Ecology

Meat, Milk and More: Policy Innovations to Shepherd Inclusive and Sustainable Livestock Systems in Africa (Malabo Montpellier Panel, 2020).Value of Agricultural Production (FAO, accessed August 25, 2022); https://www.fao.org/faostat/en/#data/QVJayne, T. & Sanchez, P. A. Agricultural productivity must improve in sub-Saharan Africa. Science 372, 1045–1047 (2021).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Dangal, S. R. S. et al. Methane emission from global livestock sector during 1890–2014: magnitude, trends and spatiotemporal patterns. Glob. Change Biol. 23, 4147–4161 (2017).Article 
ADS 

Google Scholar 
Mottet, A. et al. Climate change mitigation and productivity gains in livestock supply chains: insights from regional case studies. Reg. Env. Change 17, 129–141 (2016).Article 

Google Scholar 
Valin, H. et al. Agricultural productivity and greenhouse gas emissions: trade-offs or synergies between mitigation and food security? Environ. Res. Lett. 8, 035019 (2013).Article 
ADS 
CAS 

Google Scholar 
González-Quintero, R. et al. Yield gap analysis to identify attainable milk and meat productivities and the potential for greenhouse gas emissions mitigation in cattle systems of Colombia. Agric. Syst. 195, 103303 (2022).Article 

Google Scholar 
Crops and Livestock Products (FAO, accessed August 17,2022); https://www.fao.org/faostat/en/#data/QCLLedo, J. et al. Persistent challenges in safety and hygiene control practices in emerging dairy chains: the case of Tanzania. Food Control 105, 164–173 (2019).Article 

Google Scholar 
Häsler, B. et al. Integrated food safety and nutrition assessments in the dairy cattle value chain in Tanzania. Glob. Food Sec. 18, 102–113 (2018).Article 

Google Scholar 
Supply Utilization Accounts (FAO, accessed August 26, 2022); https://www.fao.org/faostat/en/#data/SCLMichael, S. et al. Tanzania Livestock Master Plan (International Livestock Research Institute, 2018).Tanzania Livestock Sector Analysis (2016/2017–2030/2031) (United Republic of Tanzania Ministry of Livestock and Fisheries, 2017); https://www.mifugouvuvi.go.tz/uploads/projects/1553602287-LIVESTOCK%20SECTOR%20ANALYSIS.pdfNicholson, C. et al. Assessment of Investment Priorities for Tanzania’s Dairy Sector: Report on Activities and Accomplishments (International Livestock Research Institute, 2021).Chagunda, M. G. C., Romer, D. A. M. & Roberts, D. J. Effect of genotype and feeding regime on enteric methane, non-milk nitrogen and performance of dairy cows during the winter feeding period. Livest. Sci. 122, 323–332 (2009).Article 

Google Scholar 
Notenbaert, A. et al. Towards environmentally sound intensification pathways for dairy development in the Tanga region of Tanzania. Reg. Environ. Change 20, 138 (2020).Yesuf, G. A. et al. Embedding stakeholders’ priorities into the low-emission development of the East African dairy sector. Env. Res. Lett. 16, 064032 (2021).Article 
CAS 

Google Scholar 
GLS (Greening Livestock Survey) (International Livestock Research Institute, 2019); https://data.ilri.org/portal/dataset/greeninglivestockIntended Nationally Determined Contributions (United Republic of Tanzania, 2021); https://unfccc.int/sites/default/files/NDC/2022-06/TANZANIA_NDC_SUBMISSION_30%20JULY%202021.pdfNdung’u, P. W. et al. Farm-level emission intensities of smallholder cattle (Bos indicus; B. indicus–B. taurus crosses) production systems in highlands and semi-arid regions. Animal 16, 100445 (2022).Article 
PubMed 

Google Scholar 
Goopy, J. P. et al. Severe below-maintenance feed intake increases methane yield from enteric fermentation in cattle. Br. J. Nutr. 123, 1239–1246 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Goopy, J. P. et al. A new approach for improving emission factors for enteric methane emissions of cattle in smallholder systems of East Africa—results for Nyando, Western Kenya. Agric. Syst. 161, 72–80 (2018).Article 

Google Scholar 
Supporting Low Emissions Development in the Tanzanian Dairy Cattle Sector—Reducing Enteric Methane for Food Security and Livelihoods (FAO, 2019).Gerssen-Gondelach, S. J. et al. Intensification pathways for beef and dairy cattle production systems: impacts on GHG emissions, land occupation and land use change. Agric. Ecosyst. Environ. 240, 135–147 (2017).Article 

Google Scholar 
Havlik, P. et al. Climate change mitigation through livestock system transitions. Proc. Natl Acad. Sci. USA 111, 3709–3714 (2014).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Herrero, M. et al. Greenhouse gas mitigation potentials in the livestock sector. Nat. Clim. Change 6, 452–461 (2016).Article 
ADS 

Google Scholar 
Dizyee, K., Baker, D. & Omore, A. Upgrading the smallholder dairy value chain: a system dynamics ex-ante impact assessment in Tanzania’s Kilosa district. J. Dairy Res. 86, 440–449 (2019).Article 
CAS 
PubMed 

Google Scholar 
Simões, A. R. P., Nicholson, C. F., Novakovicc, A. M. & Protil, R. M. Dynamic impacts of farm-level technology adoption on the Brazilian dairy supply chain. Int. Food Agribus. Manag. Rev. 23, 71–84 (2020).Article 

Google Scholar 
Rahimi, J. et al. Heat stress will detrimentally impact future livestock production in East Africa. Nat. Food. 2, 88–96 (2021).Article 

Google Scholar 
Mbululo, Y. & Nyihirani, F. Climate characteristics over southern highlands Tanzania. Atmos. Clim. Sci. 2, 454–463 (2012).
Google Scholar 
Kihoro, E. M., Schoneveld, G. C. & Crane, T. A. Pathways toward inclusive low-emission dairy development in Tanzania: producer heterogeneity and implications for intervention design. Agric. Syst. 190, 103073 (2021).Mruttu, H. et al. Animal Genetics Strategy and Vision for Tanzania (Tanzania Ministry of Agriculture, Livestock and Fisheries and ILRI, 2016).Agricultural Sample Survey 2018/19 Report on Livestock and Livestock Characteristics (Private Peasant Holdings) (Central Statistical Agency, 2019).2019/20 National Sample Census of Agriculture Main Report (Tanzania National Bureau of Statistics, 2022).Robinson, T. P. et al. Global Livestock Production Systems (FAO, 2011).Herrero, M. et al. Biomass use, production, feed efficiencies and greenhouse gas emissions from global livestock systems. Proc. Natl Acad. Sci. USA 110, 20888–20893 (2013).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Baseline Study of the Tanzania Dairy Value Chain (United Republic of Tanzania Ministry of Agriculture, Livestock and Fisheries, 2016).Mbwambo, N., Nandonde, S., Ndomba, C. & Desta, S. Assessment of Animal Feed Resources in Tanzania (Tanzania Ministry of Agriculture, Livestock and Fisheries and ILRI, 2016).Hartung, C., Lerer, A., Anokwa, Y., Tseng, C., Brunette, W., & Borriello, G. Open data kit: tools to build information services for developing regions. Proc. 4th ACM/IEEE International Conference on Information and Communication Technologies and Development (Association for Computing Machinery, 2010).R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2022).https://www.r-project.orgRufino, M. C. et al. Lifetime productivity of dairy cows in smallholder farming systems of the central highlands of Kenya. Animal 3, 1044–1056 (2009).Article 
CAS 
PubMed 

Google Scholar 
Hawkins, J. et al. Feeding efficiency gains can increase the greenhouse gas mitigation potential of the Tanzanian dairy sector. Sci. Rep. 11, 4190 (2021).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Python Software Foundation (Python Software Foundation, 2019); https://www.python.org/psf/Kashoma, I. P. B. et al. Predicting body weight of Tanzania shorthorn zebu cattle using heart girth measurements. Livest. Res. Rural. Dev. 23, Table 1 (2011).Galukande, E. B., Mahadevan, P. & Black, J. G. Milk production in East African zebu cattle. Anim. Sci. 4, 329–336 (1962).Article 

Google Scholar 
Gillah, K. A., Kifaro, G. C. & Madsen, J. Effects of pre partum supplementation on milk yield, reproduction and milk quality of crossbred dairy cows raised in a peri urban farm of Morogoro town Tanzania. Livest. Res. Rural. Dev. 26 (2014).Njau, F. B. C., Lwelamira, J. & Hyandye, C. Ruminant livestock production and quality of pastures in the communal grazing land of semi-arid central Tanzania. Livest. Res. Rural. Dev. 8, Table 4 (2013).Mwambene, P. L. et al. Selecting indigenous cattle populations for improving dairy production in the Southern Highlands and Eastern Tanzania. Livest. Res. Rural. Dev. 26 (2014).Rege, J. E. O. et al. Cattle of Kenya: Uses, Performance, Farmer Preferences, Measures of Genetic Diversity and Options for Improved Use (International Livestock Research Institute, 2001).Beffa, L. M. Genotype × Environment Interaction in Afrikaner Cattle. PhD thesis, Univ. of the Free State (2005).Meaker, H. J., Coetsee, T. P. N. & Lishman, A. W. The effects of age at 1st calving on the productive and reproductive-performance of beef-cows. S. Afr. J. Anim. Sci. 10, 105–113 (1980).
Google Scholar 
Chenyambuga, S. W. & Mseleko, K. F. Reproductive and lactation performances of Ayrshire and Boran crossbred cattle kept in smallholder farms in Mufindi district, Tanzania. Livest. Res. Rural. Dev. 21, 100 (2009).
Google Scholar 
Ojango, J. M. K. et al. Dairy production systems and the adoption of genetic and breeding technologies in Tanzania, Kenya, India and Nicaragua. Anim. Genet. Resour. 59, 81–95 (2016).Article 

Google Scholar 
Feedipedia—Animal Feed Resources Information System (FAO, accessed 2021); https://www.feedipedia.org/Lukuyu, B. et al. (eds) Feeding Dairy Cattle in East Africa (East Africa Dairy Development Project, 2012).Rubanza, C. D. K. et al. Biomass production and nutritive potential of conserved forages in silvopastoral traditional fodder banks (Ngitiri) of Meatu District of Tanzania. Asian-Aust. J. Anim. Sci. 19, 978–983 (2006).Article 

Google Scholar 
Food Balances (2010-) (FAO, accessed September 29, 2021); http://www.fao.org/faostat/en/#data/FBSCrop Data for the United Republic of Tanzania (FAO, accessed September 22, 2021); http://www.fao.org/faost at/en/#data/QCGilbert, 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 
2014/15 Annual Agricultural Sample Survey Report (The United Republic of Tanzania, 2016).Basic Data for Livestock and Fisheries (The United Republic of Tanzania Ministry of Livestock and Fisheries, 2013).IPCC Guidelines for National Greenhouse Gas Inventories Vol. 4 Agriculture, Forestry and Other Land Use (IPCC, 2006).2019 Refinement to the IPCC Climate Change 2014: Synthesis Report (eds Core Writing Team, Pachauri, R. K. & Meyer L. A.) (IPCC, 2019).Fertilizers by Nutrient (FAO, accessed July 6, 2022); https://www.fao.org/faostat/en/#data/RFNHutton, M. O. et al. Toward a nitrogen footprint calculator for Tanzania. Env. Res. Lett. 12, 034016 (2017).Article 

Google Scholar 
Tanzania Fertilizer Assessment (International Fertilizer Development Center, 2012); http://tanzania.countrystat.org/fileadmin/user_upload/countrystat_fenix/congo/docs/Tanzania%20Fertilizer%20Assessment%202012.pdfA Common Carbon Footprint Approach for the Dairy Sector: The IDF Guide to Standard Life Cycle Methodology (International Dairy Federation, 2015); https://www.fil-idf.org/wp-content/uploads/2016/09/Bulletin479-2015_A-common-carbon-footprint-approach-for-the-dairy-sector.CAT.pdfBruzzone, L., Bovolo, F. & Arino, O. European Space Agency land cover climate change initiative. ESA LC CCI data: high resolution land cover data via Centre for Environmental Data Analysis; https://climate.esa.int/en/projects/high-resolution-land-cover/ (2021)Characteristics of Markets for Animal Feeds Raw Materials in the East African Community: Focus on Maize Bran and Sunflower Seed Cake (Kilimo Trust, 2017).Ngunga, D. & Mwendia, S. Forage Seed System in Tanzania: A Review Report (Alliance of Biodiversity and CIAT, 2020).Nkombe, B.M. Investigation of the Potential for Forage Species to Enhance the Sustainability of Degraded Rangeland and Cropland Soils. MSc thesis, Ohio State Univ. (2016).Producer Prices (FAO, accessed 2021); http://www.fao.org/faostat/en/#data/PP More

.readcube-buybox { display: none !important;}
Protecting an overfished lobster species helps the crustaceans to grow big, according to an analysis of European lobsters in marine sanctuaries1.

