Ecology

Tigchelaar, M. et al. Nature Food 2, 673–682 (2021).Article 

Google Scholar 
Short, R. E. et al. Nature Food 2, 733–741 (2021).Article 

Google Scholar 
Golden, C. D. et al. Nature 598, 315–320 (2021).Article 
PubMed 

Google Scholar 
Hicks, C. C. et al. Nature Food 3, 851–861 (2022).Article 

Google Scholar 
Crona, B. I. et al. Nature https://doi.org/10.1038/s41586-023-05737-x (2023).Article 

Google Scholar 
Farmery, A. K. et al. One Earth 4, 28–38 (2021).Article 

Google Scholar 
Sigh, S. et al. Food Nutr. Bull. 39, 420–434 (2018).Article 
PubMed 

Google Scholar 
Larsen, T., Thilsted, S. H., Kongsbak, K. & Hansen, M. Br. J. Nutr. 83, 191–196 (2000).Article 
PubMed 

Google Scholar 
Cashion, T., Le Manach, F., Zeller, D. & Pauly, D. Fish Fish. 18, 837–844 (2017).Article 

Google Scholar 
Teisen, M. N. et al. Am. J. Clin. Nutr. 112, 74–83 (2020).Article 
PubMed 

Google Scholar 
Grieve, E. et al. BMC Public Health 23, 405 (2023).Article 
PubMed 

Google Scholar 
Mamun, A. A. et al. Front. Sustain. Food Syst. 5, 713140 (2021).Article 

Google Scholar  More

RESEARCH BRIEFINGS
22 March 2023

Since 2008, population densities of shallow-reef fishes, invertebrates and seaweeds around Australia have generally decreased near the northern limits of species’ ranges, and increased near their southern limits. Endemic invertebrates and seaweeds that prefer cold waters showed the steepest declines, and are prevented by deep-ocean barriers from moving south as temperatures rise. More

Many ocean sharks, including the grey reef shark, are endangered as a result of sharp declines in their numbers.Credit: Alexis Rosenfeld/Getty

The United Nations high seas treaty has been a long time coming. Secured earlier this month after almost 20 years of effort, it will be the first international law to offer some protection to the nearly two-thirds of the ocean that is beyond national control. These parts of the ocean currently have few, if any, meaningful safeguards against pollution, overfishing and habitat destruction. The treaty is without doubt a major achievement.Agreed under the UN Convention on the Law of the Sea, it represents several wins. Among them is the capacity to create marine protected areas through decisions of a conference of the parties to the treaty. It also recognizes that genetic resources of the high seas must benefit all of humanity. Moreover, companies planning commercial activities and organizations considering other large projects (such as potential climate interventions involving the ocean) will need to carry out environmental impact assessments.
UN forges historic deal to protect ocean life: what researchers think
Countries will be permitted to profit from exploiting marine genetic resources, but they must channel a proportion of their profits into a global fund to protect the high seas. Although the details are still to be worked out, high-income countries active in marine genetic research will be asked to contribute proportionately more to the fund.The treaty contains many opportunities for research in ocean science, for building research capacity in low- and middle-income countries, and for improving the evidence available to decision makers. Researchers working with marine genetic resources will need to register their interests with a central clearing house and commit to making data and research outputs open access.Scientists will have an important role in ensuring the treaty’s ultimate success. In part, this will involve gathering or improving the evidence to support the establishment and maintenance of strong marine protected areas and to inform stringent environmental impact assessments. Beyond that, researchers must make every effort to ensure transparency, including declaring the origin and prospective use of any genetic material, and making digital sequence information available through international repositories. This will not only enhance cooperation and capacity-building, but will also help governments to develop their own national regulations and procedures in line with the treaty.There’s also the potential for fresh scientific collaboration — for example, using emerging technologies such as telepresence, whereby scientists can take part in research cruises remotely. Marine scientists travelling to, say, the Pacific Ocean could collect samples under the guidance of colleagues elsewhere in real time. The knowledge gained from such collaborations could lead to the commercialization of new products, benefiting scientists and economies around the world.However, it is important not to overstate the treaty’s potential: notwithstanding its successes, there are deficiencies that the international community, supported by the research community, must now work to remedy.

Rena Lee, president of the high seas treaty conference, concluded proceedings on 3 March with the words “the ship has reached the shore”.Credit: Kena Betancur/AFP/Getty

As the planet warms, the Arctic’s permanent ice cover is melting, and China is planning a shipping route through the Central Arctic Ocean. This could become a regular passageway for shipping between Asia and Europe within a decade. In the Pacific, mining companies are exploring the deep sea bed for metals that they say are needed for the batteries that will power the coming green-energy transition. But these activities won’t face scrutiny under the treaty, because the treaty’s provisions don’t overrule regulations laid down by the authorities that oversee existing high seas activities. These include the International Maritime Organization, which is responsible for shipping; the International Seabed Authority, which oversees deep-sea mining; and some 17 regional fisheries management organizations tasked with regulating fisheries in various parts of the ocean, including Antarctica. Military activities and existing fishing and commercial shipping are, in fact, exempt from the treaty.
Protecting the ocean requires better progress metrics
This means, for example, that the treaty cannot create protected areas in places already covered by fishing agreements, even if that fishing is unsustainable and depleting stocks. This is a gaping hole. The overexploitation of coastal fisheries has made a frontier of the high seas, as fleets travel farther and fish for longer in search of dwindling resources. One outcome is that stocks of some highly migratory species, such as tuna, have dropped precipitously since the 1950s (M. J. Juan-Jordá et al. Proc. Natl Acad. Sci. USA 108, 20650–20655; 2011). By 2018, the Pacific bluefin tuna, for instance, was at 3.3% of 1952 levels (see go.nature.com/3mpimbh). Oceanic sharks and rays have also declined globally by 71% since 1970 (N. Pacoureau et al. Nature 589, 567–571; 2021). Once the treaty becomes law (after it has been ratified in the national parliaments of at least 60 countries), it can demand that proposed ocean activities — such as climate-intervention experiments — are subject to stringent environmental impact assessments. But it cannot do the same for activities already under way.Nor will the treaty end current offshore environmental violations. Farming waste, in the form of excessive nutrients, routinely ends up in rivers and coastal waters. From there, it makes its way to the open ocean, where it results in the formation of dead zones — vast areas devoid of life. Between 2008 and 2019, the number of these zones nearly doubled, from 400 to 700 (see go.nature.com/3mpigh1). So much plastic is now entering our seas that the oceans are thought to contain around 200 million tonnes. Meanwhile, cruise ships legally discharge more than one billion tonnes of raw sewage into international waters every year.Nonetheless, as humanity’s first serious attempt to challenge the carnage that prevails offshore, the high seas treaty is a triumph for diplomacy, particularly at a time when multilateralism is under sustained pressure. At present, just 1% of international waters are protected. That proportion is now set to grow, and this will help to maintain the health of our oceans and stem biodiversity loss. In securing this deal, the international community has given itself a fighting chance of coming good on earlier promises — most recently reiterated under the UN Convention on Biological Diversity — to protect 30% of the ocean by 2030.Full implementation, although some years away, offers scientists a once-in-a-generation opportunity to use their knowledge to support offshore conservation. In redressing our ‘out of sight, out of mind’ relationship with the oceans, the high seas treaty will allow us — supported by a burgeoning research effort — to rethink how we use our ocean commons in ways that benefit the majority. More

Most legislation to protect wildlife currently focuses on prohibiting deliberate destruction and excessive exploitation of resources. However, that approach fails to address emerging threats such as climate change. Many species will go extinct long before emissions-reduction schemes are realized.
Competing Interests
The authors declare no competing interests. More

