google Scholar 
Zimmermann, J., Kaleta, C. & Waschina, S. Gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. Genome Biol. 22, 1–35 (2021).Article 

Google Scholar 
Tseng, T. T., Tyler, B. M. & Setubal, J. C. Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology. BMC Microbiol 9, 1–9 (2009).Article 

Google Scholar 
Lucke, M., Correa, M. G. & Levy, A. The role of secretion systems, effectors, and secondary metabolites of beneficial rhizobia in interactions with plants and microbes. Front. Plant Sci. 11, 589416 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Palmer, J. L., Hilton, S., Picot, E., Bending, G. D. & Schäfer, H. Tree phyllospheres are a habitat for diverse populations of CO-oxidizing bacteria. Environ. Microbiol. 23, 6309–6327 (2021).Article 
CAS 
PubMed 

Google Scholar 
Bay, S. K. et al. Trace gas oxidizers are widespread and active members of soil microbial communities. Nat. Microbiol. 6, 246–256 (2021).Article 
CAS 
PubMed 

Google Scholar  More

Whittaker, R. J., Fernández-Palacios, J. M., Matthews, T. J., Borregaard, M. K. & Triantis, K. A. Island biogeography: taking the long view of nature’s laboratories. Science 357, eaam8326 (2017).Article 
PubMed 

Google Scholar 
Boyer, A. G. & Jetz, W. Biogeography of body size in Pacific island birds. Ecography 33, 369–379 (2010).
Google Scholar 
Heinen, J. H., van Loon, E. E., Hansen, D. M. & Kissling, W. D. Extinction‐driven changes in frugivore communities on oceanic islands. Ecography 41, 1245–1255 (2018).Article 

Google Scholar 
Sayol, F., Steinbauer, M. J., Blackburn, T. M., Antonelli, A. & Faurby, S. Anthropogenic extinctions conceal widespread evolution of flightlessness in birds. Sci. Adv. 6, eabb6095 (2020).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Steadman, D. W. & Martin, P. S. The late quaternary extinction and future resurrection of birds on Pacific islands. Earth Sci. Rev. 61, 133–147 (2003).Article 
ADS 

Google Scholar 
Blackburn, T. M., Cassey, P., Duncan, R. P., Evans, K. L. & Gaston, K. J. Avian extinction and mammalian introductions on oceanic islands. Science 305, 1955–1958 (2004).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Blackburn, T. M., Lockwood, J. L., & Cassey, P. (2009). Avian Invasions: The Ecology and Evolution of Exotic Birds (Oxford University Press, 2009).Steadman, D. W. Extinction and Biogeography of Tropical Pacific Birds (University of Chicago Press, 2006).Boyer, A. G. & Jetz, W. Extinctions and the loss of ecological function in island bird communities. Glob. Ecol. Biogeogr. 23, 679–688 (2014).Article 

Google Scholar 
Fritts, T. H. & Rodda, G. H. The role of introduced species in the degradation of island ecosystems: a case history of Guam. Annu. Rev. Ecol. Syst. 29, 113–140 (1998).Article 

Google Scholar 
Vidal, M. M. et al. Frugivores at higher risk of extinction are the key elements of a mutualistic network. Ecology 95, 3440–3447 (2014).Article 

Google Scholar 
Pires, M. M. et al. Reconstructing past ecological networks: the reconfiguration of seed-dispersal interactions after megafaunal extinction. Oecologia 175, 1247–1256 (2014).Article 
ADS 
PubMed 

Google Scholar 
Heinen, J. H., Rahbek, C. & Borregaard, M. K. Conservation of species interactions to achieve self-sustaining ecosystems. Ecography 43, 1603–1611 (2020).Article 

Google Scholar 
Moreno-Mateos, D. et al. The long-term restoration of ecosystem complexity. Nat. Ecol. Evol. 4, 676–685 (2020).Article 
PubMed 

Google Scholar 
Galetti, M. et al. Functional extinction of birds drives rapid evolutionary changes in seed size. Science 340, 1086–1090 (2013).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Dunn, R. R. Coextinction: anecdotes, models, and speculation. In Holocene Extinctions (ed. Turvey, S. T.) 167–180 (Oxford University Press, 2009).Rezende, E. L., Lavabre, J. E., Guimarães, P. R., Jordano, P. & Bascompte, J. Non-random coextinctions in phylogenetically structured mutualistic networks. Nature 448, 925–928 (2007).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Wotton, D. M. & Kelly, D. Do larger frugivores move seeds further? Body size, seed dispersal distance, and a case study of a large, sedentary pigeon. J. Biogeogr. 39, 1973–1983 (2012).Article 

Google Scholar 
Anderson, S. H., Kelly, D., Ladley, J. J., Molloy, S. & Terry, J. Cascading effects of bird functional extinction reduce pollination and plant density. Science 331, 1068–1071 (2011).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Pérez-Méndez, N., Jordano, P., García, C. & Valido, A. The signatures of Anthropocene defaunation: cascading effects of the seed dispersal collapse. Sci. Rep. 6, 1–9 (2016).Article 

Google Scholar 
Wotton, D. M. & Kelly, D. Frugivore loss limits recruitment of large-seeded trees. Proc. R. Soc. B Biol. Sci. 278, 3345–3354 (2011).Article 

Google Scholar 
Traveset, A. Effect of seed passage through vertebrate frugivores’ guts on germination: a review. Perspect. Plant Ecol. Evol. Syst. 1, 151–190 (1998).Article 

Google Scholar 
Janzen, D. H. Herbivores and the number of tree species in tropical forests. Am. Nat. 104, 501–528 (1970).Article 

Google Scholar 
Connell, J. H. On the role of natural enemies in preventing competitive exclusion in some marine animals and in rain forest trees. In Dynamics of Populations (eds Den Boer, P. J. & Gradwell, G. R.) 298–312 (Centre for Agricultural Publishing and Documentation, 1971).Farwig, N. & Berens, D. G. Imagine a world without seed dispersers: a review of threats, consequences and future directions. Basic Appl. Ecol. 13, 109–115 (2012).Article 

Google Scholar 
Meehan, H. J., McConkey, K. R. & Drake, D. R. Potential disruptions to seed dispersal mutualisms in Tonga, Western Polynesia. J. Biogeogr. 29, 695–712 (2002).Article 

Google Scholar 
Pérez-Méndez, N., Jordano, P. & Valido, A. Downsized mutualisms: consequences of seed dispersers’ body-size reduction for early plant recruitment. Perspect. Plant Ecol. Evol. Syst. 17, 151–159 (2015).Article 

Google Scholar 
Rodriguez, L. F. Can invasive species facilitate native species? Evidence of how, when, and why these impacts occur. Biol. Invasions 8, 927–939 (2006).Article 

Google Scholar 
Griffiths, C. J., Hansen, D. M., Jones, C. G., Zuël, N. & Harris, S. Resurrecting extinct interactions with extant substitutes. Curr. Biol. 21, 762–765 (2011).Article 
CAS 
PubMed 

Google Scholar 
Thibault, J.-C. & Cibois, A. Birds Of Eastern Polynesia: A Biogeographic Atlas (Lynx Edicions, 2017).Vizentin-Bugoni, J. et al. Structure, spatial dynamics, and stability of novel seed dispersal mutualistic networks in Hawaiʻi. Science 364, 78–82 (2019).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Case, S. B. & Tarwater, C. E. Functional traits of avian frugivores have shifted following species extinction and introduction in the Hawaiian Islands. Funct. Ecol. 34, 2467–2476 (2020).Article 

Google Scholar 
Albert, S., Flores, O. & Strasberg, D. Collapse of dispersal trait diversity across a long‐term chronosequence reveals a strong negative impact of frugivore extinctions on forest resilience. J. Ecol. 108, 1386–1397 (2020).Article 

Google Scholar 
Cheke, A. S. & Hume, J. P. Lost Land of the Dodo: The Ecological History of Mauritius, Réunion & Rodrigues 464 (T. & A. D. Poyser, 2008).Hammond, D. S. et al. Threats to environmentally sensitive areas from peri-urban expansion in Mauritius. Environ. Conserv. 42, 256–267 (2015).Article 

Google Scholar 
Florens, F. V., Baider, C., Seegoolam, N. B., Zmanay, Z. & Strasberg, D. Long‐term declines of native trees in an oceanic island’s tropical forests invaded by alien plants. Appl. Veg. Sci. 20, 94–105 (2017b).Article 

Google Scholar 
McConkey, K. R. & O’Farrill, G. Cryptic function loss in animal populations. Trends Ecol. Evol. 30, 182–189 (2015).Article 
PubMed 

Google Scholar 
Carpenter, J. K. et al. The forgotten fauna: Native vertebrate seed predators on islands. Funct. Ecol. 34, 1802–1813 (2020).Article 

Google Scholar 
Perea, R., Delibes, M., Polko, M., Suárez-Esteban, A. & Fedriani, J. M. Context‐dependent fruit–frugivore interactions: partner identities and spatio‐temporal variations. Oikos 122, 943–951 (2013).Article 

Google Scholar 
Dracxler, C. M. & Kissling, W. D. The mutualism–antagonism continuum in Neotropical palm–frugivore interactions: from interaction outcomes to ecosystem dynamics. Biol. Rev. 97, 527–553 (2022).Article 

Google Scholar 
Baider, C. & Florens, F. B. V. Current decline of the ‘Dodo-tree’: a case of broken-down interactions with extinct species or the result of new interactions with alien invaders? In Emerging Threats to Tropical Forests (eds Laurance, W. & Peres, C.) 199–214 (Chicago University Press, 2006).Reinegger, R. D., Oleksy, R. Z., Bissessur, P., Naujeer, H. & Jones, G. First come, first served: fruit availability to keystone bat species is potentially reduced by invasive macaques. J. Mammal. 102, 428–439 (2021).Article 

Google Scholar 
Reinegger, R. D., Oleksy, R. Z., Gazagne, E. & Jones, G. Foraging strategies of invasive Macaca fascicularis may promote plant invasion in Mauritius. Int. J. Primatol. 44, 1–31 (2022).O’Connor, S. J. & Kelly, D. Seed dispersal of matai (Prumnopitys taxifolia) by feral pigs (Sus scrofa). N.Z. J. Ecol. 36, 228–231 (2012).
Google Scholar 
Shiels, A. B. & Drake, D. R. Are introduced rats (Rattus rattus) both seed predators and dispersers in Hawaii? Biol. Invasions 13, 883–894 (2011).Article 

Google Scholar 
Florens, F. B. V. et al. Disproportionately large ecological role of a recently mass-culled flying fox in native forests of an oceanic island. J. Nat. Conserv. 40, 85–93 (2017a).Article 

Google Scholar 
Bissessur, P., Bunsy, Y., Baider, C. & Florens, F. B. V. Non-intrusive systematic study reveals mutualistic interactions between threatened island endemic species and points to more impactful conservation. J. Nat. Conserv. 49, 108–117 (2019).Article 

Google Scholar 
Hume, J. P. & Winters, R. Captive birds on Dutch Mauritius: bad-tempered parrots, warty pigeons and notes on other native animals. Hist. Biol. 28, 812–822 (2016).Article 