Access options

/* style specs start */
style{display:none!important}.LiveAreaSection-193358632 *{align-content:stretch;align-items:stretch;align-self:auto;animation-delay:0s;animation-direction:normal;animation-duration:0s;animation-fill-mode:none;animation-iteration-count:1;animation-name:none;animation-play-state:running;animation-timing-function:ease;azimuth:center;backface-visibility:visible;background-attachment:scroll;background-blend-mode:normal;background-clip:borderBox;background-color:transparent;background-image:none;background-origin:paddingBox;background-position:0 0;background-repeat:repeat;background-size:auto auto;block-size:auto;border-block-end-color:currentcolor;border-block-end-style:none;border-block-end-width:medium;border-block-start-color:currentcolor;border-block-start-style:none;border-block-start-width:medium;border-bottom-color:currentcolor;border-bottom-left-radius:0;border-bottom-right-radius:0;border-bottom-style:none;border-bottom-width:medium;border-collapse:separate;border-image-outset:0s;border-image-repeat:stretch;border-image-slice:100%;border-image-source:none;border-image-width:1;border-inline-end-color:currentcolor;border-inline-end-style:none;border-inline-end-width:medium;border-inline-start-color:currentcolor;border-inline-start-style:none;border-inline-start-width:medium;border-left-color:currentcolor;border-left-style:none;border-left-width:medium;border-right-color:currentcolor;border-right-style:none;border-right-width:medium;border-spacing:0;border-top-color:currentcolor;border-top-left-radius:0;border-top-right-radius:0;border-top-style:none;border-top-width:medium;bottom:auto;box-decoration-break:slice;box-shadow:none;box-sizing:border-box;break-after:auto;break-before:auto;break-inside:auto;caption-side:top;caret-color:auto;clear:none;clip:auto;clip-path:none;color:initial;column-count:auto;column-fill:balance;column-gap:normal;column-rule-color:currentcolor;column-rule-style:none;column-rule-width:medium;column-span:none;column-width:auto;content:normal;counter-increment:none;counter-reset:none;cursor:auto;display:inline;empty-cells:show;filter:none;flex-basis:auto;flex-direction:row;flex-grow:0;flex-shrink:1;flex-wrap:nowrap;float:none;font-family:initial;font-feature-settings:normal;font-kerning:auto;font-language-override:normal;font-size:medium;font-size-adjust:none;font-stretch:normal;font-style:normal;font-synthesis:weight style;font-variant:normal;font-variant-alternates:normal;font-variant-caps:normal;font-variant-east-asian:normal;font-variant-ligatures:normal;font-variant-numeric:normal;font-variant-position:normal;font-weight:400;grid-auto-columns:auto;grid-auto-flow:row;grid-auto-rows:auto;grid-column-end:auto;grid-column-gap:0;grid-column-start:auto;grid-row-end:auto;grid-row-gap:0;grid-row-start:auto;grid-template-areas:none;grid-template-columns:none;grid-template-rows:none;height:auto;hyphens:manual;image-orientation:0deg;image-rendering:auto;image-resolution:1dppx;ime-mode:auto;inline-size:auto;isolation:auto;justify-content:flexStart;left:auto;letter-spacing:normal;line-break:auto;line-height:normal;list-style-image:none;list-style-position:outside;list-style-type:disc;margin-block-end:0;margin-block-start:0;margin-bottom:0;margin-inline-end:0;margin-inline-start:0;margin-left:0;margin-right:0;margin-top:0;mask-clip:borderBox;mask-composite:add;mask-image:none;mask-mode:matchSource;mask-origin:borderBox;mask-position:0 0;mask-repeat:repeat;mask-size:auto;mask-type:luminance;max-height:none;max-width:none;min-block-size:0;min-height:0;min-inline-size:0;min-width:0;mix-blend-mode:normal;object-fit:fill;object-position:50% 50%;offset-block-end:auto;offset-block-start:auto;offset-inline-end:auto;offset-inline-start:auto;opacity:1;order:0;orphans:2;outline-color:initial;outline-offset:0;outline-style:none;outline-width:medium;overflow:visible;overflow-wrap:normal;overflow-x:visible;overflow-y:visible;padding-block-end:0;padding-block-start:0;padding-bottom:0;padding-inline-end:0;padding-inline-start:0;padding-left:0;padding-right:0;padding-top:0;page-break-after:auto;page-break-before:auto;page-break-inside:auto;perspective:none;perspective-origin:50% 50%;pointer-events:auto;position:static;quotes:initial;resize:none;right:auto;ruby-align:spaceAround;ruby-merge:separate;ruby-position:over;scroll-behavior:auto;scroll-snap-coordinate:none;scroll-snap-destination:0 0;scroll-snap-points-x:none;scroll-snap-points-y:none;scroll-snap-type:none;shape-image-threshold:0;shape-margin:0;shape-outside:none;tab-size:8;table-layout:auto;text-align:initial;text-align-last:auto;text-combine-upright:none;text-decoration-color:currentcolor;text-decoration-line:none;text-decoration-style:solid;text-emphasis-color:currentcolor;text-emphasis-position:over right;text-emphasis-style:none;text-indent:0;text-justify:auto;text-orientation:mixed;text-overflow:clip;text-rendering:auto;text-shadow:none;text-transform:none;text-underline-position:auto;top:auto;touch-action:auto;transform:none;transform-box:borderBox;transform-origin:50% 50%0;transform-style:flat;transition-delay:0s;transition-duration:0s;transition-property:all;transition-timing-function:ease;vertical-align:baseline;visibility:visible;white-space:normal;widows:2;width:auto;will-change:auto;word-break:normal;word-spacing:normal;word-wrap:normal;writing-mode:horizontalTb;z-index:auto;-webkit-appearance:none;-moz-appearance:none;-ms-appearance:none;appearance:none;margin:0}.LiveAreaSection-193358632{width:100%}.LiveAreaSection-193358632 .login-option-buybox{display:block;width:100%;font-size:17px;line-height:30px;color:#222;padding-top:30px;font-family:Harding,Palatino,serif}.LiveAreaSection-193358632 .additional-access-options{display:block;font-weight:700;font-size:17px;line-height:30px;color:#222;font-family:Harding,Palatino,serif}.LiveAreaSection-193358632 .additional-login >li:not(:first-child)::before{transform:translateY(-50%);content:””;height:1rem;position:absolute;top:50%;left:0;border-left:2px solid #999}.LiveAreaSection-193358632 .additional-login >li:not(:first-child){padding-left:10px}.LiveAreaSection-193358632 .additional-login >li{display:inline-block;position:relative;vertical-align:middle;padding-right:10px}.BuyBoxSection-683559780{display:flex;flex-wrap:wrap;flex:1;flex-direction:row-reverse;margin:-30px -15px 0}.BuyBoxSection-683559780 .box-inner{width:100%;height:100%}.BuyBoxSection-683559780 .readcube-buybox{background-color:#f3f3f3;flex-shrink:1;flex-grow:1;flex-basis:255px;background-clip:content-box;padding:0 15px;margin-top:30px}.BuyBoxSection-683559780 .subscribe-buybox{background-color:#f3f3f3;flex-shrink:1;flex-grow:4;flex-basis:300px;background-clip:content-box;padding:0 15px;margin-top:30px}.BuyBoxSection-683559780 .subscribe-buybox-nature-plus{background-color:#f3f3f3;flex-shrink:1;flex-grow:4;flex-basis:100%;background-clip:content-box;padding:0 15px;margin-top:30px}.BuyBoxSection-683559780 .title-readcube{display:block;margin:0;margin-right:20%;margin-left:20%;font-size:24px;line-height:32px;color:#222;padding-top:30px;text-align:center;font-family:Harding,Palatino,serif}.BuyBoxSection-683559780 .title-buybox{display:block;margin:0;margin-right:29%;margin-left:29%;font-size:24px;line-height:32px;color:#222;padding-top:30px;text-align:center;font-family:Harding,Palatino,serif}.BuyBoxSection-683559780 .title-asia-buybox{display:block;margin:0;margin-right:5%;margin-left:5%;font-size:24px;line-height:32px;color:#222;padding-top:30px;text-align:center;font-family:Harding,Palatino,serif}.BuyBoxSection-683559780 .asia-link{color:#069;cursor:pointer;text-decoration:none;font-size:1.05em;font-family:-apple-system,BlinkMacSystemFont,”Segoe UI”,Roboto,Oxygen-Sans,Ubuntu,Cantarell,”Helvetica Neue”,sans-serif;line-height:1.05em6}.BuyBoxSection-683559780 .access-readcube{display:block;margin:0;margin-right:10%;margin-left:10%;font-size:14px;color:#222;padding-top:10px;text-align:center;font-family:-apple-system,BlinkMacSystemFont,”Segoe UI”,Roboto,Oxygen-Sans,Ubuntu,Cantarell,”Helvetica Neue”,sans-serif;line-height:20px}.BuyBoxSection-683559780 .access-asia-buybox{display:block;margin:0;margin-right:5%;margin-left:5%;font-size:14px;color:#222;padding-top:10px;text-align:center;font-family:-apple-system,BlinkMacSystemFont,”Segoe UI”,Roboto,Oxygen-Sans,Ubuntu,Cantarell,”Helvetica Neue”,sans-serif;line-height:20px}.BuyBoxSection-683559780 .access-buybox{display:block;margin:0;margin-right:30%;margin-left:30%;font-size:14px;color:#222;opacity:.8px;padding-top:10px;text-align:center;font-family:-apple-system,BlinkMacSystemFont,”Segoe UI”,Roboto,Oxygen-Sans,Ubuntu,Cantarell,”Helvetica Neue”,sans-serif;line-height:20px}.BuyBoxSection-683559780 .usps-buybox{display:block;margin:0;margin-right:30%;margin-left:30%;font-size:14px;color:#222;opacity:.8px;text-align:center;font-family:-apple-system,BlinkMacSystemFont,”Segoe UI”,Roboto,Oxygen-Sans,Ubuntu,Cantarell,”Helvetica Neue”,sans-serif;line-height:20px}.BuyBoxSection-683559780 .price-buybox{display:block;font-size:30px;color:#222;font-family:-apple-system,BlinkMacSystemFont,”Segoe UI”,Roboto,Oxygen-Sans,Ubuntu,Cantarell,”Helvetica Neue”,sans-serif;padding-top:30px;text-align:center}.BuyBoxSection-683559780 .price-from{font-size:14px;padding-right:10px;color:#222;font-family:-apple-system,BlinkMacSystemFont,”Segoe UI”,Roboto,Oxygen-Sans,Ubuntu,Cantarell,”Helvetica Neue”,sans-serif;line-height:20px}.BuyBoxSection-683559780 .issue-buybox{display:block;font-size:13px;text-align:center;color:#222;font-family:-apple-system,BlinkMacSystemFont,”Segoe UI”,Roboto,Oxygen-Sans,Ubuntu,Cantarell,”Helvetica Neue”,sans-serif;line-height:19px}.BuyBoxSection-683559780 .no-price-buybox{display:block;font-size:13px;line-height:18px;text-align:center;padding-right:10%;padding-left:10%;padding-bottom:20px;padding-top:30px;color:#222;font-family:-apple-system,BlinkMacSystemFont,”Segoe UI”,Roboto,Oxygen-Sans,Ubuntu,Cantarell,”Helvetica Neue”,sans-serif}.BuyBoxSection-683559780 .vat-buybox{display:block;margin-top:5px;margin-right:20%;margin-left:20%;font-size:11px;color:#222;padding-top:10px;padding-bottom:15px;text-align:center;font-family:-apple-system,BlinkMacSystemFont,”Segoe UI”,Roboto,Oxygen-Sans,Ubuntu,Cantarell,”Helvetica Neue”,sans-serif;line-height:17px}.BuyBoxSection-683559780 .button-container{display:flex;padding-right:20px;padding-left:20px;justify-content:center}.BuyBoxSection-683559780 .button-container >*{flex:1px}.BuyBoxSection-683559780 .button-container >a:hover,.Button-505204839:hover,.Button-1078489254:hover,.Button-2808614501:hover{text-decoration:none}.BuyBoxSection-683559780 .readcube-button{background:#fff;margin-top:30px}.BuyBoxSection-683559780 .button-asia{background:#069;border:1px solid #069;border-radius:0;cursor:pointer;display:block;padding:9px;outline:0;text-align:center;text-decoration:none;min-width:80px;margin-top:75px}.BuyBoxSection-683559780 .button-label-asia,.ButtonLabel-3869432492,.ButtonLabel-3296148077,.ButtonLabel-1566022830{display:block;color:#fff;font-size:17px;line-height:20px;font-family:-apple-system,BlinkMacSystemFont,”Segoe UI”,Roboto,Oxygen-Sans,Ubuntu,Cantarell,”Helvetica Neue”,sans-serif;text-align:center;text-decoration:none;cursor:pointer}.Button-505204839,.Button-1078489254,.Button-2808614501{background:#069;border:1px solid #069;border-radius:0;cursor:pointer;display:block;padding:9px;outline:0;text-align:center;text-decoration:none;min-width:80px;max-width:320px;margin-top:10px}.Button-505204839 .readcube-label,.Button-1078489254 .readcube-label,.Button-2808614501 .readcube-label{color:#069}
/* style specs end */Subscribe to Nature+Get immediate online access to Nature and 55 other Nature journal$29.99monthlySubscribe to JournalGet full journal access for 1 year$199.00only $3.90 per issueAll prices are NET prices.VAT will be added later in the checkout.Tax calculation will be finalised during checkout.Buy articleGet time limited or full article access on ReadCube.$32.00All prices are NET prices.