In many conservation projects, women are alone on all-male teams.Credit: Getty

My career in conservation spans more than 20 countries, and workplaces ranging from universities, governments and consultancies to community-based and global non-governmental organizations (NGOs). Currently, I work as the Asia-Pacific director of gender and equity at The Nature Conservancy, one of the largest global conservation NGOs: it has more than 4,000 staff members and is active in more than 80 countries. I am responsible for ensuring that all our endeavours across the Asia-Pacific to address biodiversity loss and the climate crisis are inclusive and equitable.My career has been incredibly diverse: from monitoring saltwater crocodiles (Crocodylus porosus) in northern Australia to working with women on gender-based violence in Papua New Guinea to speaking at international climate meetings. But one theme has remained a constant: gender-based discrimination, which not only holds women back, but holds the world back from addressing the crises of climate change and biodiversity loss.Discrimination is by no means an experience unique to me or just a few women. A review of 230 peer-reviewed articles1, of which I was the lead author, confirmed a sobering truth: women everywhere are excluded from decisions about conservation and natural resources, from small and remote communities in biodiversity hotspots to large conservation organizations themselves. In every country, and in almost every setting and organization, women are routinely disadvantaged in conservation just because they are women.
Collection: Fieldwork
Unconscious bias is normal and natural, and all of us have it: it is how our brains make sense of the world. But when unexamined bias or deliberate discrimination influences decision-making, perpetuates stereotypes and keeps women from reaching their potential, they create rippling negative impacts on society and the future of our planet. Whether gender stereotypes are overtly hostile (such as ‘women are too emotional to lead fieldwork’) or seemingly benign (‘women are naturally good at organizing and supporting the team’ or ‘we need a strong, decisive leader’ — that is, a man), they hold women back in their conservation careers.An uneven playing fieldConservation has historically been a male-dominated profession. Just 3–11% of wildlife rangers are women2, and only 11% of the top-publishing authors in conservation and ecology are women3. A strong masculine culture is often associated with the profession, which can intimidate women. Many women in the sector experience sexual harassment and anxiety about their personal safety — particularly when they are the only woman on a project, which is often the case.Furthermore, women usually pay a heavy price for calling out cultures that are not inclusive. From surveying conservation professionals, I found that nearly 20% of women fear reprisal when speaking out against bias4. Their fears are warranted; many are sidelined or branded as ‘difficult’ or ‘frustrating’ if they draw attention to discrimination or poor behaviour, or try to slow down the decision-making process if it is not inclusive.In my career, I have been told that I wouldn’t be considered for an exciting project because it would be too physically demanding, be unsafe for a woman to be alone in a remote setting or require too much time away from my young family. Decisions that are made on your behalf are infuriating — and can come at both a career cost and a financial cost. Conversely, I have been offered opportunities because I have a masculine, gender-neutral name, and the people in charge assumed that I was a man before they had met me. I was then met with surprise and scepticism when I turned up and they realized that ‘Robyn James’ is a woman. I have always held my own in these situations, but the constant pressure to prove I belonged was exhausting and came at a personal cost5,6.My experiences are those of someone who holds deep and unearned privilege: I am a white cis woman with sufficient income to support my family, and I can speak and write English (the primary language of science) well. These factors increase my opportunities to contribute. Many conservationists and scientists who are women do not have those privileges. Some are also discriminated against owing to racism in a world that favours whiteness, and those who live in places where the cost of education and health care is high, wages are low and basic services such as power and Internet are intermittent face further disadvantages.As an ally and sponsor for women in conservation and science, I am determined to leverage my position to change this. I’m focused on breaking down walls and smashing the glass ceiling for women across the sector.Here are a few ways I am using the power I have to make conservation and science more inclusive. Hopefully these ideas will help others to share their solutions or to be better allies to women.Women are needed as leadersWomen who are conservation and environmental-science graduate students or are at early career stages often tell me that they don’t often see women at senior levels7, and that leaders don’t make them feel included. I am part of an informal group of women in senior positions in conservation, representing several organizations, who attend events for undergraduates and early-career professionals. We aim to share our journeys and to be visible to women who are just starting out. We model diverse leadership styles to show alternatives to masculine ‘command and control’ leadership, which these women might have more often experienced.Women routinely undersell themselves and do not apply for promotions, so we actively encourage our younger peers to apply for positions and support them by providing feedback on CVs and sharing interview techniques, for example. I am also part of a formal mentoring and sponsorship programme to support women — especially those in the lower-income countries — to navigate and excel in systems that are not designed with their success in mind. We work through issues to do with self-esteem and confidence: some women have understandably taken biased attitudes on board, and do not realize that they are worthy of progressing in their careers. I work with them to help them to understand how incredible they really are.

Conservation scientist Robyn James works with women on the Solomon Islands.Credit: Madlyn Ero

At The Nature Conservancy, we have developed a network of more than 50 women who can share their experiences and challenges in a safe supportive environment. We ensure that we work with women to address practical challenges they encounter. These efforts range from dedicated sessions on how to address gender bias in their teams and workplaces, to working through examples of how to make progress on gender equity in the field of conservation, where speaking up might clash with cultural norms or put women at risk of retaliation.Making work more inclusiveMy research with The Nature Conservancy on gender and conservation science publishing has shown that women are vastly under-represented8: less than 2% of authors were women in lower-income countries. The organization subsequently enlisted an experienced, well-published conservation scientist to work with women across the Asia-Pacific and support them in the publishing process, from developing research ideas to submitting final publications. I ensure my own published research includes authors with diverse perspectives. For example, for the three publications that were part of my PhD research1,4,8, 86% (19) of the authors are women, of which 68% (13) are first-time authors, 47% (9) are women of colour and 5 (26%) are in lower-income countries. This demonstrates that intentional efforts make a difference.Even the wording of job descriptions can exclude women. Language inherently has gendered associations, so including words such as confident, decisive, strong and outspoken in job postings has been found to attract men and deter women from applying. Many of my colleagues have felt intimidated by the tone of conservation job advertisements, which seem to be written for men. At The Nature Conservancy, we check our job descriptions and organizational plans and strategies for gendered language using a gender decoder, a tool that assesses text for masculine-coded language that could unconsciously discourage women from applying or keep women from feeling engaged with a work programme or strategy. (You can see what the decoder finds in this article here).Wherever patriarchy is deeply entrenched, men are often favoured for higher education and technical training — and women miss out. Many conservation roles have standard and mandatory educational and technical qualifications, so women are often automatically excluded from even being able to apply for a role they could otherwise be suited for.Changes in the fieldMy leadership team and I have worked to address some of the systems and processes that might inadvertently disadvantage women. For example, in the Solomon Islands, an archipelago in the south Pacific, marine conservation and research roles that require a scuba licence immediately exclude many women in the country from applying, because almost none have access to scuba training given that men are generally prioritized for training and development opportunities. In most places where The Nature Conservancy works, our employees will only ever need a mask and snorkel. Therefore, a small change in the job description means that many more women can apply. Adjusting our standard mandatory requirements has led to some fantastic women successfully applying and becoming high-performing members of our conservation teams. We now carefully omit any technical requirements that are not essential to a role or that can be easily obtained through on-the-job training.We ensure women are included in the teams that develop and implement workplace health and safety protocols, and have broadened our definition of workplace health and safety to include psychological safety and protection from gender-based violence (including sexual harassment). We worked with experienced professionals in this area to develop organization-wide guidance for our staff and partners. We also develop tailored plans depending on the country we are in to specifically address safety for women. For example, in Papua New Guinea, some women on our teams made it clear that it was unsafe for them to travel home after dark on public transport. In this country, more than two-thirds of women have experienced violence. We commissioned an official work vehicle to take staff home after hours.We ensure women have basic field equipment that is suitable for them. We provide women’s sizes in all protective gear: everything from gloves for fire protection to life jackets. This is organized before a trip or fieldwork takes place.We are also implementing protocols to ensure our conservation teams are diverse and that women are not on their own among all-male research groups. This is not only safer for women, but has repeatedly led to better conservation outcomes: the women notice things that have previously been missed. For example, in Mongolia, women in herding communities are often unable to attend important research meetings about grassland management because there is no access to toilets or because training sessions are held at times when they have caring obligations. The women on the project noticed this, and worked with the herders to ensure the infrastructure was adequate and the schedule was adjusted so that they could participate and share their unique perspectives on improving grassland conservation.Women benefit from more women being in the sector. From early-career to senior positions, representation matters. But this alone is not enough. Historically male-dominated sectors, such as conservation, that now have a relatively equal gender balance in undergraduate courses need to push for cultural change as well. This is the most difficult part of my role: challenging male leaders and systems that are not designed for women to succeed.Although we need to listen and respond to the needs of women, this is never something that should be the burden of women alone to fix. Strong leadership across our sector that prioritizes gender equity and inclusion in conservation, and provides resources to achieve it, is crucial.Women will thrive in conservation science if we keep pushing to move from equality to inclusion. Inclusion means not only that women are present, but that workplaces and programmes are designed and tailored with and for them. We shouldn’t be surprised or blame women when they don’t succeed in conservation and science workplaces and programmes that are still not actively including them. Women make up more than 50% of the population; we need to have a say in the future of our planet! More