Google Scholar 
Kingston, T., Florens, F. B. V., Oleksy, R., Ruhomaun, K. & Tatayah, V. Pteropus niger. The IUCN Red List of Threatened Species (2018).Hume, J. P. The history of the dodo Raphus cucullatus and the penguin of Mauritius. Hist. Biol. 18, 65–89 (2006).Article 

Google Scholar 
Hume, J. P. Reappraisal of the parrots (Aves: Psittacidae) from the Mascarene Islands, with comments on their ecology, morphology and affinities. Zootaxa 1513, 1–76 (2007).Article 

Google Scholar 
Hume, J. P. Systematics, morphology, and ecological history of the Mascarene starlings (Aves: Sturnidae) with the description of a new genus and species from Mauritius. Zootaxa 3849, 1–75 (2014).Article 
PubMed 

Google Scholar 
Albert, S., Flores, O., Baider, C., Florens, F. B. V. & Strasberg, D. Differing severity of frugivore loss contrasts the fate of native forests on the land of the Dodo (Mascarene archipelago). Biol. Conserv. 257, 109–131 (2021).Article 

Google Scholar 
Florens, F. B. V. Conservation in Mauritius and Rodrigues: challenges and achievements from two ecologically devastated oceanic islands. In Conservation Biology: Voices from the Tropics (eds Raven, P. H., Sodhi, N. S. & Gibson, L.) 40–50 (Wiley-Blackwell, 2013).Krivek, G., Florens, F. B. V., Baider, C., Seegobin, V. O. & Haugaasen, T. Invasive alien plant control improves foraging habitat quality of a threatened island flying fox. J. Nat. Conserv. 54, 125805 (2020).Article 

Google Scholar 
Monty, M. F., Florens, F. B. V. & Baider, C. Invasive alien plants elicit reduced production of flowers and fruits in various native forest species on the tropical island of Mauritius (Mascarenes, Indian Ocean). Trop. Conserv. Sci. 6, 35–49 (2013).Article 

Google Scholar 
Florens, F. B. V. & Baider, C. Ecological restoration in a developing island nation: how useful is the science? Restor. Ecol. 21, 1–5 (2013).Article 

Google Scholar 
Nogués-Bravo, D., Simberloff, D., Rahbek, C. & Sanders, N. J. Rewilding is the new Pandora’s box in conservation. Curr. Biol. 26, R87–R91 (2016).Article 
PubMed 

Google Scholar 
Linnebjerg, J. F., Hansen, D. M., Bunbury, N. & Olesen, J. M. Diet composition of the invasive red-whiskered bulbul Pycnonotus jocosus in Mauritius. J. Trop. Ecol. 26, 347–350 (2010).Article 

Google Scholar 
Sperry, J. H. et al. Fruit and seed traits of native and invasive plant species in Hawai’i: implications for seed dispersal by non-native birds. Biol. Invasions 23, 1819–1835 (2021).Article 

Google Scholar 
Hansen, D. M., Donlan, C. J., Griffiths, C. J. & Campbell, K. J. Ecological history and latent conservation potential: large and giant tortoises as a model for taxon substitutions. Ecography 33, 272–284 (2010).
Google Scholar 
Oleksy, R. Z. et al. The movement ecology of the Mauritian flying fox (Pteropus niger): a long-term study using solar-powered GSM/GPS tags. Mov. Ecol. 7, 1–12 (2019).Article 

Google Scholar 
Seegobin, V. O., Oleksy, R. Z. & Florens, F. B. V. Foraging and roosting patterns of a repeatedly mass-culled island flying fox offer avenues to mitigate human-wildlife conflict. Biodiversity 23, 49–60 (2022).Article 

Google Scholar 
Baider, C. et al. Status of plant conservation in oceanic islands of the Western Indian Ocean. In Proceedings of the 4th Global Botanic Gardens Congress (National Botanic Gardens of Ireland, Dublin, 2010).Humphreys, A. M., Govaerts, R., Ficinski, S. Z., Lughadha, E. N. & Vorontsova, M. S. Global dataset shows geography and life form predict modern plant extinction and rediscovery. Nat. Ecol. Evol. 3, 1043–1047 (2019).Article 
PubMed 

Google Scholar 
BGCI. State of the World’s Trees (BGCI, 2021).Vázquez-Yanes, C. & Orozco-Segovia, A. Patterns of seed longevity and germination in the tropical rainforest. Annu. Rev. Ecol. Syst. 24, 69–87 (1993).Article 

Google Scholar 
Gallaher, T., Callmander, M. W., Buerki, S. & Keeley, S. C. A long distance dispersal hypothesis for the Pandanaceae and the origins of the Pandanus tectorius complex. Mol. Phylogenet. Evol. 83, 20–32 (2015).Article 
PubMed 

Google Scholar 
Hansen, D. M., Kaiser, C. N. & Müller, C. B. Seed dispersal and establishment of endangered plants on oceanic islands: the Janzen-Connell model, and the use of ecological analogues. PLoS ONE 3, e2111 (2008).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Albert, S., Flores, O., Stahl, M., Guilhabert, F. & Strasberg, D. Tree recruitment after native frugivore extinction? A field experiment to test the impact of fruit flesh persistence in a tropical oceanic island. J. Trop. Ecol. 38, 370–376 (2022).Article 

Google Scholar 
Witmer, M. C. & Cheke, A. S. The dodo and the tambalacoque tree: an obligate mutualism reconsidered. Oikos 61, 133–137 (1991).Bosser, J., Cadet, T., Guého, J. & Marais, W. Flore des Mascareignes: La Réunion, Maurice, Rodrigues (MSIRI/ORSTOM-IRD/Kew, Mauritius, 1976-onwards).Jordano, P. Fruits and frugivory. In Seeds: The Ecology of Regeneration in Plant Communities (ed. Fenner, N.) 125–165 (CABI Publishing, 2000).van der Pijl, L. Principles of Dispersal in Higher Plants 218 (Springer-Verlag, 1969).Dominy, N. J., Svenning, J. C. & Li, W. H. Historical contingency in the evolution of primate color vision. J. Hum. Evol. 44, 25–45 (2003).Article 
PubMed 

Google Scholar 
Oba, S. et al. A Bayesian missing value estimation method for gene expression profile data. Bioinformatics 19, 2088–2096 (2003).Article 
CAS 
PubMed 

Google Scholar 
Stekhoven, D. J. & Bühlmann, P. MissForest—non-parametric missing value imputation for mixed-type data. Bioinformatics 28, 112–118 (2012).Article 
CAS 
PubMed 

Google Scholar 
Qian, H. & Jin, Y. An updated megaphylogeny of plants, a tool for generating plant phylogenies and an analysis of phylogenetic community structure. J. Plant Ecol. 9, 233–239 (2016).Article 

Google Scholar 
Jin, Y. & Qian, H. V.PhyloMaker: an R package that can generate very large phylogenies for vascular plants. Ecography 42, 1353–1359 (2019).Article 

Google Scholar 
Santos, T., Diniz-Filho, J. A., e Luis, T. R., Bini, M., & Santos, M. T. Package ‘PVR’. Phylogenetic Eigenvectors Regression and Phylogentic Signal-Representation, 3274 (2018).Hume, J. P. Extinct Birds 2nd edn (Bloomsbury, 2017).Safford, R. & Hawkins, F. The Birds of Africa: Volume VIII: The Malagasy Region: Madagascar, Seychelles, Comoros, Mascarenes 960 (Bloomsbury Publishing, 2013).Albert, S., Flores, O., Ah-Peng, C. & Strasberg, D. Forests without frugivores and frugivores without forests—an investigation into the causes of a paradox in one of the last archipelagos colonized by humans. Front. Ecol. Evol. 9, 539 (2021).Albert, S. et al. Rediscovery of the mistletoe Bakerella hoyifolia subsp. bojeri (Loranthaceae) on Reunion Island: population status assessment for its conservation. Bot. Lett. 164, 229–236 (2017).Article 

Google Scholar 
Atkinson, R. & Sevathian, J.-C. A Guide to the Plants in Mauritius 188 (Mauritian Wildlife Foundation, 2005).Austin, J. J. & Arnold, E. N. Using ancient and recent DNA to explore relationships of extinct and endangered Leiolopisma skinks (Reptilia: Scincidae) in the Mascarene islands. Mol. Phylogenet. Evol. 39, 503–511 (2006).Article 
CAS 
PubMed 

Google Scholar 
Bissessur, P., Probst, J.-M. & Florens, F. B. V. Le Merle noir ou Bulbul de Maurice Hypsipetes olivaceus. Bull. Phaethon 46, 86–90 (2017).
Google Scholar 
Bullock, D. J. The ecology and conservation of reptiles on Round Island and Gunner’s Quion, Mauritius. Biol. Conserv. 37, 135–156 (1986).Article 

Google Scholar 
Cadet, L. J. T. La végétation de l’ile de La Réunion. Etude phytoécologique et phytosociologique. PhD thesis, Université Aix-Marseille, France, 362 (1977).Cheke, A. S. The ecology of the smaller land-birds of Mauritius. In Studies of Mascarene Islands Birds (ed. Diamond, A. W.) 151–207 (Cambridge University Press, 1987).Cole, R., Ladkoo, A., Tatayah, V. & Jones, C. Mauritius Olive White-eye Recovery Programme 2007-08 (Mauritian Wildlife Foundation, Vacoas, Mauritius, 2008).Falcón, W., Moll, D. & Hansen, D. M. Frugivory and seed dispersal by chelonians: a review and synthesis. Biol. Rev. 95, 142–166 (2020).Article 
PubMed 

Google Scholar 
Guérin, R. Faune ornithologique ancienne et actuelle des îles Mascareignes, Seychelles, Comores et des îles avoisinantes, Vol. 3 (General Printing & Stationery Co., 1940–53).Günther, A. C. L. G. The Gigantic Land-tortoises (Living and Extinct) in the Collection of the British Museum 96 (Order of the Trustees, London, 1877).Hansen, D. M. Ecology, Evolution, and Conservation of Plant-Animal Interactions in Islands. PhD thesis, University of Zurich, 192 (2006).Hansen, D. M. & Müller, C. B. Invasive ants disrupt gecko pollination and seed dispersal of the endangered plant Roussea simplex in Mauritius. Biotropica 41, 202–208 (2009).Article 

Google Scholar 
Harper, G. A. & Bunbury, N. Invasive rats on tropical islands: their population biology and impacts on native species. Glob. Ecol. Conserv. 3, 607–627 (2015).Article 

Google Scholar 
Henkel, F. W. & Schmidt, W. Amphibians and Reptiles of Madagascar and the Mascarene, Seychelles, and Comoro Islands 316 (Krieger Publishing, 2000).Hume, J. P. Systematics, morphology, and ecology of pigeons and doves (Aves: Columbidae) of the Mascarene Islands, with three new species. Zootaxa 3124, 1–62 (2011).Article 

Google Scholar 
Hume, J. P. Systematics, morphology, and ecology of rails (Aves: Rallidae) of the Mascarene Islands, with one new species. Zootaxa 4626, 001–107 (2019).Article 