Additional access options:

doi: https://doi.org/10.1038/d41586-022-03708-2

References

Subjects

Conservation biology More

Morrison, M. A., Francis, M. P., Hartill, B. W. & Parkinson, D. M. Diurnal and tidal variation in the abundance of the fish fauna of a temperate tidal mudflat. Estuar. Coast. Shelf Sci. 54, 793–807 (2002).Article 
ADS 

Google Scholar 
Ribeiro, J. et al. Seasonal, tidal and diurnal changes in fish assemblages in the Ria Formosa lagoon (Portugal). Estuar. Coast. Shelf Sci. 67, 461–474 (2006).Article 
ADS 

Google Scholar 
Takemura, A., Rahman, M. S. & Park, Y. J. External and internal controls of lunar-related reproductive rhythms in fishes. J. Fish Biol. 76, 7–26 (2010).Article 
CAS 
PubMed 

Google Scholar 
Mendes, S., Turrell, W., Lütkebohle, T. & Thompson, P. Influence of the tidal cycle and a tidal intrusion front on the spatio-temporal distribution of coastal bottlenose dolphins. Mar. Ecol. Prog. Ser. 239, 221–229 (2002).Article 
ADS 

Google Scholar 
Johnston, D. W., Thorne, L. H. & Read, A. J. Fin whales Balaenoptera physalus and minke whales Balaenoptera acutorostrata exploit a tidally driven island wake ecosystem in the Bay of Fundy. Mar. Ecol. Prog. Ser. 305, 287–295 (2005).Article 
ADS 

Google Scholar 
Ichikawa, K. et al. Dugong (Dugong dugon) vocalization patterns recorded by automatic underwater sound monitoring systems. J. Acoust. Soc. Am. 119, 3726–3733 (2006).Article 
ADS 
PubMed 

Google Scholar 
Akamatsu, T. et al. Seasonal and diurnal presence of finless porpoises at a corridor to the ocean from their habitat. Mar. Biol. 157, 1879–1887 (2010).Article 

Google Scholar 
Li, S. et al. Seasonal, lunar and tidal influences on habitat use of indo-pacific humpback dolphins in Beibu gulf, China. Zool. Stud. https://doi.org/10.6620/ZS.2018.57-01 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Zamon, J. E. Seal predation on salmon and forage fish schools as a function of tidal currents in the San Juan Islands, Washington, USA. Fish. Oceanogr. 10, 353–366 (2001).Article 

Google Scholar 
Van Parijs, S. M., Hastie, G. D. & Thompson, P. M. Geographical variation in temporal and spatial vocalization patterns of male harbour seals in the mating season. Anim. Behav. 58, 1231–1239 (1999).Article 
PubMed 

Google Scholar 
Bortolotto, G. A., Danilewicz, D., Hammond, P. S., Thomas, L. & Zerbini, A. N. Whale distribution in a breeding area: Spatial models of habitat use and abundance of western South Atlantic humpback whales. Mar. Ecol. Prog. Ser. 585, 213–227 (2017).Article 
ADS 

Google Scholar 
Johnson, J. H. & Wolman, A. A. The humpback whale, Megaptera novaeangliae. Mar. Fish. Rev. 46, 30–37 (1984).
Google Scholar 
Kobayashi, N. et al. Spatial distribution and habitat use patterns of humpback whales in Okinawa, Japan. Mammal Study 41, 207–214 (2016).Article 

Google Scholar 
Mori, K., Sata, F., Yamaguchi, M., Suganuma, H. & Ueyanagi, S. Distribution, migration and local movements of humpback whale (Megaptera novaeangliae) in the adjacent waters of the Ogasawara (Bonin) Islands Japan. J. Fac. Mar. Sci. Technol. Tokai Univ. 45, 197–213 (1998).
Google Scholar 
Rasmussen, K., Calambokidis, J. & Steiger, G. H. Distribution and migratory destinations of humpback whales off the Pacific coast of Central America during the boreal winters of 1996–2003. Mar. Mammal Sci. 28, 1–13 (2012).Article 

Google Scholar 
Calambokidis, J. et al. SPLASH: structure of populations, levels of abuncance and status of humpback whales in the North Pacific. Final report for Contract AB133F-03-RP-00078, to U.S. Dept. of Comm. Western Administrative Center, Seattle, WA. https://cascadiaresearch.org/files/SPLASH-contract-Report-May08.pdf (2008).Hill, M. et al. Found: A missing breeding ground for endangered western North Pacific humpback whales in the Mariana Archipelago. Endanger. Species Res. 41, 91–103 (2020).Article 

Google Scholar 
Payne, R. S. & McVay, S. Songs of humpback whales. Science 173, 585–597 (1971).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Winn, H. E. & Winn, L. The song of the humpback whale Megaptera novaeangliae in the West Indies. Mar. Biol. 47, 97–114 (1978).Article 

Google Scholar 
Tyack, P. Interactions between singing Hawaiian humpback whales and conspecifics nearby. Behav. Ecol. Sociobiol. 8, 105–116 (1981).Article 

Google Scholar 
Herman, L. M. The multiple functions of male song within the humpback whale (Megaptera novaeangliae) mating system: Review, evaluation, and synthesis. Biol. Rev. 92, 1795–1818 (2017).Article 
PubMed 

Google Scholar 
Au, W. W. L., Mobley, J., Burgess, W. C., Lammers, M. O. & Nachtigall, P. E. Seasonal and diurnal trends of chorusing humpback whales wintering in waters off western Maui. Mar. Mammal Sci. 16, 530–544 (2000).Article 

Google Scholar 
Cerchio, S., Collins, T., Strindberg, S., Bennett, C. & Rosenbaum, H. Humpback whale singing activity off northern Angola: An indication of the migratory cycle, breeding habitat and impact of seismic surveys on singer number in Breeding. Int. Whal. Comm. P. SC/62/SH12 (2010).Kobayashi, N., Okabe, H., Higashi, N., Miyahara, H. & Uchida, S. Diel patterns in singing activity of humpback whales in a winter breeding area in Okinawan (Ryukyuan) waters. Mar. Mammal Sci. 37, 982–992 (2021).Article 

Google Scholar 
Munger, L. M., Lammers, M. O., Fisher-Pool, P. & Wong, K. Humpback whale (Megaptera novaeangliae) song occurrence at American Samoa in long-term passive acoustic recordings, 2008–2009. J. Acoust. Soc. Am. 132, 2265–2272 (2012).Article 
ADS 
PubMed 

Google Scholar 
Barlow, D. R., Fournet, M. & Sharpe, F. Incorporating tides into the acoustic ecology of humpback whales. Mar. Mammal Sci. 35, 234–251 (2019).Article 

Google Scholar 
Chenoweth, E., Gabriele, C. & Hill, D. Tidal influences on humpback whale habitat selection near headlands. Mar. Ecol. Prog. Ser. 423, 279–289 (2011).Article 
ADS 

Google Scholar 
Sousa-Lima, R. S., Clark, C. W. & Road, S. W. Modeling the effect of boat traffic on singing activity of humpback whales (Megaptera novaeangliae) in the abrolhos national marine park, Brazil. Can. Acoust 36, 174–181 (2008).
Google Scholar 
Cerchio, S., Strindberg, S., Collins, T., Bennett, C. & Rosenbaum, H. Seismic surveys negatively affect humpback whale singing activity off Northern Angola. PLoS ONE 9, e86464. https://doi.org/10.1371/journal.pone.0086464 (2014).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Darling, J. D. & Mori, K. Recent observations of humpback whales (Megaptera novaeangliae) in Japanese waters off Ogasawara and Okinawa. Can. J. Zool. 71, 325–333 (1993).Article 

Google Scholar 
Calambokidis, J. et al. Movements and population structure of humpback whales in the North Pacific. Mar. Mammal Sci. 17, 769–794 (2001).Article 