Donia, M. S. & Fischbach, M. A. Small molecules from the human microbiota. Science 349, 1254766 (2015).Koh, A., De Vadder, F., Kovatcheva-Datchary, P. & Bäckhed, F. From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell 165, 1332–1345 (2016).Article 

Google Scholar 
Koppel, N., Rekdal, V. M. & Balskus, E. P. Chemical transformation of xenobiotics by the human gut microbiota. Science 356, eaag2770 (2017).Myhrstad, M. C., Tunsjø, H., Charnock, C. & Telle-Hansen, V. H. Dietary fiber, gut microbiota, and metabolic regulation—current status in human randomized trials. Nutrients 12, 859 (2020).Article 

Google Scholar 
Lin, R., Liu, W., Piao, M. & Zhu, H. A review of the relationship between the gut microbiota and amino acid metabolism. Amino Acids 49, 2083–2090 (2017).Article 

Google Scholar 
Tyson, G. W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37–43 (2004).Article 

Google Scholar 
Flint, H. J., Scott, K. P., Louis, P. & Duncan, S. H. The role of the gut microbiota in nutrition and health. Nat. Rev. Gastroenterol. Hepatol. 9, 577–589 (2012).Article 

Google Scholar 
Lloyd-Price, J. et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569, 655–662 (2019).Article 

Google Scholar 
Yang, Q. et al. Metabolomics biotechnology, applications, and future trends: a systematic review. RSC Adv. 9, 37245–37257 (2019).Article 

Google Scholar 
Castelli, F. A. et al. Metabolomics for personalized medicine: the input of analytical chemistry from biomarker discovery to point-of-care tests. Anal. Bioanal. Chem. 414, 759–789 (2022).Article 

Google Scholar 
Dias-Audibert, F. L. et al. Combining machine learning and metabolomics to identify weight gain biomarkers. Front. Bioeng. Biotechnol. 8, 6 (2020).Article 

Google Scholar 
Zheng, C., Zhang, S., Ragg, S., Raftery, D. & Vitek, O. Identification and quantification of metabolites in 1H NMR spectra by Bayesian model selection. Bioinformatics 27, 1637–1644 (2011).Article 

Google Scholar 
Information Resources Management Association. Bioinformatics: Concepts, Methodologies, Tools, and Applications (IGI Global, 2013).Johnson, C. H. & Gonzalez, F. J. Challenges and opportunities of metabolomics. J. Cell. Physiol. 227, 2975–2981 (2012).Article 

Google Scholar 
Ayling, M., Clark, M. D. & Leggett, R. M. New approaches for metagenome assembly with short reads. Brief. Bioinform. 21, 584–594 (2020).Article 

Google Scholar 
Brumfield, K. D., Huq, A., Colwell, R. R., Olds, J. L. & Leddy, M. B. Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available neon data. PLoS ONE 15, e0228899 (2020).Article 

Google Scholar 
Garza, D. R., van Verk, M. C., Huynen, M. A. & Dutilh, B. E. Towards predicting the environmental metabolome from metagenomics with a mechanistic model. Nat. Microbiol. 3, 456–460 (2018).Article 

Google Scholar 
Noecker, C. et al. Metabolic model-based integration of microbiome taxonomic and metabolomic profiles elucidates mechanistic links between ecological and metabolic variation. MSystems 1, e00013–15 (2016).Article 

Google Scholar 
Yin, X. et al. A comparative evaluation of tools to predict metabolite profiles from microbiome sequencing data. Front. Microbiol. 11, 3132 (2020).Article 

Google Scholar 
Kettle, H., Louis, P., Holtrop, G., Duncan, S. H. & Flint, H. J. Modelling the emergent dynamics and major metabolites of the human colonic microbiota. Environ. Microbiol. 17, 1615–1630 (2015).Article 

Google Scholar 
Quinn, R. A. et al. Niche partitioning of a pathogenic microbiome driven by chemical gradients. Sci. Adv. 4, eaau1908 (2018).Article 

Google Scholar 
Wang, T., Goyal, A., Dubinkina, V. & Maslov, S. Evidence for a multi-level trophic organization of the human gut microbiome. PLoS Comput. Biol. 15, e1007524 (2019).Article 

Google Scholar 
Goyal, A., Wang, T., Dubinkina, V. & Maslov, S. Ecology-guided prediction of cross-feeding interactions in the human gut microbiome. Nat. Commun. 12, 1335 (2021).Mallick, H. et al. Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences. Nat. Commun. 10, 3136 (2019).Article 

Google Scholar 
Le, V., Quinn, T. P., Tran, T. & Venkatesh, S. Deep in the bowel: highly interpretable neural encoder–decoder networks predict gut metabolites from gut microbiome. BMC Genom. 21, 256 (2020).Reiman, D., Layden, B. T. & Dai, Y. MiMeNet: exploring microbiome–metabolome relationships using neural networks. PLoS Comput. Biol. 17, e1009021 (2021).Article 

Google Scholar 
Morton, J. T. et al. Learning representations of microbe–metabolite interactions. Nat. Methods 16, 1306–1314 (2019).Article 

Google Scholar 
Chen, R. T., Rubanova, Y., Bettencourt, J. & Duvenaud, D. Neural ordinary differential equations. In Advances in Neural Information Processing Systems 31, 6572–6583 (NeurIPS, 2018).Lu, Y., Zhong, A., Li, Q. & Dong, B. Beyond finite layer neural networks: bridging deep architectures and numerical differential equations. In International Conference on Machine Learning 3276–3285 (PMLR, 2018).Qiu, C., Bendickson, A., Kalyanapu, J. & Yan, J. Accuracy and architecture studies of residual neural network solving ordinary differential equations. Preprint at arXiv https://doi.org/10.48550/arXiv.2101.03583 (2021).Dutta, S., Rivera-Casillas, P. & Farthing, M. W. Neural ordinary differential equations for data-driven reduced order modeling of environmental hydrodynamics. Preprint at https://doi.org/10.48550/arXiv.2104.13962 (2021).Marsland III, R. et al. Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities. PLoS Comput. Biol. 15, e1006793 (2019).Article 

Google Scholar 
Franzosa, E. A. et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat. Microbiol. 4, 293–305 (2019).Article 

Google Scholar 
Swenson, T. L., Karaoz, U., Swenson, J. M., Bowen, B. P. & Northen, T. R. Linking soil biology and chemistry in biological soil crust using isolate exometabolomics. Nat. Commun. 9, 19 (2018).Article 