Google Scholar 
Jones, C. G. The larger land-birds of Mauritius. In Studies of Mascarene Island birds (ed. Diamond, A. W.) 208–300 (Cambridge University Press, 1987).Jones, C. G. Studies on the Biology of the Pink Pigeon. Columba mayeri. PhD thesis, University College of Swansea, University of Wales, UK (1995).Larosa, A. M., Smith, C. W. & Gardner, D. E. Role of alien and native birds in the dissemination of firetree (Myrica faya Ait.-Myriacaceae) and associated plants in Hawaii. Pac. Sci. 39, 372–378 (1985).
Google Scholar 
Leguat de la Fougère, F. Voyage et aventures de François Leguat et de ses compagnons en deux iles désertes des Indes Orientales, Vol. 2 (J.J. Delorme, Amsterdam, 1707).Linnebjerg, J. F., Hansen, D. M. & Olesen, J. M. Gut passage effect of the introduced red-whiskered bulbul (Pycnonotus jocosus) on germination of invasive plant species in Mauritius. Austral. Ecol. 34, 272–277 (2009).Article 

Google Scholar 
Lorence, D. H. A monograph of the Monimiaceae (Laurales) in the Malagasy region (southwest Indian Ocean). Ann. Mo. Bot. Gard. 72, 1–165 (1985).Article 

Google Scholar 
Maggs, G. et al. Quantifying drivers of supplementary food use by a reintroduced, critically endangered passerine to inform management and habitat restoration. Biol. Conserv. 238, 108240 (2019).Article 

Google Scholar 
Meyer, J. Y. & Butaud, J. F. The impacts of rats on the endangered native flora of French Polynesia (Pacific Islands): drivers of plant extinction or coup de grâce species? Biol. Invasions 11, 1569–1585 (2009).Article 

Google Scholar 
Moorhouse-Gann, R. J. et al. New universal ITS2 primers for high-resolution herbivory analyses using DNA metabarcoding in both tropical and temperate zones. Sci. Rep. 8, 1–15 (2018).Article 
CAS 

Google Scholar 
Nyhagen, D. F., Kragelund, C., Olesen, J. M. & Jones, C. G. Insular interactions between lizards and flowers: flower visitation by an endemic Mauritian gecko. J. Trop. Ecol. 17, 755–761 (2001).Article 

Google Scholar 
Nyhagen, D. F., Turnbull, S. D., Olesen, J. M. & Jones, C. G. An investigation into the role of the Mauritian flying fox, Pteropus niger, in forest regeneration. Biol. Conserv. 122, 491–497 (2005).Article 

Google Scholar 
Probst, J.-M. Les Bulbuls du genre Hypsipetes dans les Mascareignes (Océan Indien). Observations Mascarines 1, 34–36 (1988).
Google Scholar 
Probst, J. M. Capacité de vol étonnante du Bulbul orphée Pycnonotus jocosus (Ile aux Aigrettes–Ile Maurice). Bull. Phaethon 1, 14–17 (1995).
Google Scholar 
Safford, R. Conservation of the Forest-living Native Birds of Mauritius. PhD thesis, University of Kent at Canterbury, 265 (1994).Sengupta, S. Food and feeding ecology of the common myna, Acridotheres tristis (Linn.). J. Proc. Indian Natl Sci. Acad. Part B Biol. Sci. 42, 338–345 (1976).
Google Scholar 
Staub, F. Evolutionary trends in some Mauritian phanerogams in relation to their pollinators. Proc. R. Soc. Arts Sci. Maurit. 5, 7–78 (1988).
Google Scholar 
Strahm, W. A. The Conservation and Restoration of the Flora of Mauritius and Rodrigues, Vol. 2. PhD thesis, University of Reading (1993) .Sussman, R. W. & Tattersall, I. Behavior and ecology of Macaca fascicularis in Mauritius: a preliminary study. Primates 22, 192–205 (1981).Article 

Google Scholar 
Sussman, R. W. & Tattersall, I. Distribution, abundance, and putative ecological strategy of Macaca fascicularis on the island of Mauritius, southwestern Indian Ocean. Folia Primatol. 46, 28–43 (1986).Article 

Google Scholar 
Valido, A. & Olesen, J. M. The importance of lizards as frugivores and seed dispersers. In Seed Dispersal: Theory and Its Application in a Changing World (eds Dennis, A. J. et al.) 124–147 (CAB International, 2007).Vinson, J. & Vinson, J. M. Notes on the reptiles of Round Island. Maurit. Inst. Bull. 8, 49–67 (1975).
Google Scholar 
von Bethlenfalvy, G. Vertebrate Seed Dispersers in Mauritius: Fruit Traits and Fruit Traits Preferences. MSc thesis, Institute of Zoology, University of Zurich, Switzerland (2006).Wilman, H. et al. EltonTraits 1.0: species-level foraging attributes of the world’s birds and mammals: ecological archives E095-178. Ecology 95, 2027–2027 (2014).Article 

Google Scholar 
Winters, R. & Hume, J. P. The dodo, the deer and a 1647 voyage to Japan. Historical. Biology 27, 258–264 (2015).
Google Scholar 
Zuël, N. Ecology and Conservation of an Endangered Reptile Community on Round Island, Mauritius. Doctoral dissertation, University of Zurich (2009).Zuël, N. et al. Ingestion by an endemic frugivore enhances seed germination of endemic plant species but decreases seedling survival of exotics. J. Biogeogr. 39, 2021–2030 (2012).Article 

Google Scholar 
Kissling, W. D., Böhning–Gaese, K. & Jetz, W. The global distribution of frugivory in birds. Glob. Ecol. Biogeogr. 18, 150–162 (2009).Article 

Google Scholar 
Sandom, C. et al. Mammal predator and prey species richness are strongly linked at macroscales. Ecology 94, 1112–1122 (2013).Article 
PubMed 

Google Scholar 
Hume, J. P. A new subfossil bulbul (Aves: Passerines: Pycnonotidae) from Rodrigues Island, Mascarenes, southwestern Indian Ocean. Ostrich 86, 247–260 (2015).Article 

Google Scholar 
Austin, J. J., Arnold, E. N. & Jones, C. G. Reconstructing an island radiation using ancient and recent DNA: the extinct and living day geckos (Phelsuma) of the Mascarene islands. Mol. Phylogenet. Evol. 31, 109–122 (2004).Article 
CAS 
PubMed 

Google Scholar 
Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2019).Article 
CAS 
PubMed 

Google Scholar  More

World Health Organization. World malaria report 2022. (2022).Kariuki, S. N. & Williams, T. N. Human genetics and malaria resistance. Hum. Gen. 139, 801–811 (2020).Article 

Google Scholar 
Watson, J. A., White, N. J. & Dondorp, A. M. Falciparum malaria mortality in sub-Saharan Africa in the pretreatment era. Trends Parasitol. 38, 11–14 (2022).Article 
CAS 
PubMed 

Google Scholar 
Sanchez-Mazas, A. A review of HLA allele and SNP associations with highly prevalent infectious diseases in human populations. Swiss Med. Wkly. 150, w20214 (2020).PubMed 

Google Scholar 
Heijmans, C. M. C., de Groot, N. G. & Bontrop, R. E. Comparative genetics of the major histocompatibility complex in humans and nonhuman primates. Int. J. Immunogenet. 47, 243–260 (2020).Article 
CAS 
PubMed 

Google Scholar 
Neefjes, J., Jongsma, M. L., Paul, P. & Bakke, O. Towards a systems understanding of MHC class I and MHC class II antigen presentation. Nat. Rev. Immunol. 11, 823–836 (2011).Article 
CAS 
PubMed 

Google Scholar 
Zinkernagel, R. M. & Doherty, P. C. Restriction of in vitro T cell-mediated cytotoxicity in lymphocytic choriomeningitis within a syngeneic or semiallogeneic system. Nature 248, 701–702 (1974).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Colonna, M. & Samaridis, J. Cloning of Immunoglobulin-Superfamily Members Associated with HLA-C and HLA-B Recognition by Human Natural Killer Cells. Science 268, 405–408 (1995).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Hill, A. V. et al. Common west African HLA antigens are associated with protection from severe malaria. Nature 352, 595–600 (1991).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Sanchez‐Mazas, A. et al. The HLA‐B landscape of Africa: signatures of pathogen‐driven selection and molecular identification of candidate alleles to malaria protection. Mol. Ecol. 26, 6238–6252 (2017).Article 
PubMed 

Google Scholar 
Hill, A. V. et al. Molecular analysis of the association of HLA-B53 and resistance to severe malaria. Nature 360, 434–439 (1992).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Norman, P. J. et al. Co-evolution of human leukocyte antigen (HLA) class I ligands with killer-cell immunoglobulin-like receptors (KIR) in a genetically diverse population of sub-Saharan Africans. PLoS Genet. 9, e1003938 (2013).Article 
PubMed 
PubMed Central 

Google Scholar 
Sharp, P. M., Plenderleith, L. J. & Hahn, B. H. Ape origins of human malaria. Annu. Rev. Microbiol. 74, 39–63 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Liu, W. et al. Wild bonobos host geographically restricted malaria parasites including a putative new Laverania species. Nat. Commun. 8, 1635 (2017).Liu, W. et al. African origin of the malaria parasite Plasmodium vivax. Nat. Commun. 5, 3346 (2014).Article 
ADS 
PubMed 

Google Scholar 
Liu, W. et al. Origin of the human malaria parasite Plasmodium falciparum in gorillas. Nature 467, 420–425 (2010).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Liu, W. et al. Multigenomic delineation of Plasmodium species of the Laverania subgenus infecting wild-living chimpanzees and gorillas. Genome Biol. Evol. 8, 1929–1939 (2016).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
De Nys, H. M. et al. Age-related effects on malaria parasite infection in wild chimpanzees. Biol. Lett. 9, 20121160 (2013).Article 
PubMed 
PubMed Central 

Google Scholar 
De Nys, H. M. et al. Malaria parasite detection increases during pregnancy in wild chimpanzees. Malar. J. 13, 1–6 (2014).
Google Scholar 
Mapua, M. I. et al. Ecology of malaria infections in western lowland gorillas inhabiting Dzanga Sangha Protected Areas, Central African Republic. Parasitology 142, 890–900 (2015).Article 
PubMed 

Google Scholar 
Scully, E. J. et al. The ecology and epidemiology of malaria parasitism in wild chimpanzee reservoirs. Commun. Biol. 5, 1020 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Herbert, A. et al. Malaria-like symptoms associated with a natural Plasmodium reichenowi infection in a chimpanzee. Malar. J. 14, 1–8 (2015).Article 

Google Scholar 
De Nys, H. M., Löhrich, T., Wu, D., Calvignac-Spencer, S. & Leendertz, F. H. Wild African great apes as natural hosts of malaria parasites: current knowledge and research perspectives. Primate Biol. 4, 47–59 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Takemoto, H., Kawamoto, Y. & Furuichi, T. How did bonobos come to range south of the congo river? Reconsideration of the divergence of Pan paniscus from other Pan populations. Evol. Anthropol. 24, 170–184 (2015).Article 
PubMed 