Google Scholar 
Wessel, P., Smith, W. H. F., Scharroo, R., Luis, J. & Wobbe, F. Generic mapping tools: Improved version released. Eos Trans. Am. Geophys. Union 94, 409–410 (2013).Article 
ADS 

Google Scholar 
Helweg, D. A. & Herman, L. M. Diurnal patterns of behaviour and group membership of humpback whales (Megaptera novaeangliae) wintering in Hawaiian waters. Ethology 98, 298–311 (1994).Article 

Google Scholar 
Darling, J. D. & Berube, M. Interactions of singing humpback whales with other males. Mar. Mammal Sci. 17, 570–584 (2001).Article 

Google Scholar 
Whitlow, W. L. et al. Acoustic properties of humpback whale songs. J. Acoust. Soc. Am. 120, 1103–1110 (2006).Article 

Google Scholar 
Japan Coast Guard. Sailing Directions for South and East Coasts of Honshu. (1981).Tsujii, K. et al. Change in singing behavior of humpback whales caused by shipping noise. PLoS ONE 13, e0204112. https://doi.org/10.1371/journal.pone.0204112 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Ryan, J. P. et al. Humpback whale song occurrence reflects ecosystem variability in feeding and migratory habitat of the northeast Pacific. PLoS ONE 14, e0222456. https://doi.org/10.1371/journal.pone.0222456 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
R Core Team. R: A Language and Environment for Statistical Computing. 4.0.0 version. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/ (2020).Wood, S.N. Generalized Additive Models: An Introduction with R 2nd edn, (Chapman and Hall/CRC, 2017). More

Kazarov, E. The Role of Zoos in Creating a Conservation Ethic in Visitors. SIT Digital Collections (2022). at https://digitalcollections.sit.edu/isp_collection/584.Hosey, G. How does the zoo environment affect the behaviour of captive primates?. Appl. Anim. Behav. Sci. 90, 107–129 (2005).
Google Scholar 
Morgan, K. & Tromborg, C. Sources of stress in captivity. Appl. Anim. Behav. Sci. 102, 262–302 (2007).
Google Scholar 
Sherwen, S. & Hemsworth, P. The visitor effect on zoo animals: Implications and opportunities for zoo animal welfare. Animals 9, 366 (2019).PubMed Central 

Google Scholar 
Chamove, A., Hosey, G. & Schaetzel, P. Visitors excite primates in zoos. Zoo Biol. 7, 359–369 (1988).
Google Scholar 
Tetley, C. L. & O’Hara, S. J. Ratings of animal personality as a tool for improving the breeding, management and welfare of zoo mammals. Anim. Welf. UFAW J. 21(4), 463 (2012).CAS 

Google Scholar 
Stoinski, T. S., Jaicks, H. F. & Drayton, L. A. Visitor effects on the behavior of captive western lowland gorillas: The importance of individual differences in examining welfare. Zoo Biol. 31(5), 586–599 (2012).PubMed 

Google Scholar 
Queiroz, M. B. & Young, R. J. The different physical and behavioural characteristics of zoo mammals that influence their response to visitors. Animals 8(8), 139 (2018).PubMed Central 

Google Scholar 
Fanson, K. V. & Wielebnowski, N. C. Effect of housing and husbandry practices on adrenocortical activity in captive Canada lynx (Lynx canadensis). Anim. Welf. 22, 159–165 (2013).CAS 

Google Scholar 
Pirovino, M. et al. Fecal glucocorticoid measurements and their relation to rearing, behavior, and environmental factors in the population of pileated gibbons (Hylobates pileatus) held in European zoos. Int. J. Primatol. 32(5), 1161–1178 (2011).
Google Scholar 
Williams, I., Hoppitt, W. & Grant, R. The effect of auditory enrichment, rearing method and social environment on the behavior of zoo-housed psittacines (Aves: Psittaciformes); implications for welfare. Appl. Anim. Behav. Sci. 186, 85–92 (2017).
Google Scholar 
Fernandez, E., Tamborski, M., Pickens, S. & Timberlake, W. Animal–visitor interactions in the modern zoo: Conflicts and interventions. Appl. Anim. Behav. Sci. 120, 1–8 (2009).
Google Scholar 
Hosey, G. & Skyner, L. Self-injurious behavior in zoo primates. Int. J. Primatol. 28, 1431–1437 (2007).
Google Scholar 
Mallapur, A., Sinha, A. & Waran, N. Influence of visitor presence on the behaviour of captive lion-tailed macaques (Macaca silenus) housed in Indian zoos. Appl. Anim. Behav. Sci. 94, 341–352 (2005).
Google Scholar 
Davey, G. Visitors’ Effects on the Welfare of Animals in the Zoo: A Review. J. Appl. Anim. Welf. Sci. 10, 169–183 (2007).CAS 
PubMed 

Google Scholar 
Jones, H., McGregor, P., Farmer, H. & Baker, K. The influence of visitor interaction on the behavior of captive crowned lemurs (Eulemur coronatus) and implications for welfare. Zoo Biol. 35, 222–227 (2016).CAS 
PubMed 

Google Scholar 
Cook, S. & Hosey, G. R. Interaction sequences between chimpanzees and human visitors at the zoo. Zoo Biol. 14(5), 431–440 (1995).
Google Scholar 
Baker, K. C. Benefits of positive human interaction for socially-housed chimpanzees. Anim. Welf. (South Mimms, Engl.nd) 13(2), 239 (2004).CAS 

Google Scholar 
Carder, G. & Semple, S. Visitor effects on anxiety in two captive groups of western lowland gorillas. Appl. Anim. Behav. Sci. 115, 211–220 (2008).
Google Scholar 
Wood, W. Interactions among environmental enrichment, viewing crowds, and zoo chimpanzees (Pantroglodytes). Zoo Biol. 17, 211–230 (1998).
Google Scholar 
Todd, P., Macdonald, C. & Coleman, D. Visitor-associated variation in captive Diana monkey (Cercopithecus diana diana) behaviour. Appl. Anim. Behav. Sci. 107, 162–165 (2007).
Google Scholar 
Davis, N., Schaffner, C. & Smith, T. Evidence that zoo visitors influence HPA activity in spider monkeys (Ateles geoffroyii rufiventris). Appl. Anim. Behav. Sci. 90, 131–141 (2005).
Google Scholar 
Sherwen, S. L. et al. Effects of visual contact with zoo visitors on black-capped capuchin welfare. Appl. Anim. Behav. Sci. 167, 65–73 (2015).
Google Scholar 
Choo, Y., Todd, P. & Li, D. Visitor effects on zoo orangutans in two novel, naturalistic enclosures. Appl. Anim. Behav. Sci. 133, 78–86 (2011).
Google Scholar 
Sherwen, S., Magrath, M., Butler, K., Phillips, C. & Hemsworth, P. A multi-enclosure study investigating the behavioural response of meerkats to zoo visitors. Appl. Anim. Behav. Sci. 156, 70–77 (2014).
Google Scholar 
Hosey, G. & Druck, P. The influence of zoo visitors on the behaviour of captive primates. Appl. Anim. Behav. Sci. 18, 19–29 (1987).
Google Scholar 
Mitchell, G. et al. More on the ‘influence’of zoo visitors on the behaviour of captive primates. Appl. Anim. Behav. Sci. 35(2), 189–198 (1992).
Google Scholar 
Sellinger, R. & Ha, J. The effects of visitor density and intensity on the behavior of two captive jaguars (Panthera onca). J. Appl. Anim. Welfare Sci. 8, 233–244 (2005).CAS 

Google Scholar 
Azevedo, C., Lima, M., Silva, V., Young, R. & Rodrigues, M. Visitor Influence on the Behavior of Captive Greater Rheas (Rhea americana, Rheidae Aves). J. Appl. Anim. Welfare Sci. 15, 113–125 (2012).
Google Scholar 
Das Gupta, M., Das, A., Sumy, M. C. & Islam, M. M. An explorative study on visitor’s behaviour and their effect on the behaviour of primates at Chittagong zoo. Bangladesh J. Vet. Anim. Sci. 5(2), 24–32 (2017).
Google Scholar 
Hemsworth, P. Human–animal interactions in livestock production. Appl. Anim. Behav. Sci. 81, 185–198 (2003).
Google Scholar 
Stoinski, T., Czekala, N., Lukas, K. & Maple, T. Urinary androgen and corticoid levels in captive, male Western lowland gorillas (Gorilla g. gorilla): Age- and social group-related differences. Am. J. Primatol. 56, 73–87 (2002).CAS 
PubMed 

Google Scholar 
Stoinski, T., Lukas, K., Kuhar, C. & Maple, T. Factors influencing the formation and maintenance of all-male gorilla groups in captivity. Zoo Biol. 23, 189–203 (2004).
Google Scholar 
Olsson, I. & Westlund, K. More than numbers matter: The effect of social factors on behaviour and welfare of laboratory rodents and non-human primates. Appl. Anim. Behav. Sci. 103, 229–254 (2007).
Google Scholar 
Martin, J. E. Early life experiences: Activity levels and abnormal behaviours in resocialised chimpanzees. Anim Welf. 11(4), 419–436 (2002).CAS 

Google Scholar 
Birkett, L. P. & Newton-Fisher, N. E. How abnormal is the behaviour of captive, zoo-living chimpanzees?. PLoS ONE 6(6), e20101 (2011).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Ballen, C., Shine, R. & Olsson, M. Effects of early social isolation on the behaviour and performance of juvenile lizards Chamaeleo calyptratus. Anim. Behav. 88, 1–6 (2014).
Google Scholar 
Coe, C., Mendoza, S., Smotherman, W. & Levine, S. Mother-infant attachment in the squirrel monkey: Adrenal response to separation. Behav. Biol. 22, 256–263 (1978).CAS 
PubMed 

Google Scholar 
Mendoza, S., Smotherman, W., Miner, M., Kaplan, J. & Levine, S. Pituitary-adrenal response to separation in mother and infant squirrel monkeys. Dev. Psychobiol. 11, 169–175 (1978).CAS 
PubMed 

Google Scholar 
Gilbert, M. & Baker, K. Social buffering in adult male rhesus macaques (Macaca mulatta): Effects of stressful events in single vs. pair housing. J. Med. Primatol. 40, 71–78 (2010).PubMed 
PubMed Central 

Google Scholar 
Schapiro, S. Effects of social manipulations and environmental enrichment on behavior and cell-mediated immune responses in rhesus macaques. Pharmacol. Biochem. Behav. 73, 271–278 (2002).CAS 
PubMed 

Google Scholar 
Chen, W. et al. Effects of social isolation and re-socialization on cognition and ADAR1 (p110) expression in mice. PeerJ 4, e2306 (2016).PubMed 
PubMed Central 

Google Scholar 
Glatston, A., Geilvoet-Soeteman, E., Hora-Pecek, E. & Van Hooff, J. The influence of the zoo environment on social behavior of groups of cotton-topped tamarins Saguinus oedipus oedipus. Zoo Biol. 3, 241–253 (1984).
Google Scholar 
Mitchell, G. et al. Effects of visitors and cage changes on the behaviors of mangabeys. Zoo Biol. 10, 417–423 (1991).
Google Scholar 
Geissmann, T. & Orgeldinger, M. The relationship between duet songs and pair bonds in siamangs Hylobates syndactylus. Anim. Behav. 60, 805–809 (2000).CAS 
PubMed 