Google Scholar 
Litonjua, A. A. et al. Effect of prenatal supplementation with vitamin D on asthma or recurrent wheezing in offspring by age 3 years: the VDAART randomized clinical trial. JAMA 315, 362–370 (2016).Article 

Google Scholar 
Litonjua, A. A. et al. Six-year follow-up of a trial of antenatal vitamin D for asthma reduction. N. Engl. J. Med. 382, 525–533 (2020).Article 

Google Scholar 
Lee-Sarwar, K. A. et al. Integrative analysis of the intestinal metabolome of childhood asthma. J. Allergy Clin. Immunol. 144, 442–454 (2019).Article 

Google Scholar 
Lee-Sarwar, K. et al. Association of the gut microbiome and metabolome with wheeze frequency in childhood asthma. J. Allergy Clin. Immunol. 147, AB53 (2021).Article 

Google Scholar 
Harvard Willett Food Frequency Questionnaire (T.H. Chan School of Public Health, Department of Nutrition, Harvard Univ., 2015).Plan and Operation of the Third National Health and Nutrition Examination Survey, 1988–94 (National Centre for Health Statistics, 1994).Nelson, K. M., Reiber, G. & Boyko, E. J. Diet and exercise among adults with type 2 diabetes: findings from the third National Health and Nutrition Examination Survey (NHANES III). Diabetes Care 25, 1722–1728 (2002).Article 

Google Scholar 
Marriott, B. P., Olsho, L., Hadden, L. & Connor, P. Intake of added sugars and selected nutrients in the United States, National Health and Nutrition Examination Survey (NHANES) 2003-2006. Crit. Rev. Food Sci. Nutr. 50, 228–258 (2010).Article 

Google Scholar 
Moshfegh, A. Food and Nutrient Database for Dietary Studies (US Department of Agriculture, Agricultural Research Service, Food Surveys Research Group, 2022); http://www.ars.usda.gov/nea/bhnrc/fsrgRidlon, J. M., Kang, D.-J. & Hylemon, P. B. Bile salt biotransformations by human intestinal bacteria. J. Lipid Res. 47, 241–259 (2006).Article 

Google Scholar 
Bachmann, V. et al. Bile salts modulate the mucin-activated type VI secretion system of pandemic Vibrio cholerae. PLoS Negl. Trop. Dis. 9, e0004031 (2015).Article 

Google Scholar 
Ramírez-Pérez, O., Cruz-Ramón, V., Chinchilla-López, P. & Méndez-Sánchez, N. The role of the gut microbiota in bile acid metabolism. Ann. Hepatol. 16, 21–26 (2018).Article 

Google Scholar 
Jia, W., Xie, G. & Jia, W. Bile acid-microbiota crosstalk in gastrointestinal inflammation and carcinogenesis. Nat. Rev. Gastroenterol. Hepatol. 15, 111–128 (2018).Article 

Google Scholar 
Heinken, A. et al. Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease. Microbiome 7, 75 (2019).Duboc, H. et al. Connecting dysbiosis, bile-acid dysmetabolism and gut inflammation in inflammatory bowel diseases. Gut 62, 531–539 (2013).Article 

Google Scholar 
Thomas, J. P., Modos, D., Rushbrook, S. M., Powell, N. & Korcsmaros, T. The emerging role of bile acids in the pathogenesis of inflammatory bowel disease. Front. Immunol. 13, 246 (2022).Kristal, A. R., Peters, U. & Potter, J. D. Is it time to abandon the food frequency questionnaire? Cancer Epidemiol. Biomarkers Prev. 14, 2826–2828 (2005).Article 

Google Scholar 
Scalbert, A. et al. The food metabolome: a window over dietary exposure. Am. J. Clin. Nutr. 99, 1286–1308 (2014).Article 

Google Scholar 
Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).Article 

Google Scholar 
Callahan, B. J. et al. DADA: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).Article 

Google Scholar 
Evans, A. M. et al. High resolution mass spectrometry improves data quantity and quality as compared to unit mass resolution mass spectrometry in high-throughput profiling metabolomics. Metabolomics 4, 1 (2014).
Google Scholar 
Blum, R. E. et al. Validation of a food frequency questionnaire in Native American and Caucasian children 1 to 5 years of age. Matern. Child Health J. 3, 167–172 (1999).Article 

Google Scholar 
Kingma, D. P. & Ba, J. Adam: a method for stochastic optimization. Preprint at https://doi.org/10.48550/arXiv.1412.6980 (2014).Wang, T. wt1005203/mnode: initial release. Zenodo https://doi.org/10.5281/zenodo.7602940 (2023). More

Barnosky, A. D. et al. Has the Earth’s sixth mass extinction already arrived? Nature 471, 51–57 (2011).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Ceballos, G., Ehrlich, P. R. & Dirzo, R. Biological annihilation via the ongoing sixth mass extinction signaled by vertebrate population losses and declines. Proc. Natl Acad. Sci. USA 114, E6089–E6096 (2017).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Cowie, R. H., Bouchet, P. & Fontaine, B. The Sixth Mass Extinction: fact, fiction or speculation? Biol. Rev. 97, 640–663 (2022).Article 
PubMed 

Google Scholar 
Dirzo, R. et al. Defaunation in the anthropocene. Science 345, 401–406 (2014).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Ceballos, G. et al. Accelerated modern human–induced species losses: entering the sixth mass extinction. Sci. Adv. 1, e1400253 (2015).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Pimm, S. L. et al. The biodiversity of species and their rates of extinction, distribution, and protection. Science 344, 1246752 (2014).Article 
CAS 
PubMed 

Google Scholar 
Urban, M. et al. Accelerating extinction risk from climate change. Science 348, 571–573 (2015).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Pincheira-Donoso, D. et al. Temporal and spatial patterns of vertebrate extinctions during the Anthropocene. Preprint at bioRxiv https://doi.org/10.1101/2022.05.05.490605 (2022).Brook, B. W., Sodhi, N. S. & Bradshaw, C. J. A. Synergies among extinction drivers under global change. Trends Ecol. Evol. 23, 453–460 (2008).Article 
PubMed 

Google Scholar 
Pacifici, M. et al. Assessing species vulnerability to climate change. Nat. Clim. Change 5, 215–224 (2015).Article 
ADS 

Google Scholar 
Thomas, C. D. et al. Extinction risk from climate change. Nature 427, 145–148 (2004).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Warren, R. et al. Quantifying the benefit of early climate change mitigation in avoiding biodiversity loss. Nat. Clim. Change 3, 678–682 (2013).Article 
ADS 

Google Scholar 
Román-Palacios, C. & Wiens, J. J. Recent responses to climate change reveal the drivers of species extinction and survival. Proc. Natl Acad. Sci. USA 117, 4211–4217 (2020).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Gaston, K. J., Jackson, S. F., Cantú-Salazar, L. & Cruz-Piñón, G. The ecological performance of protected areas. Annu. Rev. Ecol. Evol. Syst. 39, 93–113 (2008).Article 

Google Scholar 
Saout, S. L. et al. Protected areas and effective biodiversity conservation. Science 342, 803–805 (2013).Article 
ADS 
PubMed 

Google Scholar 
Watson, J. E. M., Dudley, N., Segan, D. B. & Hockings, M. The performance and potential of protected areas. Nature 515, 67–73 (2014).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Araújo, M. B., Alagador, D., Cabeza, M., Noguésbravo, D. & Thuiller, W. Climate change threatens European conservation areas. Ecol. Lett. 14, 484–492 (2011).Article 
PubMed 
PubMed Central 