Google Scholar 
Takemoto, H., Kawamoto, Y. & Furuichi, T. The formation of Congo River and the origin of bonobos: A new hypothesis. in Bonobos: unique in mind, brain, and behavior (eds. Hare, B. & Yamamoto, S.) 235-248 (Oxford University Press, 2017).Takemoto, H. et al. The mitochondrial ancestor of bonobos and the origin of their major haplogroups. PLoS One. 12, e0174851 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Pilbrow, V. & Groves, C. Evidence for divergence in populations of bonobos (Pan paniscus) in the Lomami-Lualaba and Kasai-Sankuru regions based on preliminary analysis of craniodental variation. Int. J. Primatol. 34, 1244–1260 (2013).Article 

Google Scholar 
de Groot, N. G., Stevens, J. M. & Bontrop, R. E. Does the MHC confer protection against malaria in bonobos? Trends Immunol. 39, 768–771 (2018).Article 
PubMed 

Google Scholar 
Sidney, J., Peters, B., Frahm, N., Brander, C. & Sette, A. HLA class I supertypes: a revised and updated classification. BMC Immunol. 9, 1 (2008).Article 
PubMed 
PubMed Central 

Google Scholar 
Wroblewski, E. E. et al. Bonobos maintain immune system diversity with three functional types of MHC-B. J. Immunol. 198, 3480–3493 (2017).Article 
CAS 
PubMed 

Google Scholar 
Bjorkman, P. et al. The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigens. Nature 329, 512–518 (1987).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Guethlein, L. A., Norman, P. J., Hilton, H. G. & Parham, P. Co-evolution of MHC class I and variable NK cell receptors in placental mammals. Immunol. Rev. 267, 259–282 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wroblewski, E. E. et al. Signature patterns of MHC diversity in three Gombe communities of wild chimpanzees reflect fitness in reproduction and immune defense against SIVcpz. PLoS. Biol. 13, e1002144 (2015).Article 
PubMed 
PubMed Central 

Google Scholar 
Li, Y. et al. Eastern chimpanzees, but not bonobos, represent a simian immunodeficiency virus reservoir. J. Virol. 18, 10776–10791 (2012).Article 

Google Scholar 
Yang, C. et al. Sequence variations in the non-repetitive regions of the liver stage-specific antigen-1 (LSA-1) of Plasmodium falciparum from field isolates,. Mol. Biochem Parasitol. 71, 291–294 (1995).Article 
CAS 
PubMed 

Google Scholar 
Fidock, D. A. et al. Plasmodium falciparum liver stage antigen-1 is well conserved and contains potent B and T cell determinants. J. Immunol. 153, 190–204 (1994).Article 
CAS 
PubMed 

Google Scholar 
Aurrecoechea, C. et al. PlasmoDB: a functional genomic database for malaria parasites. Nucl. Acids Res. 37, D539–D543 (2009).Article 
CAS 
PubMed 

Google Scholar 
Hughes, A. L. & Yeager, M. Natural selection at major histocompatibility complex loci of vertebrates. Annu. Rev. Genet. 32, 415–435 (1998).Article 
CAS 
PubMed 

Google Scholar 
Trowsdale, J. The MHC, disease and selection. Immunol. Lett. 137, 1–8 (2011).Article 
CAS 
PubMed 

Google Scholar 
Crow, J. & Kimura, M. An Introduction To Population Genetics Theory. (Alpha Editions, 1970).Prado-Martinez, J. et al. Great ape genetic diversity and population history. Nature 499, 471 (2013).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Digitale, J. C. et al. HLA alleles B* 53:01 and C* 06:02 are associated with higher risk of P. falciparum parasitemia in a cohort in Uganda. Front. Immunol. 12, 650028 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Lyke, K. E. et al. Association of HLA alleles with Plasmodium falciparum severity in Malian children. Tissue Antigens. 77, 562–571 (2011).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Osafo-Addo, A. D. et al. HLA-DRB1*04 allele is associated with severe malaria in northern Ghana. Am. J. Trop. Med. 78, 251–255 (2008).Article 

Google Scholar 
Jallow, M. et al. Genome-wide and fine-resolution association analysis of malaria in West Africa. Nat. Genet. 41, 657–665 (2009).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Malaria Genomic Epidemiology Network. Insights into malaria susceptibility using genome-wide data on 17,000 individuals from Africa, Asia and Oceania. Nat. Commun. 10, 5732 (2019).Article 
ADS 
CAS 

Google Scholar 
Ravenhall, M. et al. Novel genetic polymorphisms associated with severe malaria and under selective pressure in North-eastern Tanzania. PLoS Genet. 14, e1007172 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Damena, D., Denis, A., Golassa, L. & Chimusa, E. R. Genome-wide association studies of severe P. falciparum malaria susceptibility: progress, pitfalls and prospects. BMC Med. Genom. 12, 1–14 (2019).Article 
CAS 

Google Scholar 
Kennedy, A. E., Ozbek, U. & Dorak, M. T. What has GWAS done for HLA and disease associations? Int. J. Immunogenet. 44, 195–211 (2017).Article 
CAS 
PubMed 

Google Scholar 
Tukwasibwe, S. et al. Variations in killer-cell immunoglobulin-like receptor and human leukocyte antigen genes and immunity to malaria. Cell. Mol. Immunol. 17, 799–806 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Leffler, E. M. et al. Multiple instances of ancient balancing selection shared between humans and chimpanzees. Science 339, 1578–1582 (2013).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Phillips, M. et al. Malaria. Nat. Rev. Dis. Prim. 3, 17050 (2017).Article 
PubMed 

Google Scholar 
Samandary, S. et al. Associations of HLA-A, HLA-B and HLA-C alleles frequency with prevalence of herpes simplex virus infections and diseases across global populations: implication for the development of an universal CD8+ T-cell epitope-based vaccine. Hum. Immunol. 75, 715–729 (2014).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Miranda-Katz, M. et al. Novel HLA-B7-restricted human metapneumovirus epitopes enhance viral clearance in mice and are recognized by human CD8+ T cells. Sci. Rep. 11, 20769 (2021).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Appanna, R., Ponnampalavanar, S., Lum Chai See, L. & Sekaran, S. D. Susceptible and protective HLA class 1 alleles against dengue fever and dengue hemorrhagic fever patients in a Malaysian population. PloS One 5, e13029 (2010).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Gao, X. et al. Effect of a single amino acid change in MHC class I molecules on the rate of progression to AIDS. NEJM 344, 1668–1675 (2001).Article 
CAS 
PubMed 

Google Scholar 
Sharp, P. M. & Hahn, B. H. Origins of HIV and the AIDS pandemic. Cold Spring Harb. Perspect. Med. 1, a006841 (2011).Article 
PubMed 
PubMed Central 

Google Scholar 
Barbian, H. J. et al. CHIIMP: An automated high‐throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees. Ecol. Evol. 8, 7946–7963 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Sullivan, K. M., Mannucci, A., Kimpton, C. P. & Gill, P. A rapid and quantitative DNA sex test: fluorescence-based PCR analysis of X-Y homologous gene amelogenin. Biotechniques 15, 636–638 (1993). 640-631.CAS 
PubMed 

Google Scholar 
de Groot, N. G. et al. Nomenclature report 2019: major histocompatibility complex genes and alleles of Great and Small Ape and Old and New World monkey species. Immunogenet 72, 25–36 (2020).Article 

Google Scholar 
Zhang, J., Kobert, K., Flouri, T. & Stamatakis, A. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30, 614–620 (2014).Article 
CAS 
PubMed 

Google Scholar 
Thomsen, M., Lundegaard, C., Buus, S., Lund, O. & Nielsen, M. MHCcluster, a method for functional clustering of MHC molecules. Immunogenet 65, 655–665 (2013).Article 
CAS 

Google Scholar 
Maibach, V. & Vigilant, L. Reduced bonobo MHC class I diversity predicts a reduced viral peptide binding ability compared to chimpanzees. BMC Evol. Biol. 19, 1–15 (2019).Article 

Google Scholar 
Wroblewski, E. E., Parham, P. & Guethlein, L. A. Two to tango: co-evolution of hominid natural killer cell receptors and MHC. Front. Immunol. 10 https://doi.org/10.3389/fimmu.2019.00177 (2019).Raymond, M. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Hered. 86, 248–249 (1995).Article 

Google Scholar 
Rousset, F. GENEPOP’007: a complete re‐implementation of the GENEPOP software for Windows and Linux. Mol. Ecol. Resour. 8, 103–106 (2008).Article 
PubMed 

Google Scholar 
Wilson, M. L. et al. Lethal aggression in Pan is better explained by adaptive strategies than human impacts. Nature 513, 414–417 (2014).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Cheng, L., Samuni, L., Lucchesi, S., Deschner, T. & Surbeck, M. Love thy neighbour: behavioural and endocrine correlates of male strategies during intergroup encounters in bonobos. Anim. Behav. 187, 319–330 (2022).Article 

Google Scholar 
Lucchesi, S. et al. Beyond the group: how food, mates, and group size influence intergroup encounters in wild bonobos. Behav. Ecol. 31, 519–532 (2020).Article 

Google Scholar 
Plumptre, A., Robbins, M. M. & Williamson, E. A. Gorilla beringei. The IUCN Red List of Threatened Species 2019: e.T39994A115576640. (2019).Maisels, F., Bergl, R. A. & Williamson, E. A. Gorilla gorilla (amended version of 2016 assessment). The IUCN Red List of Threatened Species 2018: e.T9404A136250858. (2018).Humle, T., Maisels, F., Oates, J.F., Plumptre, A. & Williamson, E.A. Pan troglodytes (errata version published in 2018). The IUCN Red List of Threatened Species 2016: e.T15933A129038584. (2016).Fruth, B. et al. Pan paniscus (errata version published in 2016). The IUCN Red List of Threatened Species 2016: e.T15932A102331567. (2016). More

Strains belonging to the same species display distinct growth dynamics on the marine polysaccharide alginateWe first quantified the growth dynamics of the 12 Vibrionaceae strains (Supplementary Table 1) on alginate in well-mixed batch cultures. Growth of populations was initiated at approximately the same inoculum density (105 colony forming units (c.f.u.) ml−1). We tracked the growth dynamics by measuring the optical density at 600 nm and compared the maximum population size reached over the course of 36 h (Fig. 1 and S1). We found significant differences in the maximal optical density achieved by different strains within each species (Fig. 1 and S1). In V. splendidus, strains 12B01 and FF6 reached a lower maximum population size compared to strains 1S124 and 13B01 (Fig. 1 and S1A). In V. cyclitrophicus, strain ZF270 reached a lower maximum population size compared to strains 1F175, 1F111, and ZF28 (Fig. 1 and S1A). Similarly, in V. sp. F13, strain 9ZC77 reached a lower maximum population size than strains 9CS106, 9ZC13, and ZF57 (Fig. 1 and S1A). These findings suggest that some strains are limited in their growth abilities in well-mixed environments, perhaps as a consequence of differences in the amount and activity of enzymes they release (Supplementary Table 1).Fig. 1: Vibrionaceae strains differ in their growth dynamics on the marine polysaccharide alginate under well-mixed conditions.Maximum optical density (measured at 600 nm) achieved by populations of strains belonging to Vibrio splendidus, Vibrio cyclitrophicus, and Vibrio sp. F13 during the course of a 36 h growth cycle on the same concentration (0.1% weight/volume) of the polysaccharide alginate. Points and error bars indicate the mean of measurements across populations within each ecotype (npopulations = 3) and the 95% confidence interval (CI), respectively. Different letters indicate statistically significant differences between strains within one species (One-way ANOVA and Dunnett’s post-hoc test; V. splendidus: p  More