Google Scholar 
Palombit, R. Pair bonds in monogamous apes: A comparison of the siamang hylobates syndactylus and the white-handed gibbon hylobates lar. Behaviour 133, 321–356 (1996).
Google Scholar 
Rutberg, A. The evolution of monogamy in primates. J. Theor. Biol. 104, 93–112 (1983).ADS 
CAS 
PubMed 

Google Scholar 
Giorgi, A., Montebovi, G., Vitale, A. & Alleva, E. A behavioural case study of early social isolation of a subadult white-handed gibbon (Hylobates lar). Folia Primatol. 89, 287–294 (2018).
Google Scholar 
Skynner, L. A., Amory, J. R. & Hosey, G. The effect of visitors on the self-injurious behaviour of a male pileated gibbon (Hylobates pileatus). Zool. Garten 74(1), 38–41 (2004).
Google Scholar 
Smith, K. & Kuhar, C. Siamangs (Hylobates syndactylus) and white-cheeked gibbons (Hylobates leucogenys) show few behavioral differences related to zoo attendance. J. Appl. Anim. Welfare Sci. 13, 154–163 (2010).CAS 

Google Scholar 
Lukas, K. E. et al. Longitudinal study of delayed reproductive success in a pair of white-cheeked gibbons (Hylobates leucogenys). Zoo Biol. 21, 413–434 (2002).
Google Scholar 
Cooke, C. & Schillaci, M. Behavioral responses to the zoo environment by white handed gibbons. Appl. Anim. Behav. Sci. 106, 125–133 (2007).
Google Scholar 
Mootnick, A. & Baker, E. Masturbation in captiveHylobates (gibbons). Zoo Biol. 13, 345–353 (1994).
Google Scholar 
Geissmann, T. Reassessment of age of sexual maturity in gibbons (hylobates spp.). American Journal of Primatology 23, 11–22 (1991).Altmann, J. Observational study of behavior: Sampling methods. Behaviour 49(3–4), 227–266 (1974).CAS 
PubMed 

Google Scholar 
Pomerantz, O. & Terkel, J. Effects of positive reinforcement training techniques on the psychological welfare of zoo-housed chimpanzees (Pan troglodytes). Am. J. Primatol. 71, 687–695 (2009).PubMed 

Google Scholar 
Orgeldinger, M. Protective and territorial behavior in captive siamangs (Hylobates syndactylus). Zoo Biol. 16, 309–325 (1997).
Google Scholar 
Fox, J. et al. Package ‘car’. Vienna: R Foundation for Statistical Computing, 16 https://cran.uni-muenster.de/web/packages/car/car.pdf (2012).Magnusson, A., Skaug, H., Nielsen, A., Berg, C., Kristensen, K., Maechler, M., van Bentham, K., Bolker, B., Brooks, M. & Brooks, M. M. Package ‘glmmtmb’. R Package Version 0.2. 0 (2017).Hartig, F., & Hartig, M. F. Package ‘DHARMa’. Vienna, Austria: R Development Core Team (2017).Troisi, A. Displacement activities as a behavioral measure of stress in nonhuman primates and human subjects. Stress 5, 47–54 (2002).PubMed 

Google Scholar 
Baker, K. & Aureli, F. Behavioural indicators of anxiety: An empirical test in chimpanzees. Behaviour 134, 1031–1050 (1997).
Google Scholar 
Vick, S. J. & Paukner, A. Variation and context of yawns in captive chimpanzees (Pan troglodytes). Am. J. Primatol. Off. J. Am. Soc. Primatol. 72(3), 262–269 (2010).
Google Scholar 
Norscia, I. & Palagi, E. When play is a family business: Adult play, hierarchy, and possible stress reduction in common marmosets. Primates 52, 101–104 (2010).PubMed 

Google Scholar 
Held, S. & Špinka, M. Animal play and animal welfare. Anim. Behav. 81, 891–899 (2011).
Google Scholar 
Davey, G. Visitor behavior in zoos: A review. Anthrozoös 19, 143–157 (2006).
Google Scholar 
Nimon, A. & Dalziel, F. Cross-species interaction and communication: a study method applied to captive siamang (Hylobates syndactylus) and long-billed corella (Cacatua tenuirostris) contacts with humans. Appl. Anim. Behav. Sci. 33, 261–272 (1992).
Google Scholar 
Suomi, S. Early determinants of behaviour: Evidence from primate studies. Br. Med. Bull. 53, 170–184 (1997).CAS 
PubMed 

Google Scholar 
Anderson, J. & Chamove, A. Self-aggression and social aggression in laboratory-reared macaques. J. Abnorm. Psychol. 89, 539–550 (1980).CAS 
PubMed 

Google Scholar 
Mallapur, A. & Choudhury, B. Behavioral abnormalities in captive nonhuman primates. J. Appl. Anim. Welfare Sci. 6, 275–284 (2003).CAS 

Google Scholar 
Barlow, C., Caldwell, C. & Lee, P. Individual differences and response to visitors in zoo-housed diana monkeys (Cercopithecus diana diana). Cabdirect.org (2022). at https://www.cabdirect.org/cabdirect/abstract/20123180753.Gartner, M. & Weiss, A. Studying primate personality in zoos: Implications for the management, welfare and conservation of great apes. International Zoo Yearbook 52, 79–91 (2018).
Google Scholar 
Mitchell, G., Raymond, E., Ruppenthal, G. & Harlow, H. Long-term effects of total social isolation upon behavior of rhesus monkeys. Psychol. Rep. 18, 567–580 (1966).
Google Scholar 
Martín, O., Vinyoles, D., García-Galea, E. & Maté, C. Improving the welfare of a zoo-housed male drill (Mandrillus leucophaeus poensis) aggressive toward visitors. J. Appl. Anim. Welfare Sci. 19, 323–334 (2016).
Google Scholar 
Ross, S., Melber, L., Gillespie, K. & Lukas, K. The impact of a modern, naturalistic exhibit design on visitor behavior: A cross-facility comparison. Visitor Stud. 15, 3–15 (2012).
Google Scholar 
Quadros, S., Goulart, V., Passos, L., Vecci, M. & Young, R. Zoo visitor effect on mammal behaviour: Does noise matter?. Appl. Anim. Behav. Sci. 156, 78–84 (2014).
Google Scholar 
Bonnie, K., Ang, M. & Ross, S. Effects of crowd size on exhibit use by and behavior of chimpanzees (Pan troglodytes) and Western lowland gorillas (Gorilla gorilla) at a zoo. Appl. Anim. Behav. Sci. 178, 102–110 (2016).
Google Scholar  More

Podos, J. Correlated evolution of morphology and vocal signal structure in Darwin’s finches. Nature 409, 185–188 (2001).ADS 
CAS 
PubMed 

Google Scholar 
Bradbury, J. W. & Vehrencamp, S. Principles of Animal Communication (Sinauer Associated, 1998).
Google Scholar 
Podos, J. & Warren, P. S. The evolution of geographic variation in birdsong. Adv. Study Behav. 37, 403–458 (2007).
Google Scholar 
Charlton, B. D., Owen, M. A. & Swaisgood, R. R. Coevolution of vocal signal characteristics and hearing sensitivity in forest mammals. Nat. Commun. 10, 1–7 (2019).CAS 

Google Scholar 
Soltis, J. Vocal communication in African elephants (Loxodonta africana). Zoo Biol. 29, 192–209 (2010).PubMed 

Google Scholar 
King, S. L. & Janik, V. M. Bottlenose dolphins can use learned vocal labels to address each other. Proc. Natl. Acad. Sci. 110, 13216–13221 (2013).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Ravignani, A. et al. Ontogeny of vocal rhythms in harbor seal pups: An exploratory study. Curr. Zool. 65, 107–120 (2019).PubMed 

Google Scholar 
Rauber, R. & Manser, M. B. Effect of group size and experience on the ontogeny of sentinel calling behaviour in meerkats. Anim. Behav. 171, 129–138 (2021).
Google Scholar 
Janik, V. M. & Slater, P. J. Vocal learning in mammals. Adv. Study Behav. 26, 59–100 (1997).
Google Scholar 
Fitch, W. T. Production of vocalizations in mammals. In Encyclopedia of Language and Linguistics 2nd edn, Vol. 1 115–121 (Elsevier, 2006).
Google Scholar 
Fletcher, N. H. A frequency scaling rule in mammalian vocalization. In Handbook of Behavioral Neuroscience Vol. 19 51–56 (Elsevier, 2010).
Google Scholar 
Fant, G. Acoustic Theory of Speech Production (Mouton, 1960).
Google Scholar 
Taylor, A. & Reby, D. The contribution of source–filter theory to mammal vocal communication research. J. Zool. 280, 221–236 (2010).
Google Scholar 
Fitch, W. T., Neubauer, J. & Herzel, H. Calls out of chaos: The adaptive significance of nonlinear phenomena in mammalian vocal production. Anim. Behav. 63, 407–418 (2002).
Google Scholar 
Domning, D. P. & Hayek, L. A. C. Interspecific and intraspecific morphological variation in manatees (Sirenia: Trichechus). Mar. Mamm. Sci. 2, 87–144 (1986).
Google Scholar 
Anderson, P. K. & Barclay, R. M. R. Acoustic signals of solitary Dugongs: Physical characteristics and behavioral correlates. J. Mamm. 76, 1226–1237 (1995).
Google Scholar 
Sousa-Lima, R., Paglia, A. P. & Da Fonseca, G. Signature information and individual recognition in the isolation calls of Amazonian manatees, Trichechus inunguis (Mammalia: Sirenia). Anim. Behav. 63, 301–310 (2002).
Google Scholar 
Sousa-Lima, R. S., Paglia, A. P. & Fonseca, G. A. B. Gender, age, and identity in the isolation calls of Antillean manatees (Trichechus manatus manatus). Aquat. Mamm. 34, 109–122 (2008).
Google Scholar 
O’Shea, T. J. & Poché, L. B. Aspects of underwater sound communication in Florida manatees (Trichechus manatus latirostris). J. Mamm. 87, 1061–1071 (2006).
Google Scholar 
Rosas, F. C. W. Biology, conservation and status of the Amazonian manatee Trichechus inunguis. Mamm. Rev. 24, 49–59 (1994).
Google Scholar 
Meirelles, A. C. O. & Carvalho, V. L. Peixe-boi marinho: biologia e conservação no Brasil. Aquasis, Bambu Editora e Artes Gráficas, São Paulo (2016).Alvarez-Alemán, A., Beck, C. A. & Powell, J. A. First report of a Florida manatee (Trichechus manatus latirostris) in Cuba. Aquat. Mamm. 36, 148 (2010).
Google Scholar 
Castelblanco-Martínez, D. N. et al. First documentation of long-distance travel by a Florida manatee to the Mexican Caribbean. Ethol. Ecol. Evol. 1–12 (2021).Packard, J. M. & Wetterqvist, O. F. Evaluation of manatee habitat systems on the northwestern Florida coast. Coast. Manag. 14, 279–310 (1986).
Google Scholar 
Luna, F. D. O. et al. Genetic connectivity of the West Indian manatee in the southern range and limited evidence of hybridization with Amazonian manatees. Front. Mar. Sci. 7, 1089 (2021).
Google Scholar 
Hartman, D. Ecology and behavior of the manatee (Trichechus manatus) in Florida. Spec. Publ. Am. Soc. Mammal. 5, 153 (1979).
Google Scholar 
D’AffonsecaNeto, J. A. & Vergara-Parente, J. E. Sirenia (peixe-boi-da-Amazônia, Peixe-boi-marinho). In Tratado de Animais Selvagens: medicina veterinária (eds Cubas, Z. S. et al.) 701–714 (Roca, 2006).
Google Scholar 
Deutsch, C. J., Reid, J. P., Bonde, R. K., Easton, D. E., Kochman, H. I. & O’Shea, T. J. Seasonal movements, migratory behavior, and site fidelity of West Indian manatees along the Atlantic coast of the United States. Wildl. Monogr. 1–77 (2003).Laist, D. W. & Reynolds, J. E. III. Influence of power plants and other warm-water refuges on Florida manatees. Mar. Mamm. Sci. 21, 739–764 (2005).
Google Scholar 
Reynolds, J. E. Aspects of the social behaviour and herd structure of a semi-isolated colony of West Indian manatees, Trichechus manatus. Mammalia 45, 431–452 (1981).
Google Scholar 
Dantas, G. A. Ontogenia do padrão vocal individual do peixe-boi da Amazônia Trichechus inunguis (Sirenia, trichechidae). Dissertação (Instituto Nacional de Pesquisas da Amazônia, 2009).
Google Scholar 
Brady, B., Moore, J. & Love, K. Behavior related vocalizations of the Florida manatee (Trichechus manatus latirostris). Mar. Mamm. Sci. 1–15 (2021).Nowacek, D. P., Casper, B. M., Wells, R. S., Nowacek, S. M. & Mann, D. A. Intraspecific and geographic variation of West Indian manatee (Trichechus manatus spp.) vocalizations. J. Acoust. Soc. Am. 114, 66–69 (2003).ADS 
PubMed 