Google Scholar 
Chen, Y., Zhang, J., Jiang, J., Nielsen, S. & He, F. Assessing the effectiveness of China’s protected areas to conserve current and future amphibian diversity. Divers. Distrib. 23, 146–157 (2017).Article 

Google Scholar 
Jenkins, C. N. & Joppa, L. Expansion of the global terrestrial protected area system. Biol. Conserv. 142, 2166–2174 (2009).Article 

Google Scholar 
Johnston, A. et al. Observed and predicted effects of climate change on species abundance in protected areas. Nat. Clim. Change 3, 1055–1061 (2013).Article 
ADS 

Google Scholar 
Lehikoinen, P., Santangeli, A., Jaatinen, K., Rajasärkkä, A. & Lehikoinen, A. Protected areas act as a buffer against detrimental effects of climate change-evidence from large-scale, long-term abundance data. Glob. Change Biol. 25, 304–313 (2018).Article 
ADS 

Google Scholar 
Coetzee, B. W. T., Robertson, M. P., Erasmus, B. F. N., Rensburg, B. J. V. & Thuiller, W. Ensemble models predict Important Bird Areas in southern Africa will become less effective for conserving endemic birds under climate change. Glob. Ecol. Biogeogr. 18, 701–710 (2009).Article 

Google Scholar 
Araújo, M. B., Cabeza, M., Thuiller, W., Hannah, L. & Williams, P. H. Would climate change drive species out of reserves? An assessment of existing reserve‐selection methods. Glob. Change Biol. 10, 1618–1626 (2004).Article 
ADS 

Google Scholar 
Pouzols, F. M. et al. Global protected area expansion is compromised by projected land-use and parochialism. Nature 516, 383–386 (2014).Article 
ADS 

Google Scholar 
Monzn, J., Moyer-Horner, L. & Palamar, M. B. Climate change and species range dynamics in protected areas. Bioscience 61, 752–761 (2011).Article 

Google Scholar 
Newbold, T., Oppenheimer, P., Etard, A. & Williams, J. J. Tropical and Mediterranean biodiversity is disproportionately sensitive to land-use and climate change. Nat. Ecol. Evol. 4, 1630–1638 (2020).Article 
PubMed 

Google Scholar 
Liu, X. et al. Animal invaders threaten protected areas worldwide. Nat. Commun. 11, 2892 (2020).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Carlson, C. J. et al. Climate change increases cross-species viral transmission risk. Nature 607, 555–562 (2022).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Mi, C., Huettmann, F. & Guo, Y. Climate envelope predictions indicate an enlarged suitable wintering distribution for Great Bustards (Otis tarda dybowskii) in China for the 21st century. Peerj 4, e1630–e1630 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Guisan, A. et al. Predicting species distributions for conservation decisions. Ecol. Lett. 16, 1424–1435 (2013).Article 
PubMed 
PubMed Central 

Google Scholar 
Zhu, G., Papeş, M., Giam, X., Cho, S.-H. & Armsworth, P. R. Are protected areas well-sited to support species in the future in a major climate refuge and corridor in the United States? Biol. Conserv. 255, 108982 (2021).Article 

Google Scholar 
Gutiérrez, J. A. & Duivenvoorden, J. F. Can we expect to protect threatened species in protected areas? A case study of the genus Pinus in Mexico. Rev. Mexicana Biodivers. 81, 875–882 (2010).
Google Scholar 
Velásquez-Tibatá, J., Salaman, P. & Graham, C. H. Effects of climate change on species distribution, community structure, and conservation of birds in protected areas in Colombia. Reg. Environ. Change 13, 235–248 (2013).Article 

Google Scholar 
Riquelme, C. et al. Protected areas’ effectiveness under climate change: a latitudinal distribution projection of an endangered mountain ungulate along the Andes Range. Peerj 6, e5222 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Bazzichetto, M. et al. Plant invasion risk: a quest for invasive species distribution modelling in managing protected areas. Ecol. Indic. 95, 311–319 (2018).Article 

Google Scholar 
Hannah, L. et al. Protected area needs in a changing climate. Front. Ecol. Environ. 5, 131–138 (2007).Article 

Google Scholar 
Cox, N. et al. A global reptile assessment highlights shared conservation needs of tetrapods. Nature 695, 285–290 (2022).Article 
ADS 

Google Scholar 
IUCN. The IUCN red list of threatened species. http://www.iucnredlist.org/ (2021).Wake, D. B. & Vredenburg, V. T. Are we in the midst of the sixth mass extinction? A view from the world of amphibians. Proc. Natl Acad. Sci. USA 105, 11466–11473 (2008).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Cordier, J. M. et al. A global assessment of amphibian and reptile responses to land-use changes. Biol. Conserv. 253, 108863 (2021).Article 

Google Scholar 
Powers, R. P. & Jetz, W. Global habitat loss and extinction risk of terrestrial vertebrates under future land-use-change scenarios. Nat. Clim. Change 9, 323–329 (2019).Article 
ADS 

Google Scholar 
Pounds, J. A. et al. Widespread amphibian extinctions from epidemic disease driven by global warming. Nature 439, 161–167 (2006).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Scheele, B. C. et al. Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity. Science 363, 1459–1463 (2019).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Blaustein, A. R. & Kiesecker, J. M. Complexity in conservation: lessons from the global decline of amphibian populations. Ecol. Lett. 5, 597–608 (2002).Article 

Google Scholar 
Kraus, F. Impacts from invasive reptiles and amphibians. Annu. Rev. Ecol. Evol. Syst. 46, 75–97 (2015).Article 

Google Scholar 
Alford, R. A., Bradfield, K. S. & Richards, S. J. Global warming and amphibian losses. Nature 447, E3–E4 (2007).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Hof, C., Araújo, M. B., Jetz, W. & Rahbek, C. Additive threats from pathogens, climate and land-use change for global amphibian diversity. Nature 480, 516–519 (2011).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Rohr, J. R. & Raffel, T. R. Linking global climate and temperature variability to widespread amphibian declines putatively caused by disease. Proc. Natl Acad. Sci. USA 107, 8269–8274 (2008).Article 
ADS 

Google Scholar 
Pincheira‐Donoso, D. et al. The global macroecology of brood size in amphibians reveals a predisposition of low‐fecundity species to extinction. Glob. Ecol. Biogeogr. 30, 1299–1310 (2021).Article 

Google Scholar 
Smith, M. A. & Green, D. M. Dispersal and the metapopulation paradigm in amphibian ecology and conservation: are all amphibian populations metapopulations? Ecography 28, 110–128 (2005).Article 

Google Scholar 
Borzée, A. et al. Climate change-based models predict range shifts in the distribution of the only Asian plethodontid salamander: Karsenia koreana. Sci. Rep. 9, 11838 (2019).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Heller, N. E. & Zavaleta, E. S. Biodiversity management in the face of climate change: a review of 22 years of recommendations. Biol. Conserv. 142, 14–32 (2009).Article 

Google Scholar 
Haight, J. & Hammill, E. Protected areas as potential refugia for biodiversity under climatic change. Biol. Conserv. 241, 108258 (2020).Article 

Google Scholar 
Thomas, C. D. et al. Protected areas facilitate species’ range expansions. Proc. Natl Acad. Sci. USA 109, 14063–14068 (2012).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Lawson, C. R., Bennie, J. J., Thomas, C. D., Hodgson, J. A. & Wilson, R. J. Active management of protected areas enhances metapopulation expansion under climate change. Conserv. Lett. 7, 111–118 (2014).Article 

Google Scholar 
Beale, C. M., Baker, N. E., Brewer, M. J. & Lennon, J. J. Protected area networks and savannah bird biodiversity in the face of climate change and land degradation. Ecol. Lett. 16, 1061–1068 (2013).Article 
PubMed 