Asner, G. P., Elmore, A. J., Olander, L. P., Martin, R. E. & Harris, A. T. Grazing systems, ecosystem responses, and global change. Annu. Rev. Environ. Resour. 29, 261–299 (2004).Article 

Google Scholar 
Millenium Ecosystem Assessment Board. Ecosystems and Human Well-Being: Wetlands and Water: Synthesis (Island Press, Washington, DC, 2005).Lind, J., Sabates-Wheeler, R., Caravani, M., Kuol, L. B. D. & Nightingale, D. M. Newly evolving pastoral and post-pastoral rangelands of Eastern Africa. Pastoralism 10, 24 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Hoffman, T. & Vogel, C. Climate change impacts on African rangelands. Rangelands 30, 12–17 (2008).Article 

Google Scholar 
Joyce, L. A. et al. Climate change and North American rangelands: Assessment of mitigation and adaptation strategies. Rangeland Ecol. Manage. 66, 512–528 (2013).Article 

Google Scholar 
Stringer, L. C., Reed, M. S., Dougill, A. J., Seely, M. K. & Rokitzki, M. Implementing the UNCCD: Participatory challenges. Nat. Resour. Forum 31, 198–211 (2007).Article 

Google Scholar 
Vågen, T.-G., Winowiecki, L. A., Tondoh, J. E., Desta, L. T. & Gumbricht, T. Mapping of soil properties and land degradation risk in Africa using MODIS reflectance. Geoderma 263, 216–225 (2016).Article 
ADS 

Google Scholar 
Stevens, N., Lehmann, C. E. R., Murphy, B. P. & Durigan, G. Savanna woody encroachment is widespread across three continents. Glob. Chang. Biol. 23, 235–244 (2017).Article 
ADS 
PubMed 

Google Scholar 
Muñoz, P. et al. Land degradation, poverty and inequality (2019).Bond, W. & Keeley, J. Fire as a global ‘herbivore’: the ecology and evolution of flammable ecosystems. Trends Ecol. Evol. 20, 387–394 (2005).Article 
PubMed 

Google Scholar 
Lehmann, C. E. R., Archibald, S. A., Hoffmann, W. A. & Bond, W. J. Deciphering the distribution of the savanna biome. New Phytol. 191, 197–209 (2011).Article 
PubMed 

Google Scholar 
Staver, A. C., Archibald, S. & Levin, S. A. The global extent and determinants of savanna and forest as alternative biome states. Science 334, 230–232 (2011).Article 
ADS 
CAS 
MATH 
PubMed 

Google Scholar 
Fuhlendorf, S. D., Fynn, R. W. S., McGranahan, D. A. & Twidwell, D. Heterogeneity as the basis for rangeland management in Rangeland Systems: Processes, Management and Challenges, Springer Series on Environmental Management (ed. Briske, D. D.), 169–196 (Springer International Publishing, 2017).Liao, C., Agrawal, A., Clark, P. E., Levin, S. A. & Rubenstein, D. I. Landscape sustainability science in the drylands: mobility, rangelands and livelihoods. Landsc. Ecol. 35, 2433–2447 (2020).Article 

Google Scholar 
Galvin, K. A. Transitions: pastoralists living with change. Annu. Rev. Anthropol. 38, 185–198 (2009).Article 

Google Scholar 
López-i Gelats, F., Fraser, E. D. G., Morton, J. F. & Rivera-Ferre, M. G. What drives the vulnerability of pastoralists to global environmental change? A qualitative meta-analysis. Glob. Environ. Change 39, 258–274 (2016).Obiri, J. F. Invasive plant species and their disaster-effects in dry tropical forests and rangelands of Kenya and Tanzania. Jàmbá: Journal of Disaster Risk Studies 3, 417–428 (2011).Kioko, J., Kiringe, J. W. & Seno, S. O. Impacts of livestock grazing on a savanna grassland in Kenya. J. Arid Land 4, 29–35 (2012).Article 

Google Scholar 
Kotiaho, J. S. et al. The IPBES assessment report on land degradation and restoration. Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem (2018).Western, D., Mose, V. N., Worden, J. & Maitumo, D. Predicting extreme droughts in savannah Africa: A comparison of proxy and direct measures in detecting biomass fluctuations, trends and their causes. PLoS One 10, e0136516 (2015).Article 
PubMed 
PubMed Central 

Google Scholar 
Dai, A. Drought under global warming: a review. WIREs Climate Change 2, 45–65 (2011).Article 

Google Scholar 
Holechek, J. L., Cibils, A. F., Bengaly, K. & Kinyamario, J. I. Human population growth, African pastoralism, and rangelands: A perspective. Rangeland Ecol. Manage. 70, 273–280 (2017).Article 

Google Scholar 
Midgley, G. F. & Bond, W. J. Future of African terrestrial biodiversity and ecosystems under anthropogenic climate change. Nat. Clim. Chang. 5, 823–829 (2015).Article 
ADS 

Google Scholar 
Hill, M. J. & Guerschman, J. P. The MODIS global vegetation fractional cover product 2001–2018: Characteristics of vegetation fractional cover in grasslands and savanna woodlands. Remote Sensing 12, 406 (2020).Article 
ADS 

Google Scholar 
Lake, P. S. Resistance, resilience and restoration. Ecol. Manage. Restor. 14, 20–24 (2013).Article 

Google Scholar 
Hodgson, D., McDonald, J. L. & Hosken, D. J. What do you mean, ‘resilient’?. Trends Ecol. Evol. 30, 503–506 (2015).Article 
PubMed 

Google Scholar 
Tilman, D. & Downing, J. A. Biodiversity and stability in grasslands. Nature 367, 363–365 (1994).Article 
ADS 

Google Scholar 
Fedrigo, J. K. et al. Temporary grazing exclusion promotes rapid recovery of species richness and productivity in a long-term overgrazed Campos grassland. Restor. Ecol. 26, 677–685 (2018).Article 

Google Scholar 
Ruppert, J. C. et al. Quantifying drylands’ drought resistance and recovery: the importance of drought intensity, dominant life history and grazing regime. Glob. Chang. Biol. 21, 1258–1270 (2015).Article 
ADS 
PubMed 

Google Scholar 
Homewood, K. M. Policy, environment and development in African rangelands. Environ. Sci. Policy 7, 125–143 (2004).Article 

Google Scholar 
Caro, T. & Davenport, T. R. B. Wildlife and wildlife management in Tanzania. Conserv. Biol. 30, 716–723 (2016).Article 
PubMed 

Google Scholar 
Bollig, M. & Schulte, A. Environmental change and pastoral perceptions: degradation and indigenous knowledge in two African pastoral communities. Hum. Ecol. 27, 493–514 (1999).Article 

Google Scholar 
Veldhuis, M. P. et al. Cross-boundary human impacts compromise the Serengeti-Mara ecosystem. Science 363, 1424–1428 (2019).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Nicholson, S. E. Climate and climatic variability of rainfall over Eastern Africa. Rev. Geophys. 55, 590–635 (2017).Article 
ADS 

Google Scholar 
2012 Population and Housing Census (National Bureau of Statistics, Ministry of Finance, 2013).Kiffner, C., Nagar, S., Kollmar, C. & Kioko, J. Wildlife species richness and densities in wildlife corridors of Northern Tanzania. J. Nat. Conserv. 31, 29–37 (2016).Article 

Google Scholar 
Foley, C. A. H. & Faust, L. J. Rapid population growth in an elephant Loxodonta africana population recovering from poaching in Tarangire National Park, Tanzania. Oryx 44, 205–212 (2010).Article 

Google Scholar 
Kebacho, L. L. Large-scale circulations associated with recent interannual variability of the short rains over East Africa. Meteorol. Atmos. Phys. 134, 10 (2021).Article 
ADS 

Google Scholar 
Wainwright, C. M., Finney, D. L., Kilavi, M., Black, E. & Marsham, J. H. Extreme rainfall in East Africa, October 2019-January 2020 and context under future climate change. Weather 76, 26–31 (2021).Article 
ADS 

Google Scholar 
Abukari, H. & Mwalyosi, R. B. Comparing pressures on national parks in Ghana and Tanzania: The case of mole and Tarangire National Parks. Global Ecol. Conserv. 15, e00405 (2018).Article 

Google Scholar 
Kaswamila, A. An analysis of the contribution of community wildlife management areas on livelihood in Tanzania. Sustain. Natl. Res. Manag. 139–54 (2012).NTRI. Maps | NTRI – Northern Tanzania Rangelands Initiative. https://www.ntri.co.tz/maps/ (2016). Accessed: 2021-3-29.Mworia, J., Kinyamario, J. & John, E. Impact of the invader Ipomoea hildebrandtii on grass biomass, nitrogen mineralisation and determinants of its seedling establishment in Kajiado, Kenya. Afr. J. Range Forage Sci. 25, 11–16 (2008).Article 

Google Scholar 
Manyanza, N. M. & Ojija, F. Invasion, impact and control techniques for invasive Ipomoea hildebrandtii on Maasai steppe rangelands. NATO Adv. Sci. Inst. Ser. E Appl. Sci. 17, 12 (2021).Thaiyah, A. G. et al. Acute, sub-chronic and chronic toxicity of Solanum incanum L in sheep in Kenya. Kenya Veterinarian 35, 1–8 (2011).
Google Scholar 
Roques, K. G., O’Connor, T. G. & Watkinson, A. R. Dynamics of shrub encroachment in an African savanna: relative influences of fire, herbivory, rainfall and density dependence. J. Appl. Ecol. 38, 268–280 (2001).Article 

Google Scholar 
Riginos, C. & Herrick, J. E. Monitoring rangeland health: a guide for pastoralists and other land managers in Eastern Africa. Version II (2010).Farr, T. G. et al. The shuttle radar topography mission. Rev. Geophys. 45, RG2004 (2007).QGIS Development Team. QGIS Geographic Information System. QGIS Association (2022).Gorelick, N. et al. Google Earth Engine: Planetary-scale geospatial analysis for everyone. Remote Sens. Environ. 202, 18–27 (2017).Article 
ADS 