Google Scholar 
Rycyk, A. M. et al. First characterization of vocalizations and passive acoustic monitoring of the vulnerable African manatee (Trichechus senegalensis). J. Acoust. Soc. Am. 150, 3028–3037 (2021).ADS 
PubMed 

Google Scholar 
Landrau-Giovannetti, N., Mignucci-Giannoni, A. A. & Reidenberg, J. S. Acoustical and anatomical determination of sound production and transmission in West Indian (Trichechus manatus) and Amazonian (T. inunguis) manatees. Anat. Rec. 297, 1896–1907 (2014).
Google Scholar 
Morton, E. On the occurrence and significance of motivation-structural rules in some bird and mammal sounds. Am. Nat. 111, 855–869 (1977).
Google Scholar 
Borges, J. C. et al. Growth pattern differences of captive born Antillean manatee (Trichechus manatus) calves and those rescued in the Brazilian northeastern coast. J. Zoo Wildl. Med. 43, 494–500 (2012).PubMed 

Google Scholar 
Lima, D. S., Vergara-Parente, J. E., Young, R. J. & Paszkiewicz, E. Training of Antillean manatee Trichechus manatus manatus Linnaeus, 1758 as a management technique for individual welfare. Lat. Am. J. Mar. Mamm. 4, 61–68 (2005).
Google Scholar 
K. Lisa Yang Center for Conservation Bioacoustics at the Cornell Lab of Ornithology. Raven Pro: Interactive Sound Analysis Software (Version 1.5) [Computer software]. https://ravensoundsoftware.com/ (The Cornell Lab of Ornithology, 2022).Zollinger, S. A., Podos, J., Nemeth, E., Goller, F. & Brumm, H. On the relationship between, and measurement of, amplitude and frequency in birdsong. Anim. Behav. 84, e1–e9 (2012).
Google Scholar 
Sokal, R. R. & Rohlf, F. J. Biometry (W. H. Freeman and Co., 1995).MATH 

Google Scholar 
Charrier, I. & Harcourt, R. G. Individual vocal identity in mother and pup Australian sea lions (Neophoca cinerea). J. Mamm. 87, 929–938 (2006).
Google Scholar 
Green, S. & Salkind, N. J. Using SPSS for Windows and Macintosh: Analyzing and Understanding Data 4th edn. (Prentice Hall, 2003).
Google Scholar 
Charlton, B. D. et al. Cues to body size in the formant spacing of male koala (Phascolarctos cinereus) bellows: Honesty in an exaggerated trait. J. Exp. Biol. 214(20), 3414–3422 (2011).PubMed 

Google Scholar 
IBM Corp. Released 2020. IBM SPSS Statistics for Windows, Version 27.0.Best, R. C. The aquatic mammals and reptiles of the Amazon. In The Amazon 371–412 (Springer, 1984).
Google Scholar 
Gerhardt, H. C. The evolution of vocalization in frogs and toads. Annu. Rev. Ecol. Syst. 25, 293–324 (1994).
Google Scholar 
Mendoza, P. et al. Growth curve of Amazonian manatee (Trichechus inunguis) in captivity. Aquat. Mamm. 45 (2019).Schwarz, L. K. Methods and models to determine perinatal status of Florida manatee carcasses. Mar. Mamm. Sci. 24, 881–898 (2008).
Google Scholar 
Hauser, M. D., Chomsky, N. & Fitch, W. T. The faculty of language: What is it, who has it, and how did it evolve?. Science 298, 1569–1579 (2002).ADS 
CAS 
PubMed 

Google Scholar 
Marler, P. & Peters, S. Developmental overproduction and selective attrition: New processes in the epigenesis of birdsong. Dev. Psychol. J. Int. Soc. Dev. Psychol. 15.4, 369–378 (1982).
Google Scholar 
Casey, C., Reichmuth, C., Costa, D. P. & Le Boeuf, B. The rise and fall of dialects in northern elephant seals. Proc. R. Soc. B 285, 2018–2176 (2018).
Google Scholar 
Hunter, M. E. et al. Puerto Rico and Florida manatees represent genetically distinct groups. Conserv. Genet. 13, 1623–1635 (2012).
Google Scholar 
Castelblanco-Martínez, D. N. et al. Analysis of body condition indices reveals different ecotypes of the Antillean manatee. Sci. Rep. 11, 1–14 (2021).
Google Scholar 
McCracken, K. G. & Sheldon, F. H. Avian vocalizations and phylogenetic signal. Proc. Natl. Acad. Sci. 94, 3833–3836 (1997).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Moron, J. R. et al. Whistle variability of Guiana dolphins in South America: Latitudinal variation or acoustic adaptation? Mar. Mamm. Sci. 1–32 (2018)Luís, A. R. et al. Vocal universals and geographic variations in the acoustic repertoire of the common bottlenose dolphin. Sci. Rep. 11, 1–9 (2021).
Google Scholar 
Ey, E. & Fisher, J. The ‘Acoustic adaptations hypothesis’ a review of the evidence from birds, anurans and mammals. Bioacoustics 19, 21–48 (2009).
Google Scholar 
Miksis-Olds, J. L. & Tyack, P. L. Manatee (Trichechus manatus) vocalization usage in relation to environmental noise levels. J. Acoust. Soc. Am. 125, 1806–1815 (2009).ADS 
PubMed 

Google Scholar 
Sun, W., Wang, Z., Jamalabdollahi, M. & Reza Zekavat, S. A. Experimental study on the difference between acoustic communication channels in freshwater rivers/lakes and in oceans. In 2014 48th Asilomar Conference on Signals, Systems and Computers, 333–337 (2004)Rivera Chavarría, M., Castro, J. & Camacho, A. The relationship between acoustic habitat, hearing and tonal vocalizations in the Antillean manatee (Trichechus manatus manatus, Linnaeus, 1758). Biol. Open 4, 1237–1242 (2015).PubMed 
PubMed Central 

Google Scholar 
Gaspard, J. C. III. et al. Audiogram and auditory critical ratios of two Florida manatees (Trichechus manatus latirostris). J. Exp. Biol. 215, 1442–1447 (2012).PubMed 

Google Scholar 
Gerstein, E. R., Gerstein, L., Forsythe, S. E. & Blue, J. E. The underwater audiogram of the West Indian manatee (Trichechus manatus). J. Acoust. Soc. Am. 105, 3575–3583 (1999).ADS 
CAS 
PubMed 

Google Scholar 
Klishin, V., Pezo, R., Popov, V., Ya, A. & Supin. Some characteristics of hearing of the Brazilian manatee, Trichechus inunguis. Aquat. Mamm. 16 (1990).Johnson, M., de Soto, N. A. & Madsen, P. T. Studying the behaviour and sensory ecology of marine mammals using acoustic recording tags: A review. Mar. Ecol. Prog. Ser. 395, 55–73 (2009).ADS 