Google Scholar 
D’Amen, M. et al. Will climate change reduce the efficacy of protected areas for amphibian conservation in Italy? Biol. Conserv. 144, 989–997 (2011).Article 

Google Scholar 
Singh, M. Evaluating the impact of future climate and forest cover change on the ability of Southeast (SE) Asia’s protected areas to provide coverage to the habitats of threatened avian species. Ecol. Indic. 114, 106307 (2020).Article 

Google Scholar 
Hole, D. G. et al. Projected impacts of climate change on a continent‐wide protected area network. Ecol. Lett. 12, 420–431 (2009).Article 
PubMed 

Google Scholar 
Lehikoinen, P. et al. Increasing protected area coverage mitigates climate-driven community changes. Biol. Conserv. 253, 108892 (2021).Article 

Google Scholar 
Araújo, M. B., Thuiller, W. & Pearson, R. G. Climate warming and the decline of amphibians and reptiles in Europe. J. Biogeogr. 33, 1712–1728 (2006).Article 

Google Scholar 
Girardello, M., Griggio, M., Whittingham, M. J. & Rushton, S. P. Models of climate associations and distributions of amphibians in Italy. Ecol. Res. 25, 103–111 (2010).Article 

Google Scholar 
McMenamin, S. K., Hadly, E. A. & Wright, C. K. Climatic change and wetland desiccation cause amphibian decline in Yellowstone National Park. Proc. Natl Acad. Sci. USA 105, 16988–16993 (2008).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Ficetola, G. F. & Maiorano, L. Contrasting effects of temperature and precipitation change on amphibian phenology, abundance and performance. Oecologia 181, 683–693 (2016).Article 
ADS 
PubMed 

Google Scholar 
Bickford, D., Howard, S. D., Ng, D. J. J. & Sheridan, J. A. Impacts of climate change on the amphibians and reptiles of Southeast Asia. Biodivers. Conserv. 19, 1043–1062 (2010).Article 

Google Scholar 
Manne, L. L., Brooks, T. M. & Pimm, S. L. Relative risk of extinction of passerine birds on continents and islands. Nature 399, 258–261 (1999).Article 
ADS 
CAS 

Google Scholar 
Jenkins, C. N., Pimm, S. L. & Joppa, L. N. Global patterns of terrestrial vertebrate diversity and conservation. Proc. Natl Acad. Sci. USA 110, E2602–E2610 (2013).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Pearson, R. G. et al. Life history and spatial traits predict extinction risk due to climate change. Nat. Clim. Change 4, 217–221 (2014).Article 
ADS 

Google Scholar 
Wauchope, H. S. et al. Protected areas have a mixed impact on waterbirds, but management helps. Nature 605, 103–107 (2022).Article 
ADS 
CAS 
PubMed 

Google Scholar 
WWF. Tropical and Subtropical Moist Broadleaf Forest Ecoregions (World Wide Fund for Nature, 2019).Rodrigues, A. S. L. et al. Global gap analysis: priority regions for expanding the global protected-area network. Bioscience 54, 1092–1100 (2004).Article 

Google Scholar 
Hidasi‐Neto, J., Loyola, R. & Cianciaruso, M. V. Global and local evolutionary and ecological distinctiveness of terrestrial mammals: identifying priorities across scales. Divers. Distrib. 21, 548–559 (2015).Article 

Google Scholar 
Martin, J.-L., Maris, V. & Simberloff, D. S. The need to respect nature and its limits challenges society and conservation science. Proc. Natl Acad. Sci. USA 113, 6105–6112 (2016).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Czech, B., Krausman, P. & Devers, P. Economic associations among causes of species endangerment in the United States. Bioscience 50, 593–601 (2000).Article 

Google Scholar 
CBD. First draft of the post-2020 global biodiversity framework. https://www.cbd.int/doc/c/abb5/591f/2e46096d3f0330b08ce87a45/wg2020-03-03-en.pdf (2021).Roll, U. et al. The global distribution of tetrapods reveals a need for targeted reptile conservation. Nat. Ecol. Evol. 1, 1677–1682 (2017).Article 
PubMed 

Google Scholar 
Ficetola, G. F. et al. An evaluation of the robustness of global amphibian range maps. J. Biogeogr. 41, 211–221 (2014).Article 

Google Scholar 
Aiello‐Lammens, M. E., Boria, R. A., Radosavljevic, A., Vilela, B. & Anderson, R. P. spThin: an R package for spatial thinning of species occurrence records for use in ecological niche models. Ecography 38, 541–545 (2015).Article 

Google Scholar 
Erfanian, M. B., Sagharyan, M., Memariani, F. & Ejtehadi, H. Predicting range shifts of three endangered endemic plants of the Khorassan-Kopet Dagh floristic province under global change. Sci. Rep. 11, 9159 (2021).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Brown, J. L., Cameron, A., Yoder, A. D. & Vences, M. A necessarily complex model to explain the biogeography of the amphibians and reptiles of Madagascar. Nat. Commun. 5, 5046 (2014).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Gaston, K. J. Rarity as double jeopardy. Nature 394, 229–230 (1998).Article 
ADS 
CAS 

Google Scholar 
Hijmans, R. J., Cameron, S. E., Parra, J. L., Jones, P. G. & Jarvis, A. Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 25, 1965–1978 (2005).Article 

Google Scholar 
Li, X., Liu, X., Kraus, F., Tingley, R. & Li, Y. Risk of biological invasions is concentrated in biodiversity hotspots. Front. Ecol. Environ. 14, 411–417 (2016).Article 

Google Scholar 
Naimi, B., Hamm, N. A. S., Groen, T. A., Skidmore, A. K. & Toxopeus, A. G. Where is positional uncertainty a problem for species distribution modelling? Ecography 37, 191–203 (2014).Article 

Google Scholar 
Xin, X., Wu, T. & Zhang, J. Introduction of CMIP5 experiments carried out with the climate system models of beijing climate center. Adv. Clim. Change Res. 4, 41–49 (2013).Article 

Google Scholar 
Voldoire, A. et al. The CNRM-CM5.1 global climate model: description and basic evaluation. Clim. Dyn. 40, 2091–2121 (2013).Article 

Google Scholar 
Watanabe, S. et al. MIROC-ESM 2010: model description and basic results of CMIP5-20c3m experiments. Geosci. Model Dev. 4, 845–872 (2011).Article 
ADS 

Google Scholar 
Mi, C. et al. Temperate and tropical lizards are vulnerable to climate warming due to increased water loss and heat stress. Proc. R. Soc. Lond. B. Biol. Sci. 289, 20221074 (2022).
Google Scholar 
Naimi, B. & Araújo, M. B. sdm: a reproducible and extensible R platform for species distribution modelling. Ecography 39, 368–375 (2016).Article 

Google Scholar 
Holt, B. G. et al. An update of Wallace’s zoogeographic regions of the world. Science 339, 74–78 (2013).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Barbet-Massin, M., Jiguet, F., Albert, C. H. & Thuiller, W. Selecting pseudo-absences for species distribution models: how, where and how many?: How to use pseudo-absences in niche modelling? Methods Ecol. Evol. 3, 327–338 (2012).Article 

Google Scholar 
Andrade, A. F. A., de, Velazco, S. J. E. & Júnior, P. D. M. ENMTML: an R package for a straightforward construction of complex ecological niche models. Environ. Modell. Softw. 125, 104615 (2020).Article 

Google Scholar 
Senay, S. D., Worner, S. P. & Ikeda, T. Novel three-step pseudo-absence selection technique for improved species distribution modelling. PLos ONE 8, e71218 (2013).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Thuiller, W. BIOMOD–optimizing predictions of species distributions and projecting potential future shifts under global change. Glob. Change Biol. 9, 1353–1362 (2003).Article 
ADS 