Google Scholar 
Didan, K. MOD13Q1 MODIS/Terra Vegetation Indices 16-Day L3 Global 250m SIN Grid V006 [Data set] (NASA EOSDIS Land Processes DAAC, 2015).Friedl, M. & Sulla-Menashe, D. MCD12Q1 MODIS/Terra+ Aqua Land Cover Type Yearly L3 Global 500m SIN Grid V006 (NASA EOSDIS Land Processes DAAC, 2019).Vermote, E. MOD09A1 MODIS/Terra Surface Reflectance 8-day L3 Global 500m SIN Grid V006. NASA EOSDIS Land Processes DAAC 10 (2015).Funk, C. et al. The climate hazards infrared precipitation with stations–a new environmental record for monitoring extremes. Scientific Data 2, 1–21 (2015).Article 

Google Scholar 
Zeileis, A. & Grothendieck, G. zoo: S3 infrastructure for regular and irregular time series. arXiv:math/0505527 (2005).R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. (2016).Scaramuzza, P. & Barsi, J. Landsat 7 scan line corrector-off gap-filled product development in Proceeding of Pecora 16, 23–27 (2005).
Google Scholar 
Huete, A. et al. Overview of the radiometric and biophysical performance of the MODIS vegetation indices. Remote Sens. Environ. 83, 195–213 (2002).Article 
ADS 

Google Scholar 
Rikimaru, A., Roy, P. S. & Miyatake, S. Tropical forest cover density mapping. Trop. Ecol. 39–47 (2002).Diek, S., Fornallaz, F., Schaepman, M. E. & De Jong, R. Barest pixel composite for agricultural areas using landsat time series. Remote Sensing 9, 1245 (2017).Article 
ADS 

Google Scholar 
Qi, J., Chehbouni, A., Huete, A. R., Kerr, Y. H. & Sorooshian, S. A modified soil adjusted vegetation index. Remote Sens. Environ. 48, 119–126 (1994).Article 
ADS 

Google Scholar 
Adams, B. et al. Mapping forest composition with Landsat time series: An evaluation of seasonal composites and harmonic regression. Remote Sensing 12, 610 (2020).Article 
ADS 

Google Scholar 
Nwanganga, F. & Chapple, M. Practical machine learning in R (John Wiley and Sons, Indianapolis, 2020).Adam, E., Mutanga, O., Odindi, J. & Abdel-Rahman, E. M. Land-use/cover classification in a heterogeneous coastal landscape using RapidEye imagery: evaluating the performance of random forest and support vector machines classifiers. Int. J. Remote Sens. 35, 3440–3458 (2014).Article 

Google Scholar 
Mansour, K., Mutanga, O., Adam, E. & Abdel-Rahman, E. M. Multispectral remote sensing for mapping grassland degradation using the key indicators of grass species and edaphic factors. Geocarto Int. 31, 477–491 (2016).Article 

Google Scholar 
Hunter, F. D. L., Mitchard, E. T. A., Tyrrell, P. & Russell, S. Inter-Seasonal time series imagery enhances classification accuracy of grazing resource and land degradation maps in a savanna ecosystem. Remote Sensing 12, 198 (2020).Article 
ADS 

Google Scholar 
Yang, L. et al. Estimating surface downward shortwave radiation over china based on the gradient boosting decision tree method. Remote Sensing 10, 185 (2018).Article 
ADS 

Google Scholar 
Pham, T. D. et al. Estimating mangrove Above-Ground biomass using extreme gradient boosting decision trees algorithm with fused Sentinel-2 and ALOS-2 PALSAR-2 data in Can Gio biosphere reserve, Vietnam. Remote Sensing 12, 777 (2020).Article 
ADS 

Google Scholar 
Adobe Inc. Adobe illustrator.Lenth, R. V. emmeans: Estimated marginal means, aka Least-Squares means. R package version 1.5.4 (2021).Royall, R. M. The effect of sample size on the meaning of significance tests. Am. Stat. 40, 313–315 (1986).MATH 

Google Scholar 
Rue, H., Martino, S. & Chopin, N. Approximate bayesian inference for latent Gaussian models by using integrated nested Laplace approximations. J. R. Stat. Soc. Series B Stat. Methodol. 71, 319–392 (2009).Lindgren, F. & Rue, H. Bayesian spatial modelling with R-INLA. J. Stat. Softw. 63, 1–25 (2015).Article 

Google Scholar 
Bakka, H. et al. Spatial modelling with R-INLA: A review. arXiv:1802.06350 [stat] (2018).Lobora, A. L. et al. Modelling habitat conversion in Miombo woodlands: Insights from Tanzania. J. Land Use Sci. 1747423X.2017.1331271 (2017).Bright, E. A., Rose, A. N., Urban, M. L. & McKee, J. LandScan 2017 High-Resolution global population data set. Tech. Rep., Oak Ridge National Lab.(ORNL), Oak Ridge, TN (United States) (2018).Gilbert, M. et al. Global distribution data for cattle, buffaloes, horses, sheep, goats, pigs, chickens and ducks in 2010. Sci Data 5, 180227 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Yang, Y., Fang, J., Ma, W. & Wang, W. Relationship between variability in aboveground net primary production and precipitation in global grasslands. Geophys. Res. Lett. 35 (2008).Guo, Q. et al. Spatial variations in aboveground net primary productivity along a climate gradient in Eurasian temperate grassland: effects of mean annual precipitation and its seasonal distribution. Glob. Chang. Biol. 18, 3624–3631 (2012).Article 
ADS 

Google Scholar 
Wang, X., Yue, Y. & Faraway, J. J. Bayesian Regression Modeling with INLA (Chapman and Hall/CRC, 2018).Côté, I. M. & Darling, E. S. Rethinking ecosystem resilience in the face of climate change. PLoS Biol. 8, e1000438 (2010).Article 
PubMed 
PubMed Central 

Google Scholar 
O’Loughlin, J. et al. Climate variability and conflict risk in East Africa, 1990–2009. Proc. Natl. Acad. Sci. 109, 18344–18349 (2012).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Ongoma, V., Chen, H., Gao, C., Nyongesa, A. M. & Polong, F. Future changes in climate extremes over Equatorial East Africa based on CMIP5 multimodel ensemble. Nat. Hazards 90, 901–920 (2018).Article 

Google Scholar 
Homewood, K. & Rodgers, W. A. Pastoralism, conservation and the overgrazing controversy. Conservation in Africa: People, policies and practice 111–128 (1987).Scoones, I. Exploiting heterogeneity: habitat use by cattle in dryland Zimbabwe. J. Arid Environ. 29, 221–237 (1995).Article 
ADS 

Google Scholar 
Goldman, M. J. & Riosmena, F. Adaptive capacity in Tanzanian Maasailand: Changing strategies to cope with drought in fragmented landscapes. Glob. Environ. Change 23, 588–597 (2013).Article 
PubMed 
PubMed Central 

Google Scholar 
Selemani, I. S. & Others. Communal rangelands management and challenges underpinning pastoral mobility in Tanzania: a review. Livestock Res. Rural Dev. 26, 1–12 (2014).Middleton, N. Rangeland management and climate hazards in drylands: dust storms, desertification and the overgrazing debate. Nat. Hazards 92, 57–70 (2018).Article 

Google Scholar 
Sallu, S. M., Twyman, C. & Stringer, L. C. Resilient or vulnerable livelihoods? Assessing livelihood dynamics and trajectories in rural Botswana. Ecology and Society 15 (2010).Oba, G. & Lusigi, W. J. An overview of drought strategies and land use in African pastoral systems (Agricultural Administration Unit, Overseas Development Institute, 1987).Russell, S., Tyrrell, P. & Western, D. Seasonal interactions of pastoralists and wildlife in relation to pasture in an African savanna ecosystem. J. Arid Environ. 154, 70–81 (2018).Article 
ADS 

Google Scholar 
Girvetz, E. et al. Future climate projections in Africa: Where are we headed? In The Climate-Smart Agriculture Papers: Investigating the Business of a Productive, Resilient and Low Emission Future 15–27 (Springer International Publishing, 2019).Lyon, B. & DeWitt, D. G. A recent and abrupt decline in the East African long rains. Geophys. Res. Lett. 39 (2012).Liebmann, B. et al. Climatology and interannual variability of boreal spring wet season precipitation in the Eastern Horn of Africa and implications for its recent decline. J. Clim. 30, 3867–3886 (2017).Article 
ADS 

Google Scholar 
Shongwe, M. E., van Oldenborgh, G. J., van den Hurk, B. & van Aalst, M. Projected changes in mean and extreme precipitation in Africa under global warming. part II: East Africa. J. Clim. 24, 3718–3733 (2011).Dunning, C. M., Black, E. & Allan, R. P. Later wet seasons with more intense rainfall over Africa under future climate change. J. Clim. 31, 9719–9738 (2018).Article 
ADS 

Google Scholar 
Rowell, D. P., Booth, B. B. B., Nicholson, S. E. & Good, P. Reconciling past and future rainfall trends over East Africa. J. Clim. 28, 9768–9788 (2015).Article 
ADS 

Google Scholar 
Vizy, E. K. & Cook, K. H. Mid-Twenty-First-Century changes in extreme events over Northern and Tropical Africa. J. Clim. 25, 5748–5767 (2012).Article 
ADS 

Google Scholar 
Gebremeskel Haile, G. et al. Droughts in East Africa: Causes, impacts and resilience. Earth-Sci. Rev. 193, 146–161 (2019).Kendon, E. J. et al. Enhanced future changes in wet and dry extremes over Africa at convection-permitting scale. Nat. Commun. 10, 1794 (2019).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Finney, D. L. et al. Effects of explicit convection on future projections of mesoscale circulations, rainfall, and rainfall extremes over Eastern Africa. J. Clim. 33, 2701–2718 (2020).Article 
ADS 

Google Scholar 
Prins, H. H. T. & Loth, P. E. Rainfall patterns as background to plant phenology in Northern Tanzania. J. Biogeogr. 15, 451–463 (1988).Article 

Google Scholar 
Ngondya, I. B., Treydte, A. C., Ndakidemi, P. A. & Munishi, L. K. Invasive plants: ecological effects, status, management challenges in Tanzania and the way forward. J. Biodivers. Environ. Sci. (JBES) 10, 204–217 (2017).
Google Scholar 
Drusch, M. et al. Sentinel-2: ESA’s optical High-Resolution mission for GMES operational services. Remote Sens. Environ. 120, 25–36 (2012).Article 
ADS 

Google Scholar 
Rapinel, S. et al. Evaluation of Sentinel-2 time-series for mapping floodplain grassland plant communities. Remote Sens. Environ. 223, 115–129 (2019).Article 
ADS 

Google Scholar 
Li, W. et al. Accelerating savanna degradation threatens the Maasai Mara socio-ecological system. Glob. Environ. Change 60, 102030 (2020).Article 

Google Scholar 
Wonkka, C. L., Twidwell, D., Franz, T. E., Taylor, C. A. & Rogers, W. E. Persistence of a severe drought increases desertification but not woody dieback in semiarid savanna. Rangeland Ecol. Manage. 69, 491–498 (2016).Article 

Google Scholar 
Vierich, H. I. D. & Stoop, W. A. Changes in West African savanna agriculture in response to growing population and continuing low rainfall. Agric. Ecosyst. Environ. 31, 115–132 (1990).Article 