Google Scholar  More

We aimed to understand the impact of changing pCO2 (400 vs. 800 ppm, representing current and projected year 2100 concentrations) on Prochlorococcus and Synechococcus and its effects on their interactions with the co-cultured heterotrophic “helper” bacterium Alteromonas sp. EZ55. Consistent with our previous research [7], EZ55 was more strongly affected by year 2100 pCO2 than any of the photoautotrophs in our study despite the primary dependence of the latter organisms’ metabolism on CO2. Strikingly, elevated pCO2 tended to reduce or eliminate the effect of co-culture on EZ55, with far fewer genes being significantly differentially transcribed relative to axenic EZ55 at the same pCO2. Thus, pCO2 strongly impacted the metabolic conversation between cyanobacteria and EZ55. Our detailed analysis of differentially regulated metabolic pathways suggested three mutually reinforcing mechanisms underlying this dynamic interaction: (i) pCO2 impacts on the release of ‘leaky’ cyanobacteria-derived metabolites, (ii) alteration of the dynamics of competition over inorganic nutrients between the co-cultured organisms, and (iii) modulation of bacterial and phytoplankton stress states. We explore each of these mechanisms in further detail below.Carbon cycling of “leaky” metabolites in co-cultureThe media we used for coculturing phytoplankton and bacteria contained no exogenous carbon sources; therefore, EZ55 was dependent on cyanobacterial exudates to grow, and it is likely that much of its changed transcription reflected changing availability of extracellular metabolites in the medium. The significant upregulation of carbon catabolism and transport genes as well as chemotaxis genes in co-cultures relative to axenic EZ55 supports the view that bacterial remineralization of cyanobacteria-secreted organic compounds is a driving force in these simple ecosystems. Additionally, changes in transcription of carbohydrate catabolism and transport genes provide clues as to which metabolites were being secreted under different experimental conditions (Fig. 5).Fig. 5: Proposed reconstruction of Alteromonas EZ55 ecophysiology.Reconstructions are shown for four different community contexts (axenic culture, or co-culture with Prochlorococcus MIT9312, Synechococcus WH8102, or Synechococcus CC9311) at 400 or 800 ppm pCO2, reflecting possible changes in the availability of C compounds, growth limiting factors, and stress conditions consistent with differential gene transcription observations. EZ55 image was obtained by cryoelectron microscopy from the sessions reported in Hennon et al. [7]. Background colors for each partner correspond to the bar colors in Fig. 3.Full size imageLike all oxygenic phototrophs, the cyanobacteria studied here fix carbon using the enzyme rubisco, which also catalyzes the undesirable photorespiration reaction leading to the production of 2PG instead of photosynthate. Phytoplankton in the field and in culture have been observed to excrete low molecular weight carboxylic acids including glycolate [39,40,41]. Photorespiratory glycolate is one of the most abundant sources of carbon in the oceans [38] and a preferred growth substrate for some marine heterotrophic bacteria [42]. Moreover the bacterial glcD gene for converting glycolate to glyoxylate is ubiquitously transcribed in the ocean [41, 43]. Although EZ55 lacks a specific transporter for glycolate, it can be taken up by the cell using the same transporters used for acetate and lactate uptake [44, 45], both of which were upregulated in co-culture conditions at 400 ppm (Fig. 3). Our data also showed differential regulation of enzymes involved in glycolate catabolism pathways, with at least one pathway upregulated in co-culture with each cyanobacterial strain (Fig. 3). We further demonstrated that EZ55 cultures were capable of growth on glycolate as a sole source of carbon, possibly using a novel GlcDF fusion protein (Fig. S11) and/or a plant-like LOX/GOX enzyme (Fig. 4). Thus, photorespiratory byproducts are likely a source of carbon for EZ55 in these cultures, particularly in the presence of MIT9312, which has no detectable enzymes for reclaiming 2PG on its own.There was also evidence that EZ55 utilized amino acids, organic acids, and fatty acids produced by phytoplankton under certain conditions in these cultures (Fig. S9). Lactate, acetate, and propanoate transporters and catabolism pathways were upregulated in co-culture with all cyanobacteria, as was pyruvate dehydrogenase with MIT9312, but only at 400 ppm. Both valine and glycine catabolism were also upregulated at 400 ppm in co-culture with the two Synechococcus strains, and fatty acid catabolism was upregulated in co-culture with MIT9312 and CC9311 at 400 ppm pCO2. Most of these substances have been directly or indirectly observed in cyanobacterial cultures in previous studies. For example, glycolate, lactate, acetate, and pyruvate have been directly measured in Prochlorococcus spent media [39], and co-culture with Prochlorococcus can fulfill the SAR11 growth requirement for glycine and pyruvate [46]. Fatty acid catabolism genes may have targeted membrane vesicles which are abundantly released by Prochlorococcus and other marine bacteria and may be a significant source of carbon for heterotrophs in the ocean [47, 48]; if so, future studies should investigate if WH8102 produces fewer vesicles than the other two cyanobacteria, explaining the differential transcription of beta-oxidation genes observed here.Valine, fatty acid, and propanoate catabolic pathways intersect with the formation of propanoyl-coA which in bacteria is generally fed into the TCA cycle through the methylcitrate pathway [49], which was significantly downregulated at 400 ppm in co-culture with all cyanobacteria even though other genes in these pathways were upregulated. Therefore, it is not clear what the ultimate fate of carbon from these sources is, although it is possible that EZ55 may be able to convert propanoyl-coA into a TCA cycle intermediate through another alternative pathway (e.g. as has been described in Mycobacterium tuberculosis via the methylmalonyl pathway [50]).Notably, gene transcription related to the utilization of all these products declined at 800 ppm pCO2 (Figs. 3, S8, S9). This was not unexpected for enzymes in the glycolate utilization pathways, as the increased CO2/O2 ratio at 800 ppm should decrease the rate of photorespiration relative to carbon fixation and therefore the availability of photorespiratory metabolites like glycolate [51, 52]. It is not clear, however, why organic and fatty acids would be less abundant in cyanobacterial exudates at 800 ppm. One possibility is that cyanobacteria release fewer of these compounds into the medium at high pCO2 because of a change in their internal redox state under these conditions favoring full oxidation of photosynthate. If future pCO2 conditions fundamentally alter the character of phytoplankton exudates, this could have profound implications for evolution and ecosystem functioning in future oceans.Evidence for inorganic nutrient limitation and competitionAutotrophic cyanobacteria and heterotrophic EZ55 were unlikely to compete over carbon under our experimental conditions, but we observed evidence of competition over inorganic nutrients such as N, P, and Fe. EZ55 phosphate, ammonium, and iron transporters, nitrogen regulatory protein P-II, and glutamine synthetase (the primary gateway for N assimilation in bacteria) were all more highly transcribed for all co-cultures compared to axenic cultures at 400 ppm pCO2 (Fig. S6), suggesting a switch from axenic carbon limitation to nutrient limitation in the presence of a continual supply of photosynthetically derived carbon (Fig. 5). On the other hand, few nutrient transporters were upregulated compared to axenic under 800 ppm pCO2. Although gene transcription data alone is not sufficient to conclude whether Alteromonas is limited by inorganic or organic nutrients, the reduced importance of nutrient acquisition suggests that EZ55 is carbon limited under these conditions just as it is in the absence of cyanobacteria.There were comparatively few species-specific changes in EZ55 nutrient transporter gene transcription. One example was an ammonium transporter, which was strongly upregulated in co-culture with both open ocean cyanobacteria (MIT9312 and WH8102) at 400 ppm pCO2. This may reflect a response to a comparatively high affinity for N in cyanobacteria adapted to the permanently oligotrophic open ocean, making them much stronger competitors for limiting N than coastal CC9311. N competition with EZ55 has been observed to increase the relative competitive fitness of Prochlorococcus vs. Synechococcus (coastal strain WH7803) in 3-way co-cultures [53]. In contrast, WH8102 appears to have higher N demand under 800 ppm pCO2, significantly upregulating a nitrate transporter and several genes related to urea utilization (Fig. S2). This may be explained by the enhanced transcription of carbon fixation genes and faster exponential growth rates observed in WH8102 at elevated pCO2, increasing N demand, and may indicate that WH8102 was C limited at 400 ppm.It is important to note that different N sources were provided in PEv medium (in which axenic EZ55 and MIT9312 co-cultures were grown) and SEv medium (in which CC9311 and WH8102 co-cultures were grown), with NH4+ in the former and NO3- in the latter. However, we do not think this difference can explain the observed changes in gene regulation, since EZ55 is capable of growth using either N source. It is interesting to note, however, that EZ55’s ammonium transporter was upregulated in both media types (Fig. S6), suggesting it may be benefitting from ammonium excreted by Synechococcus in SEv co-cultures.Impacts of co-culture and pCO2 on stress conditionsEZ55 showed less transcription of stress-related genes at 400 than 800 ppm pCO2, and also less evidence of stress in co-culture with any cyanobacterium than in axenic culture by itself. Nearly every gene in the EZ55 genome related to protection from H2O2 was downregulated in co-culture at 400 ppm, as were a suite of other stress-related genes (Fig. 2); on the other hand, many of these genes were significantly upregulated relative to axenic conditions at 800 ppm. Additionally, at 800 ppm there was a pronounced difference in EZ55 H2O2 defense gene transcription between cyanobacterial partners. As we described previously [7], both monofunctional catalases were downregulated at 800 ppm in co-culture with MIT9312, as were 2 of 3 alkylhydroperoxide reductase genes (although the third was significantly upregulated). In contrast, the monofunctional catalase genes were significantly upregulated in co-culture with WH8102 at 800 ppm. Elevated transcription of genes involved in the biosynthesis of glycine betaine, an osmoprotectant which has also been shown to function as an antioxidant [54, 55], provides further evidence for increased oxidative stress in co-culture with Synechococcus at 800 ppm in EZ55.Some indication of the mechanism behind EZ55’s changing stress level under co-culture and elevated pCO2 can be seen in the dynamics of three stress-related RNA polymerase sigma factors. Both rpoE and rpoH, responsible for controlling envelope and heat stress regulons, respectively, were downregulated at 400 ppm in co-culture relative to axenic and 800 ppm conditions; rpoE was significantly upregulated at 800 ppm pCO2. These trends are consistent with starvation-induced oxidative stress under both axenic and 800 ppm conditions, as discussed above. In contrast, rpoS was upregulated at 400 ppm pCO2, strongly so in co-culture with MIT9312. RpoS is a specialized sigma factor that accumulates under conditions of nutrient deprivation or as cells enter the stationary phase and serves to increase general stress resistance [56, 57]. For example, in Escherichia coli RpoS was shown to play a crucial role for survival during nitrogen deprivation [58]. While the decoupling of the transcription of oxidative stress genes like catalase from rpoS transcription was unexpected, rpoS trends are consistent with EZ55 being nutrient limited at 400 ppm pCO2 (Fig. S6) and with the upregulation of catalase in co-culture with MIT9312, but not WH8102 or CC9311, at 400 ppm (Fig. 2).In contrast to EZ55, differentially transcribed genes related to stress responses were rare in cyanobacteria at 800 ppm. While both MIT9312 and WH8102 had significant growth impairments at 800 ppm (Fig. S1), there was little evidence of a stress-specific gene transcription response in either strain. DNA mismatch repair genes were enriched as a group at 800 ppm in Prochlorococcus, although the only individual stress-related protein that was differentially transcribed was a HLI protein that was strongly downregulated at 800 ppm. No stress-related genes or gene sets were enriched in WH8102, and the small number of differentially transcribed stress genes in CC9311 (e.g., heat-shock and HLI proteins) were all downregulated at 800 ppm. This could indicate a dependence of both MIT9312 and WH8102 on their co-cultured EZ55 partner for protection, as neither of these cyanobacterial genomes contains catalase or several other stress-response genes common in heterotrophic bacteria. It could also indicate that they have different stress response mechanisms than those that have been characterized in heterotrophic bacteria; for instance, several hypothetical proteins of unknown function were differentially regulated in each cyanobacterium between the pCO2 conditions. Finally, it is possible that the stresses experienced by MIT9312 and WH8102 occurred in the initial days after transfer into fresh media (i.e., the significantly extended lag period observed for both), and were alleviated by the late log phase when the cultures were sampled for RNA sequencing.Summary overview of metabolic responsesWe have shown that the response to elevated pCO2 in our algal:bacterial co-cultures was driven more by interspecies interactions than by CO2-specific responses themselves. While it is important to note that we do not have direct culture-based evidence for some of these claims, we feel that gene transcription evidence is strong for several conclusions regarding the interactions in our cultures (Fig. 5).First, increased pCO2 appears to have fundamentally altered the amount and/or types of carbon compounds secreted by all three cyanobacterial strains examined, placing EZ55 into a stationary-phase metabolic state nearly indistinguishable to being in culture media with no added carbon source at all. We suggest that this is driven directly by the higher CO2:O2 ratio, which lowered the rate of photorespiration and subsequent release of 2PG and/or glycolate and indirectly may have reduced the amount of incompletely oxidized carbon released by cyanobacteria by changing the intracellular redox state [59]. Possibly because of the changing supply of carbon, EZ55 also appeared to transition away from a state of nutrient competition with its cyanobacterial partners, exemplified by decreased transcription of nutrient transporters at elevated pCO2 (Fig. S6).Second, co-culture at 400 ppm clearly reduced stress on EZ55 relative to either axenic growth or co-culture growth at 800 ppm, possibly due to the provision of a more reliable source of C as described above by the cyanobacterial partner under these conditions. In contrast, both MIT9312 and WH8102 clearly experienced elevated stress, potentially related to the changes in EZ55’s metabolism under these conditions. One of the major conclusions from our previous work [7] was the finding that EZ55 reduced catalase transcription at 800 ppm pCO2, eliminating the “helper” effect that Prochlorococcus depends on to grow in culture [13, 14]. In this work we see that the catalase response in co-culture with MIT9312 was opposite that in co-culture with the two Synechococcus strains. One possible explanation for this lies in the fact that MIT9312, unlike the other three strains in this study, did not possess a complete 2PG catabolism pathway and therefore likely excreted this product where it was subsequently catabolized by EZ55. We confirmed by genomic analysis (Figs. S10–S13) and culture experiments (Fig. 4) that EZ55 was able to grow on glycolate as a sole carbon source, and that its intracellular H2O2 concentration was elevated compared to growth on glucose. We suggest that more 2PG was secreted by MIT9312 at 400 ppm pCO2 due to the lower CO2:O2 ratio, and that growth on this carbon source increased EZ55’s internal oxidative stress load, resulting in higher transcription of H2O2 defenses such as catalase (Fig. 2). If true, this provides one possible explanation of why the “helper” relationship broke down at elevated pCO2 – by leaking 2PG as a readily available growth substrate for EZ55 at 400 ppm, MIT9312 forced EZ55 to maintain a high degree of intracellular ROS defense, leading to the well-characterized ability of EZ55 to cross-protect Prochlorococcus strains from the relatively lower H2O2 concentrations in the bulk environment, and allowing MIT9312 to eliminate two energetically costly enzymatic pathways. When higher pCO2 reduced the rate of photorespiration, EZ55’s need to produce excess catalase decreased, resulting in lower levels of protection, and concomitant growth impairments, for MIT9312.This is an example of how leaky Black Queen functions allow organisms like Prochlorococcus to streamline their metabolism while simultaneously creating stable interdependencies within their communities. However, it also shows how Black Queen-stabilized exchanges can break down. If our hypothesized relationship between pCO2 and catalase production is correct, then this system depends on the passive release of a metabolic by-product that evolved under a set of atmospheric pCO2 conditions that have been largely stable for thousands of years – but this leaves the system particularly vulnerable to the rapid changes in pCO2 currently taking place and may leave Prochlorococcus with no protection at all in the future ocean. If Prochlorococcus is outcompeted by less-streamlined competitors, this could reduce the overall efficiency of primary production in the open ocean gyres with possible positive feedbacks on CO2 accumulation in the atmosphere. Subsequent experiments should examine whether Prochlorococcus can overcome this imbalance through adaptive evolution quickly enough to avoid serious disruptions of its current niche.In conclusion, these results provide further support for the observation that axenic cultures do not provide a good window into the behavior of natural communities. The metabolism of Alteromonas sp. EZ55, a ubiquitous consumer in the ocean, was strongly dependent on its community context, and relatively subtle shifts in the chemical environment induced by elevated pCO2 were sufficient to significantly remodel its physiology. Moreover, the transcriptional response of EZ55 to changing pCO2 was much greater than that of any of the photoautotrophs examined, suggesting that more work is needed to understand the often-ignored heterotrophic bacteria associated with marine primary producers and how they will respond to global ocean change. Thus, further research is indicated on some of our core findings and hypotheses (e.g., the role of 2PG, and the nature of the carbon exchanged between the cyanobacteria and Alteromonas) via metabolomics or direct substrate measurements. These results further highlight the importance of laboratory experiments using co-cultures as an experimentally tractable intermediate between oversimplified axenic cultures and overly complicated natural communities. They also highlight the dominant role that primary producers play in determining the metabolism and interactions of the organisms that depend on them for sustenance. More