Google Scholar 
Williams, J. N. et al. Using species distribution models to predict new occurrences for rare plants. Divers. Distrib. 15, 565–576 (2009).Article 

Google Scholar 
Graham, C. H. et al. The influence of spatial errors in species occurrence data used in distribution models. J. Appl. Ecol. 45, 239–247 (2008).Article 

Google Scholar 
Elith, J. et al. Novel methods improve prediction of species’ distributions from occurrence data. Ecography 29, 129–151 (2006).Article 

Google Scholar 
Mi, C., Huettmann, F., Guo, Y., Han, X. & Wen, L. Why choose Random Forest to predict rare species distribution with few samples in large undersampled areas? Three Asian crane species models provide supporting evidence. Peerj 5, e2849 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Drake, J. M., Randin, C. & Guisan, A. Modelling ecological niches with support vector machines. J. Appl. Ecol. 43, 424–432 (2006).Article 

Google Scholar 
Allouche, O., Tsoar, A. & Kadmon, R. Assessing the accuracy of species distribution models: prevalence, kappa and the true skill statistic (TSS). J. Appl. Ecol. 43, 1223–1232 (2006).Article 

Google Scholar 
McPherson, J., Jetz, W. & Rogers, D. J. The effects of species’ range sizes on the accuracy of distribution models: ecological phenomenon or statistical artefact? J. Appl. Ecol. 41, 811–823 (2004).Article 

Google Scholar 
Wang, B. et al. Australian wheat production expected to decrease by the late 21st century. Glob. Change Biol. 24, 2403–2415 (2017).Article 
ADS 

Google Scholar 
Gallardo, B. et al. Protected areas offer refuge from invasive species spreading under climate change. Glob. Change Biol. 23, 5331–5343 (2017).Article 
ADS 

Google Scholar 
Thuiller, W., Lafourcade, B., Engler, R. & Araújo, M. B. BIOMOD – a platform for ensemble forecasting of species distributions. Ecography 32, 369–373 (2009).Article 

Google Scholar 
UNEP-WCMC, I. and. The world database on protected areas (WDPA). https://www.protectedplanet.net/en#4_43.25_111_0 (2014).Asamoah, E. F., Beaumont, L. J. & Maina, J. M. Climate and land-use changes reduce the benefits of terrestrial protected areas. Nat. Clim. Change 11, 1105–1110 (2021).Article 
ADS 

Google Scholar 
Brennan, A. et al. Functional connectivity of the world’s protected areas. Science 376, 1101–1104 (2022).You, Z. et al. Pitfall of big databases. Proc. Natl Acad. Sci. USA 115, 201813323 (2018).Article 

Google Scholar 
Nelson, A. & Chomitz, K. M. Effectiveness of strict vs. multiple use protected areas in reducing tropical forest fires: a global analysis using matching methods. PLoS ONE 6, e22722 (2011).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Albuquerque, F. & Beier, P. Rarity-weighted richness: a simple and reliable alternative to integer programming and heuristic algorithms for minimum set and maximum coverage problems in conservation planning. PLoS ONE 10, e0119905 (2015).Article 
PubMed 
PubMed Central 

Google Scholar 
Tang, C. Q. et al. Identifying long-term stable refugia for relict plant species in East Asia. Nat. Commun. 9, 4488 (2018).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Kier, G. & Barthlott, W. Measuring and mapping endemism and species richness: a new methodological approach and its application on the flora of Africa. Biodivers. Conserv 10, 1513–1529 (2001).Article 

Google Scholar 
Albuquerque, F. & Gregory, A. The geography of hotspots of rarity-weighted richness of birds and their coverage by Natura 2000. PLoS ONE 12, e0174179 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Jennings, M. D. Gap analysis: concepts, methods, and recent results. Landsc. Ecol. 15, 5–20 (2000).Article 

Google Scholar 
Romero‐Muñoz, A. et al. Increasing synergistic effects of habitat destruction and hunting on mammals over three decades in the Gran Chaco. Ecography 43, 954–966 (2020).Article 

Google Scholar 
Brooks, T. M. et al. Global biodiversity conservation priorities. Science 313, 58–61 (2006).Article 
ADS 
CAS 
PubMed 

Google Scholar  More

Ellis, E. C. et al. People have shaped most of terrestrial nature for at least 12,000 years. Proc. Natl. Acad. Sci. USA 118, e2023483118 (2021).Article 
CAS 

Google Scholar 
Williams, B. A. et al. Change in terrestrial human footprint drives continued loss of intact ecosystems. One Earth 3, 371–382 (2020).Article 

Google Scholar 
Kuipers, K. J. J. et al. Habitat fragmentation amplifies threats from habitat loss to mammal diversity across the world’s terrestrial ecoregions. One Earth 4, 1505–1513 (2021).Article 

Google Scholar 
Venter, O. et al. Sixteen years of change in the global terrestrial human footprint and implications for biodiversity conservation. Nat. Commun. 7, 12558 (2016).Article 
CAS 

Google Scholar 
Watson, J. E. M. & Venter, O. Mapping the continuum of humanity’s footprint on land. One Earth 1, 175–180 (2019).Article 

Google Scholar 
Foley, J. A. et al. Global consequences of land use. Science 309, 570–574 (2005).Article 
CAS 

Google Scholar 
Glidden, C. K. et al. Human-mediated impacts on biodiversity and the consequences for zoonotic disease spillover. Curr. Biol. 31, R1342–R1361 (2021).Article 
CAS 

Google Scholar 
Grobbelaar, A. A. et al. Resurgence of yellow fever in Angola, 2015-2016. Emerg. Infect. Dis. 22, 1854–1855 (2016).Article 

Google Scholar 
Gubler, D. J. Epidemic dengue/dengue hemorrhagic fever as a public health, social and economic problem in the 21st century. Trends Microbiol. 10, 100–103 (2002).Article 
CAS 

Google Scholar 
Hotez, P. J. Neglected tropical diseases in the Anthropocene: the cases of Zika, Ebola, and other infections. PLoS Negl. Trop. Dis. 10, e0004648 (2016).Article 

Google Scholar 
Paixão, E. S., Teixeira, M. G. & Rodrigues, L. C. Zika, chikungunya and dengue: the causes and threats of new and re-emerging arboviral diseases. BMJ Glob. Health 3, e000530 (2018).Article 

Google Scholar 
Rosenberg, R. et al. Vital signs: trends in reported vectorborne disease cases – United States and territories, 2004-2016. Morb. Mortal. Wk. Rep. 67, 496–501 (2018).Article 

Google Scholar 
World Malaria Report 2020: 20 Years of Global Progress and Challenges (WHO, 2020); https://apps.who.int/iris/handle/10665/337660Lambin, E. F., Tran, A., Vanwambeke, S. O., Linard, C. & Soti, V. Pathogenic landscapes: interactions between land, people, disease vectors, and their animal hosts. Int. J. Health Geogr. 9, 54 (2010).Article 

Google Scholar 
Shocket, M. S. et al. Transmission of West Nile and five other temperate mosquito-borne viruses peaks at temperatures between 23 °C and 26 °C. eLife 9, e58511 (2020).Article 
CAS 

Google Scholar 
Kilpatrick, A. M. & Randolph, S. E. Drivers, dynamics, and control of emerging vector-borne zoonotic diseases. Lancet 380, 1946–1955 (2012).Article 

Google Scholar 
Franklinos, L. H. V., Jones, K. E., Redding, D. W. & Abubakar, I. The effect of global change on mosquito-borne disease. Lancet Infect. Dis. 19, e302–e312 (2019).Article 

Google Scholar 
Keys, P. W., Barnes, E. A. & Carter, N. H. A machine-learning approach to human footprint index estimation with applications to sustainable development. Environ. Res. Lett. 16, 044061 (2021).Article 