Google Scholar 
Fynn, R. W. S. & O’Connor, T. G. Effect of stocking rate and rainfall on rangeland dynamics and cattle performance in a semi-arid savanna, South Africa. J. Appl. Ecol. 37, 491–507 (2000).Article 

Google Scholar 
Wang, S., Chen, W., Xie, S. M., Azzari, G. & Lobell, D. B. Weakly supervised deep learning for segmentation of remote sensing imagery. Remote Sensing 12, 207 (2020).Article 
ADS 

Google Scholar 
Alananga, S., Makupa, E. R., Moyo, K. J., Matotola, U. C. & Mrema, E. F. Land administration practices in Tanzania: A replica of past mistakes. Journal of Property, Planning and Environmental Law (2019).Huggins, C. Village land use planning and commercialization of land in Tanzania. LANDac Research Brief 1 (2016).Stein, H., Maganga, F. P., Odgaard, R., Askew, K. & Cunningham, S. The formal divide: Customary rights and the allocation of credit to agriculture in Tanzania. J. Dev. Stud. 52, 1306–1319 (2016).Article 

Google Scholar 
Hall, D. G. M., Reeve, M. J., Thomasson, A. J. & Wright, V. F. Water retention, porosity and density of field soils (No. Tech. Monograph N9, 1977).Moore, D. C. & Singer, M. J. Crust formation effects on soil erosion processes. Soil Sci. Soc. Am. J. 54, 1117–1123 (1990).Article 
ADS 

Google Scholar 
Cotler, H. & Ortega-Larrocea, M. P. Effects of land use on soil erosion in a tropical dry forest ecosystem, Chamela watershed, Mexico. Catena 65, 107–117 (2006).Article 

Google Scholar 
Bach, E. M., Baer, S. G., Meyer, C. K. & Six, J. Soil texture affects soil microbial and structural recovery during grassland restoration. Soil Biol. Biochem. 42, 2182–2191 (2010).Article 
CAS 

Google Scholar 
Butz, R. J. Traditional fire management: historical fire regimes and land use change in pastoral East Africa. Int. J. Wildland Fire 18, 442–450 (2009).Article 

Google Scholar  More

Pawlowski, J. et al. CBOL Protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLOS Biol. 10, e1001419 (2012).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
del Campo, J. et al. The others: our biased perspective of eukaryotic genomes. Trends Ecol. Evol. 29, 252–259 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Handbook of the Protists (Springer, 2017). https://doi.org/10.1007/978-3-319-28149-0.Lang, B. F., O’Kelly, C., Nerad, T., Gray, M. W. & Burger, G. The closest unicellular relatives of animals. Curr. Biol. 12, 1773–1778 (2002).Article 
CAS 
PubMed 

Google Scholar 
del Campo, J. et al. Ecological and evolutionary significance of novel protist lineages. Eur. J. Protistol. 55, 4–11 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Grau-Bové, X. et al. Dynamics of genomic innovation in the unicellular ancestry of animals. Life 6, e26036 (2017).
Google Scholar 
Gawryluk, R. M. R. et al. Non-photosynthetic predators are sister to red algae. Nature 572, 240–243 (2019).Article 
CAS 
PubMed 

Google Scholar 
Gabr, A., Grossman, A. R. & Bhattacharya, D. Paulinella, a model for understanding plastid primary endosymbiosis. J. Phycol. 56, 837–843 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Gao, Z., Karlsson, I., Geisen, S., Kowalchuk, G. & Jousset, A. Protists: Puppet masters of the rhizosphere microbiome. Trends Plant Sci. 24, 165–176 (2019).Article 
CAS 
PubMed 

Google Scholar 
Caron, D. A. New accomplishments and approaches for assessing protistan diversity and ecology in natural ecosystems. Bioscience 59, 287–299 (2009).Article 

Google Scholar 
Gooday, A. J., Schoenle, A., Dolan, J. R. & Arndt, H. Protist diversity and function in the dark ocean: Challenging the paradigms of deep-sea ecology with special emphasis on foraminiferans and naked protists. Eur. J. Protistol. 75, 125721 (2020).Article 
PubMed 

Google Scholar 
Stoecker, D. K., Johnson, M. D., de Vargas, C. & Not, F. Acquired phototrophy in aquatic protists. Aquat. Microb. Ecol. 57, 279–310 (2009).Article 

Google Scholar 
Strom, S. L., Benner, R., Ziegler, S. & Dagg, M. J. Planktonic grazers are a potentially important source of marine dissolved organic carbon. Limnol. Oceanogr. 42, 1364–1374 (1997).Article 
ADS 
CAS 

Google Scholar 
Orsi, W. D. et al. Identifying protist consumers of photosynthetic picoeukaryotes in the surface ocean using stable isotope probing. Environ. Microbiol. 20, 815–827 (2018).Article 
CAS 
PubMed 

Google Scholar 
Corno, G. & Jürgens, K. Direct and indirect effects of protist predation on population size structure of a bacterial strain with high phenotypic plasticity. Appl. Environ. Microbiol. 72, 78–86 (2006).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Mahé, F. et al. Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests. Nat. Ecol. Evol. 1, 91 (2017).Article 
PubMed 

Google Scholar 
Ruppert, K. M., Kline, R. J. & Rahman, M. S. Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Glob. Ecol. Conserv. 17, e00547 (2019).Article 

Google Scholar 
Epstein, S. & López-García, P. “Missing” protists: a molecular prospective. Biodivers. Conserv. 17, 261–276 (2008).Article 

Google Scholar 
López-García, P., Rodríguez-Valera, F., Pedrós-Alió, C. & Moreira, D. Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409, 603–607 (2001).Article 
ADS 
PubMed 

Google Scholar 
Lovejoy, C., Massana, R. & Pedrós-Alió, C. Diversity and distribution of marine microbial eukaryotes in the Arctic Ocean and adjacent seas. Appl. Environ. Microbiol. 72, 3085–3095 (2006).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Worden, A. Z., Cuvelier, M. L. & Bartlett, D. H. In-depth analyses of marine microbial community genomics. Trends Microbiol. 14, 331–336 (2006).Article 
CAS 
PubMed 

Google Scholar 
Countway, P. D. et al. Distinct protistan assemblages characterize the euphotic zone and deep sea (2500 m) of the western North Atlantic (Sargasso Sea and Gulf Stream). Environ. Microbiol. 9, 1219–1232 (2007).Article 
CAS 
PubMed 

Google Scholar 
Massana, R. & Pedrós-Alió, C. Unveiling new microbial eukaryotes in the surface ocean. Curr. Opin. Microbiol. 11, 213–218 (2008).Article 
PubMed 

Google Scholar 
Alexander, E. et al. Microbial eukaryotes in the hypersaline anoxic L’Atalante deep-sea basin. Environ. Microbiol. 11, 360–381 (2009).Article 
CAS 
PubMed 

Google Scholar 
Stoeck, T. et al. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol. Ecol. 19, 21–31 (2010).Article 
CAS 
PubMed 

Google Scholar 
Logares, R. et al. Patterns of rare and abundant marine microbial eukaryotes. Curr. Biol. 24, 813–821 (2014).Article 
CAS 
PubMed 

Google Scholar 
de Vargas, C. et al. Eukaryotic plankton diversity in the sunlit ocean. Science 348, 150 (2015).Article 

Google Scholar 
Fell, J. W., Scorzetti, G., Connell, L. & Craig, S. Biodiversity of micro-eukaryotes in Antarctic Dry Valley soils with More

Moore, J. An overview of parasite-induced behavioral alterations – and some lessons from bats. J. Exp. Biol. 216, 11–17 (2012).Article 

Google Scholar 
Nunn, C. L. & Altizer, S. Infectious Diseases in Primates: Behavior, Ecology and Evolution (Oxford University Press, 2006).Book 

Google Scholar 
Hutchings, M. R., Athanasiadou, S., Kyriazakis, I. & Gordon, I. J. Nutrition and Behaviour Group Symposium on ‘Exploitation of medicinal properties of plants by animals and man through food intake and foraging behaviour’: Can animals use foraging behaviour to combat parasites?. Proc. Nutr. Soc. 62, 361–370 (2003).Article 

Google Scholar 
Hawley, D. M., Etienne, R. S., Ezenwa, V. O. & Jolles, A. E. Does animal behavior underlie covariation between hosts’ exposure to infectious agents and susceptibility to infection? Implications for disease dynamics. Integr. Comp. Biol. 51, 528–539 (2011).Article 

Google Scholar 
Rimbach, R. et al. Brown spider monkeys (Ateles hybridus): a model for differentiating the role of social networks and physical contact on parasite transmission dynamics. Philos. Trans. R. Soc. B Biol. Sci. 370, 20140110 (2015).Article 

Google Scholar 
Friant, S., Ziegler, T. E. & Goldberg, T. L. Changes in physiological stress and behaviour in semi-free-ranging red-capped mangabeys (Cercocebus torquatus) following antiparasitic treatment. Proc. R. Soc. B Biol. Sci. 283, 20161201 (2016).Article 

Google Scholar 
Hudson, P. J. & Dobson, A. P. Macroparasites: Observed patterns in naturally fluctuating animal populations. In Ecology of infectious diseases in natural populations (eds Grenfell, B. T. & Dobson, A. P.) 144–176 (Cambridge University Press, 1995). https://doi.org/10.1017/CBO9780511629396.006.Chapter 

Google Scholar 
Murray, D. L., Lloyd, B. K. & Cary, J. R. Do parasitism and nutritional status interact to affect production in snowshoe hares?. Ecology 79, 1209–1222 (1998).Article 

Google Scholar 
Coop, R. L. & Holmes, P. H. Nutrition and parasite interaction. Int. J. Parasitol. 26, 951–962 (1996).Article 
CAS 

Google Scholar 
Møller, A. P., de Lope, F., Moreno, J., González, G. & Pérez, J. J. Ectoparasites and host energetics: House martin bugs and house martin nestlings. Oecologia 98, 263–268 (1994).Article 
ADS 

Google Scholar 
Munger, J. C. & Karasov, W. H. Sublethal parasites and host energy budgets: Tapeworm infection in white-footed mice. Ecology 70, 904–921 (1989).Article 

Google Scholar 
Hicks, O. et al. The energetic cost of parasitism in a wild population. Proc. R. Soc. B Biol. Sci. 285, 20180489 (2018).Article 

Google Scholar 
Sánchez, C. A. et al. On the relationship between body condition and parasite infection in wildlife: A review and meta-analysis. Ecol. Lett. 21, 1869–1884 (2018).Article 

Google Scholar 
Kyriazakis, I., Tolkamp, B. J. & Hutchings, M. R. Towards a functional explanation for the occurrence of anorexia during parasitic infections. Anim. Behav. 56, 265–274 (1998).Article 
CAS 

Google Scholar 
Hart, B. L. Behavioral adaptations to pathogens and parasites: Five strategies. Neurosci. Biobehav. Rev. 14, 273–294 (1990).Article 
CAS 

Google Scholar 
Lopes, P. C., Block, P. & König, B. Infection-induced behavioural changes reduce connectivity and the potential for disease spread in wild mice contact networks. Sci. Rep. 6, 1–10 (2016).Article 

Google Scholar 
Pelletier, F. & Festa-Bianchet, M. Effects of body mass, age, dominance and parasite load on foraging time of bighorn rams. Ovis canadensis. Behav. Ecol. Sociobiol. 56, 546–551 (2004).Article 

Google Scholar 
Bonneaud, C. et al. Assessing the cost of mounting an immune response. Am. Nat. 161, 367–379 (2003).Article 

Google Scholar 
Hart, B. L. The behavior of sick animals. Vet. Clin. North Am. Small Anim. Pract. 21, 225–237 (1991).Article 
CAS 

Google Scholar 
Poulin, R. Meta-analysis of parasite-induced behavioural changes. Anim. Behav. 48, 137–146 (1994).Article 

Google Scholar 
Janson, C. H. Toward an experiemental socioecology of primates. Examples from Argentine brown capuchin monkeys (Cebus apella nigritus). In Adaptive Radiations of Neotropical Primates (eds Janson, C. H. et al.) 309–325 (Plenum Press, 1996).Chapter 

Google Scholar 
Robinson, J. G. Seasonal variation in use of time and space by the wedge-capped capuchin monkey, Cebus olivaceus: Implications for foraging theory. Smithson. Contrib. Zool. https://doi.org/10.5479/si.00810282.431 (1986).Article 

Google Scholar 
Saj, T., Sicotte, P. & Paterson, J. D. Influence of human food consumption on the time budget of vervets. Int. J. Primatol. 20, 977–994 (1999).Article 

Google Scholar 
Ghai, R. R., Fugère, V., Chapman, C. A., Goldberg, T. L. & Davies, T. J. Sickness behaviour associated with non-lethal infections in wild primates. Proc. Biol. Sci. 282, 20151436 (2015).
Google Scholar 
Blersch, R. et al. Sick and tired: Sickness behaviour, polyparasitism and food stress in a gregarious mammal. Behav. Ecol. Sociobiol. 75, 169 (2021).Article 

Google Scholar 
Müller-Klein, N. et al. Physiological and social consequences of gastrointestinal nematode infection in a nonhuman primate. Behav. Ecol. 30, 322–335 (2019).Article 

Google Scholar 
Chapman, C. A. et al. Social behaviours and networks of vervet monkeys are influenced by gastrointestinal parasites. PLoS ONE 11, e0161113 (2016).Article 

Google Scholar 
Owen-Ashley, N. T. & Wingfield, J. C. Acute phase responses of passerine birds: characterization and seasonal variation. J. Ornithol. 148, 583–591 (2007).Article 

Google Scholar 
Owen-Ashley, N. T. & Wingfield, J. C. Seasonal modulation of sickness behavior in free-living northwestern song sparrows (Melospiza melodia morphna). J. Exp. Biol. 209, 3062–3070 (2006).Article 

Google Scholar 
Janson, C. H. & Di Bitetti, M. S. Experimental analysis of food detection in capuchin monkeys: Effects of distance, travel speed, and resource size. Behav. Ecol. Sociobiol. 41, 17–24 (1997).Article 

Google Scholar 
Di Bitetti, M. S. Food-associated calls in the tufted capuchin monkey (Cebus apella). PhD Thesis. (Stony Brook University, New York, 2001).Di Bitetti, M. S. & Janson, C. H. Reproductive socioecology of tufted capuchins (Cebus apella nigritus) in Norteastern Argentina. Int. J. Primatol. 22, 127–142 (2001).Article 

Google Scholar 
Janson, C., Baldovino, M. C. & Di Bitetti, M. The group life cycle and demography of brown capuchin monkeys (Cebus [apella] nigritus) in Iguazú National Park, Argentina. In Long-Term Field Studies of Primates (eds Kappeler, P. M. & Watts, D. P.) 185–212 (Springer, Berlin, 2012). https://doi.org/10.1007/978-3-642-22514-7_9.Chapter 

Google Scholar 
Robinson, J. C. & Galán Saúco, V. Bananas and plantains. (Crop production science in horticulture series N. 19, CAB International, 2010). https://doi.org/10.1079/9781845936587.0000Tiddi, B., Pfoh, R. & Agostini, I. The impact of food provisioning on parasite infection in wild black capuchin monkeys: A network approach. Primates 60, 297–306 (2019).Article 

Google Scholar 
Agostini, I., Vanderhoeven, E., Di Bitetti, M. S. & Beldomenico, P. M. Experimental testing of reciprocal effects of nutrition and parasitism in wild black capuchin monkeys. Sci. Rep. 7, 1–11 (2017).Article 

Google Scholar 
de Vries, H., Netto, W. J. & Hanegraaf, P. L. H. Matman: a program for the analysis of sociometric matrices and behavioural transition matrices. Behaviour 125, 157–175 (1993).Article 

Google Scholar 
Martin, P. & Bateson, P. Measuring Behaviour (Cambridge University Press, 1993). https://doi.org/10.1017/cbo9780511810893.Book 

Google Scholar 
Cox, D. D. & Todd, A. C. Survey of gastrointestinal parasitism in Wisconsin dairy cattle. J. Am. Vet. Med. Assoc. 141, 706–709 (1962).CAS 

Google Scholar 
Ballweber, L. R., Beugnet, F., Marchiondo, A. A. & Payne, P. A. American association of veterinary parasitologists’ review of veterinary fecal flotation methods and factors influencing their accuracy and use—Is there really one best technique?. Vet. Parasitol. 204, 73–80 (2014).Article 
CAS 

Google Scholar 
Godfrey, S. S. Networks and the ecology of parasite transmission: a framework for wildlife parasitology. Int. J. Parasitol. Parasites Wildl. 2, 235–245 (2013).Article 

Google Scholar 
Sosa, S., Sueur, C. & Puga-Gonzalez, I. Network measures in animal social network analysis: Their strengths, limits, interpretations and uses. Methods Ecol. Evol. 2020, 1–12 (2020).
Google Scholar 
Sosa, S. et al. A multilevel statistical toolkit to study animal social networks: The Animal Network Toolkit Software (ANTs) R package. Sci. Rep. 10, 12507 (2020).Article 
ADS 
CAS 

Google Scholar 
Croft, D. P., Madden, J. R., Franks, D. W. & James, R. Hypothesis testing in animal social networks. Trends Ecol. Evol. 26, 502–507 (2011).Article 

Google Scholar 
Farine, D. R. Animal social network inference and permutations for ecologists in R using asnipe. Methods Ecol. Evol. 4, 1187–1194 (2013).Article 

Google Scholar 
Burnham, K. P. & Anderson, D. R. Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach (2nd ed). Ecological Modelling (Springer, 2002). https://doi.org/10.1016/j.ecolmodel.2003.11.004Bates, D., Maechler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).Article 

Google Scholar 
Barton, K. MuMIn: Multi-model inference. R package version 1.15.6. 63 (2016). citeulike:11961261Carlton, E. D., Demas, G. E. & French, S. S. Leptin, a neuroendocrine mediator of immune responses, inflammation, and sickness behaviors. Horm. Behav. 62, 272–279 (2012).Article 
CAS 

Google Scholar 
Tizard, I. Sickness behavior, its mechanisms and significance. Anim. Health Res. Rev. 9, 87–99 (2008).Article 

Google Scholar 
Inoue, W. & Luheshi, G. N. Acute starvation alters lipopolysaccharide-induced fever in leptin-dependent and -independent mechanisms in rats. Am. J. Physiol. Regul. Integr. Comp. Physiol. 299, R1709-19 (2010).Article 

Google Scholar 
Macdonald, L., Radler, M., Paolini, A. G. & Kent, S. Calorie restriction attenuates LPS-induced sickness behavior and shifts hypothalamic signaling pathways to an antiinflammatory bias. Am. J. Physiol. Regul. Integr. Comp. Physiol. 301, 172–184 (2011).Article 

Google Scholar 
Wisse, B. E. et al. Physiological regulation of hypothalamic IL-1β gene expression by leptin and glucocorticoids: implications for energy homeostasis. Am. J. Physiol. Endocrinol. Metab. 287, R1107–R1113 (2004).Article 

Google Scholar 
Pohl, J., Woodside, B. & Luheshi, G. N. Changes in hypothalamically mediated acute-phase inflammatory responses to lipopolysaccharide in diet-induced obese rats. Endocrinology 150, 4901–4910 (2009).Article 
CAS 

Google Scholar 
Bretscher, P. On analyzing how the Th1/Th2 phenotype of an immune response is determined: classical observations must not be ignored. Front. Immunol. 10, 1–7 (2019).Article 

Google Scholar 
Poppi, D. P., Sykes, A. R. & Dynes, R. A. The effect of endoparasitism on host nutrition – the implications for nutrient manipulation. Proc. New Zeal. Soc. Anim. Prod. 50, 237–243 (1990).
Google Scholar 
Coulson, G., Cripps, J. K., Garnick, S., Bristow, V. & Beveridge, I. Parasite insight: assessing fitness costs, infection risks and foraging benefits relating to gastrointestinal nematodes in wild mammalian herbivores. Philos. Trans. R. Soc. B Biol. Sci. 373, 197 (2018).Article 

Google Scholar 
Worsley-Tonks, K. E. L. & Ezenwa, V. O. Anthelmintic treatment affects behavioural time allocation in a free-ranging ungulate. Anim. Behav. 108, 47–54 (2015).Article 

Google Scholar 
Jones, O. R., Anderson, R. M. & Pilkington, J. G. Parasite-induced anorexia in a free-ranging mammalian herbivore: An experimental test using Soay sheep. Can. J. Zool. 84, 685–692 (2006).Article 

Google Scholar 
Cripps, J. K., Martin, J. K. & Coulson, G. Anthelmintic treatment does not change foraging strategies of female eastern grey kangaroos, Macropus giganteus. PLoS ONE 11, e0147384 (2016).Article 

Google Scholar 
Giles, N. Predation risk and reduced foraging activity in fish: experiments with parasitized and non-parasitized three-spined sticklebacks, Gasterosteus aculeatus L.. J. Fish Biol. 31, 37–44 (1987).Article 

Google Scholar 
Knutie, S. A., Wilkinson, C. L., Wu, Q. C., Ortega, C. N. & Rohr, J. R. Host resistance and tolerance of parasitic gut worms depend on resource availability. Oecologia 183, 1031–1040 (2017).Article 
ADS 

Google Scholar 
Lopes, P. C., French, S. S., Woodhams, D. C. & Binning, S. A. Metabolic response of dolphins to short-term fasting reveals physiological changes that differ from the traditional fasting model. J. Exp. Biol. 224, jeb225847 (2021).Article 

Google Scholar 
Behringer, D. C., Butler, M. J. & Shields, J. D. Ecology: Avoidance of disease by social lobsters. Nature 441, 421 (2006).Article 
ADS 
CAS 

Google Scholar 
Poirotte, C. et al. Mandrills use olfaction to socially avoid parasitized conspecifics. Sci. Adv. 3, e1601721 (2017).Article 
ADS 

Google Scholar  More