Google Scholar 
Venter, O. et al. Global terrestrial human footprint maps for 1993 and 2009. Sci. Data 3, 160067 (2016).Article 

Google Scholar 
Di Marco, M., Ferrier, S., Harwood, T. D., Hoskins, A. J. & Watson, J. E. M. Wilderness areas halve the extinction risk of terrestrial biodiversity. Nature 573, 582–585 (2019).Article 

Google Scholar 
Hill, J. E., DeVault, T. L., Wang, G. & Belant, J. L. Anthropogenic mortality in mammals increases with the human footprint. Front. Ecol. Environ. 18, 13–18 (2020).Article 

Google Scholar 
Elsen, P. R., Monahan, W. B. & Merenlender, A. M. Topography and human pressure in mountain ranges alter expected species responses to climate change. Nat. Commun. 11, 1974 (2020).Article 
CAS 

Google Scholar 
Su, J., Yin, H. & Kong, F. Ecological networks in response to climate change and the human footprint in the Yangtze River Delta urban agglomeration, China. Landsc. Ecol. 36, 2095–2112 (2021).Article 

Google Scholar 
Hansen, A. J. et al. A policy-driven framework for conserving the best of Earth’s remaining moist tropical forests. Nat. Ecol. Evol. 4, 1377–1384 (2020).Article 

Google Scholar 
Dos Santos, C. V. B., da Paixão Sevá, A., Werneck, G. L. & Struchiner, C. J. Does deforestation drive visceral leishmaniasis transmission? A causal analysis. Proc. R. Soc. B 288, 20211537 (2021).Article 

Google Scholar 
MacDonald, A. J. & Mordecai, E. A. Amazon deforestation drives malaria transmission, and malaria burden reduces forest clearing. Proc. Natl. Acad. Sci. USA 116, 22212–22218 (2019).Article 
CAS 

Google Scholar 
Honório, N. A. et al. Dispersal of Aedes aegypti and Aedes albopictus (Diptera: Culicidae) in an urban endemic dengue area in the State of Rio de Janeiro, Brazil. Mem. Inst. Oswaldo Cruz 98, 191–198 (2003).Article 

Google Scholar 
Rodrigues, N. B. et al. Brazilian Aedes aegypti as a competent vector for multiple complex arboviral coinfections. J. Infect. Dis. 224, 101–108 (2021).Article 

Google Scholar 
Weinstein, J. S., Leslie, T. F. & von Fricken, M. E. Spatial associations between land use and infectious disease: Zika virus in Colombia. Int. J. Environ. Res. Public Health 17, E1127 (2020).Article 

Google Scholar 
Heukelbach, J., Alencar, C. H., Kelvin, A. A., de Oliveira, W. K. & Pamplona de Góes Cavalcanti, L. Zika virus outbreak in Brazil. J. Infect. Dev. Countr. 10, 116–120 (2016).Article 

Google Scholar 
Lowe, R. et al. The Zika virus epidemic in Brazil: from discovery to future implications. Int. J. Environ. Res. Public Health 15, E96 (2018).Article 

Google Scholar 
Alves, M. C. G. P., de Matos, M. R., de Lourdes Reichmann, M. & Dominguez, M. H. Estimation of the dog and cat population in the State of São Paulo. Rev. Saude Publica 39, 891–897 (2005).Article 

Google Scholar 
Mordecai, E. A. et al. Thermal biology of mosquito-borne disease. Ecol. Lett. 22, 1690–1708 (2019).Article 

Google Scholar 
Gage, K. L., Burkot, T. R., Eisen, R. J. & Hayes, E. B. Climate and vectorborne diseases. Am. J. Prev. Med. 35, 436–450 (2008).Article 

Google Scholar 
Doenças e Agravos de Notificação – 2007 em Diante (SINAN) (DATASUS, Ministério da Saúde do Brasil, 2021); https://datasus.saude.gov.br/acesso-a-informacao/doencas-e-agravos-de-notificacao-de-2007-em-diante-sinan/SIVEP – MALÁRIA Notificação de Casos (Ministério da Saúde do Brasil, 2021); http://200.214.130.44/sivep_malaria/R Core Team. R: A language and environment for statistical computing (R Foundation for Statistical Computing, 2020); https://www.R-project.org/Sorichetta, A. et al. High-resolution gridded population datasets for Latin America and the Caribbean in 2010, 2015, and 2020. Sci. Data 2, 150045 (2015).Article 

Google Scholar 
Harris, I., Osborn, T. J., Jones, P. & Lister, D. Version 4 of the CRU TS monthly high-resolution gridded multivariate climate dataset. Sci. Data 7, 109 (2020).Article 

Google Scholar 
Souza at. al. Reconstructing three decades of land use and land cover changes in Brazilian biomes with Landsat archive and Earth Engine. Remote Sens. 12, https://doi.org/10.3390/rs12172735 (2020).Fountain-Jones, N. M. et al. How to make more from exposure data? An integrated machine learning pipeline to predict pathogen exposure. J. Anim. Ecol. 88, 1447–1461 (2019).Article 

Google Scholar 
Breiman, L. Random forests. Mach. Learn. 45, 5–32 (2001).Article 

Google Scholar 
Genuer, R., Poggi, J.-M. & Tuleau-Malot, C. Variable selection using random forests. Pattern Recogn. Lett. 31, 2225–2236 (2010).Article 

Google Scholar 
Wei, T. et al. Package ‘corrplot’. Statistician 56, e24 (2017).
Google Scholar 
Ratner, B. The correlation coefficient: its values range between +1/−1, or do they? J. Target. Meas. Anal. Mark. 17, 139–142 (2009).Article 

Google Scholar 
Ishwaran, H. & Kogalur, U. B. Fast unified random forests for survival, regression, and classification (RF-SRC) (2019).O’Brien, R. & Ishwaran, H. A random forests quantile classifier for class imbalanced data. Pattern Recognit. 90, 232–249 (2019).Article 

Google Scholar 
Silge, J. & Mahoney, M. spatialsample: spatial resampling infrastructure. R version 0.2.1 (2023).Bhatt, S. et al. The global distribution and burden of dengue. Nature 496, 504–507 (2013).Article 
CAS 

Google Scholar 
Weaver, S. C. & Forrester, N. L. Chikungunya: evolutionary history and recent epidemic spread. Antivir. Res. 120, 32–39 (2015).Article 
CAS 

Google Scholar 
Puntasecca, C. J., King, C. H. & LaBeaud, A. D. Measuring the global burden of chikungunya and Zika viruses: a systematic review. PLoS Negl. Trop. Dis. 15, e0009055 (2021).Article 

Google Scholar 
Baeza, A., Santos-Vega, M., Dobson, A. P. & Pascual, M. The rise and fall of malaria under land-use change in frontier regions. Nat. Ecol. Evol. 1, 108 (2017).Article 

Google Scholar 
de Araújo Pedrosa, F. & de Alencar Ximenes, R. A. Sociodemographic and environmental risk factors for American cutaneous leishmaniasis (ACL) in the State of Alagoas, Brazil. Am. J. Trop. Med. Hyg. 81, 195–201 (2009).Article 

Google Scholar 
Gonçalves, N. V. et al. Cutaneous leishmaniasis: spatial distribution and environmental risk factors in the state of Pará, Brazilian Eastern Amazon. J. Infect. Dev. Countr. 13, 939–944 (2019).Article 

Google Scholar 
Leishmaniasis (Pan American Health Organization, 2022); https://www.paho.org/en/topics/leishmaniasisHarhay, M. O., Olliaro, P. L., Costa, D. L. & Costa, C. H. N. Urban parasitology: visceral leishmaniasis in Brazil. Trends Parasitol. 27, 403–409 (2011).Article 

Google Scholar  More