Randolph, S. E. & Rogers, D. J. The arrival, establishment and spread of exotic diseases: Patterns and predictions. Nat. Rev. Microbiol. 8, 361–371 (2010).Article 
PubMed 

Google Scholar 
Boussès, P., Dehecq, J. S., Brengues, C. & Fontenille, D. Inventaire actualisé des moustiques (Diptera : Culicidae) de l’île de La Réunion, océan Indien. Bulletin de la Société de pathologie exotique 106, 113–125 (2013).Article 
PubMed 

Google Scholar 
Delatte, H. et al. Geographic distribution and developmental sites of Aedes albopictus (Diptera: Culicidae) during a Chikungunya epidemic event. Vector-Borne Zoonotic Dis. 8, 25–34 (2008).Article 
PubMed 

Google Scholar 
Gomard, Y., Lebon, C., Mavingui, P. & Atyame, C. M. Contrasted transmission efficiency of Zika virus strains by mosquito species Aedes aegypti, Aedes albopictus and Culex quinquefasciatus from Reunion Island. Parasites Vectors https://doi.org/10.1186/s13071-020-04267-z (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Vazeille, M., Dehecq, J.-S. & Failloux, A.-B. Vectorial status of the Asian tiger mosquito Aedes albopictus of La Réunion Island for Zika virus: Ae. Albopictus of la réunion island. Med. Vet. Entomol. 32, 251–254 (2018).Article 
PubMed 

Google Scholar 
Youssouf, H. et al. Rift valley fever outbreak, Mayotte, France, 2018–2019. Emerg. Infect. Dis. 26, 769–772 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Sang, R. et al. Rift valley fever virus epidemic in Kenya, 2006/2007: The entomologic investigations. Am. J. Trop. Med. Hyg. 83, 28–37 (2010).Article 
PubMed 
PubMed Central 

Google Scholar 
Cardinale, E. et al. West Nile virus infection in horses, Indian ocean. Comp. Immunol. Microbiol. Infect. Dis. 53, 45–49 (2017).Article 
PubMed 

Google Scholar 
Bouyer, J., Yamada, H., Pereira, R., Bourtzis, K. & Vreysen, M. J. B. Phased conditional approach for mosquito management using sterile insect technique. Trends Parasitol. 36, 325–336 (2020).Article 
PubMed 

Google Scholar 
Lees, R. S., Carvalho, D. O. & Bouyer, J. Potential Impact of Integrating the Sterile Insect Technique into the Fight against Disease-Transmitting Mosquitoes 1081–1118 (CRC Press, 2021). https://doi.org/10.1201/9781003035572-33.Book 

Google Scholar 
Gouagna, L. C. et al. Strategic approach, advances, and challenges in the development and application of the SIT for area-wide control of Aedes albopictus mosquitoes in Reunion Island. Insects 11, 770 (2020).Article 
PubMed Central 

Google Scholar 
Bouyer, J. & Lefrançois, T. Boosting the sterile insect technique to control mosquitoes. Trends Parasitol. 30, 271–273 (2014).Article 
PubMed 

Google Scholar 
Soghigian, J. et al. Genetic evidence for the origin of Aedes aegypti, the yellow fever mosquito, in the southwestern Indian Ocean. Mol. Ecol. 29, 3593–3606 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Bouyer, J. & Vreysen, M. J. B. Yes, irradiated sterile male mosquitoes can be sexually competitive!. Trends Parasitol. 36, 877–880 (2020).Article 
PubMed 

Google Scholar 
Owino, E. A. et al. Field evaluation of natural human odours and the biogent-synthetic lure in trapping Aedes aegypti, vector of dengue and chikungunya viruses in Kenya. Parasites Vectors 7, 451 (2014).
Article 
PubMed 
PubMed Central 

Google Scholar 
Kröckel, U., Andreas, R., Eiras, Á. & Geier, M. New tools for surveillance of adult yellow fever mosquitoes: Comparison of trap catches with human landing rates in an urban environment. J. Am. Mosq. Control Assoc. 22, 229–238 (2006).Article 
PubMed 

Google Scholar 
Haramboure, M. et al. Modelling the control of Aedes albopictus mosquitoes based on sterile males release techniques in a tropical environment. Ecol. Model. 424, 109002 (2020).Article 

Google Scholar 
Farajollahi, A. et al. Field efficacy of BG-sentinel and industry-standard traps for Aedes albopictus (Diptera: Culicidae) and West Nile Virus Surveillance. J. Med. Entomol. 46, 919–925 (2009).Article 
PubMed 

Google Scholar 
Roiz, D. et al. Trapping the Tiger: Efficacy of the novel BG-sentinel 2 with several attractants and carbon dioxide for collecting Aedes albopictus (Diptera: Culicidae) in Southern France. J. Med. Entomol. 53, 460–465 (2016).Article 
PubMed 

Google Scholar 
Wilke, A. B. B. et al. Assessment of the effectiveness of BG-sentinel traps baited with CO2 and BG-Lure for the surveillance of vector mosquitoes in miami-dade County Florida. PLoS ONE 14, e0212688 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Staunton, K. M. et al. Effect of BG-lures on the male aedes (Diptera: Culicidae) sound trap capture rates. J. Med. Entomol. 58, 2425–2431 (2021).Article 
PubMed 
PubMed Central 

Google Scholar 
Visser, T. M. et al. Optimisation and field validation of odour-baited traps for surveillance of Aedes aegypti adults in Paramaribo Suriname. Parasites Vectors 13, 121 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Owino, E. A. et al. An improved odor bait for monitoring populations of Aedes aegypti-vectors of dengue and chikungunya viruses in Kenya. Parasites Vectors 8, 253 (2015).Article 
PubMed 
PubMed Central 

Google Scholar 
Le Goff, G. et al. Comparison of efficiency of BG-sentinel traps baited with mice, mouse-litter, and CO2 lures for field sampling of male and female aedes albopictus mosquitoes. Insects 8, 95 (2017).Article 
PubMed Central 

Google Scholar 
Nielsen, G. D., Petersen, S. H., Vinggaard, A. M., Hansen, L. F. & Wolkoff, P. Ventilation, CO2 production, and CO2 exposure effects in conscious, restrained CF-1 mice. Pharmacol. Toxicol. 72, 163–168 (1993).
Article 
PubMed 

Google Scholar 
Gouagna, L. C., Dehecq, J.-S., Fontenille, D., Dumont, Y. & Boyer, S. Seasonal variation in size estimates of Aedes albopictus population based on standard mark–release–recapture experiments in an urban area on Reunion Island. Acta Trop. 143, 89–96 (2015).Article 
PubMed 

Google Scholar 
Dekker, T., Geier, M. & Cardé, R. T. Carbon dioxide instantly sensitizes female yellow fever mosquitoes to human skin odours. J. Exp. Biol. 208, 2963–2972 (2005).Article 
PubMed 

Google Scholar 
Grant, A. J. & O’Connell, R. J. Age-related changes in female mosquito carbon dioxide detection. J. Med. Entomol. 44, 617–623 (2007).Article 
PubMed 

Google Scholar 
Bohbot, J. & Vogt, R. G. Antennal expressed genes of the yellow fever mosquito (Aedes aegypti L.); characterization of odorant-binding protein 10 and takeout. Insect Biochem. Mol. Biol. 35, 961–979 (2005).Article 
PubMed 

Google Scholar 
Hartberg, W. K. Observations on the mating behaviour of Aedes aegypti in nature. Bull. World Health Organ. 45, 847 (1971).PubMed 
PubMed Central 

Google Scholar 
Cator, L. J., Arthur, B. J., Ponlawat, A. & Harrington, L. C. Behavioral observations and sound recordings of free-flight mating swarms of Ae. aegypti (Diptera: Culicidae) in Thailand. J. Med. Entomol. 48, 941–946 (2011).Article 
PubMed 

Google Scholar 
Lacroix, R., Delatte, H., Hue, T. & Reiter, P. Dispersal and survival of male and female Aedes albopictus(Diptera: Culicidae) on Réunion Island. J. Med. Entomol. 46, 1117–1124 (2009).Article 
PubMed 

Google Scholar 
Pombi, M. et al. Field evaluation of a novel synthetic odour blend and of the synergistic role of carbon dioxide for sampling host-seeking Aedes albopictus adults in Rome, Italy. Parasites Vectors 7, 580 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Cilek, J. E., Hallmon, C. F. & Johnson, R. Semi-field comparison of the Bg Lure, nonanal, and 1-Octen-3-OL to attract adult mosquitoes in northwestern Florida. J. Am. Mosq. Control Assoc. 27, 393–397 (2011).Article 
PubMed 

Google Scholar 
Bagny Beilhe, L., Delatte, H., Juliano, S. A., Fontenille, D. & Quilici, S. Ecological interactions in Aedes species on Reunion Island. Med. Vet. Entomol. 27, 387–397 (2013).Article 
PubMed 

Google Scholar 
Golstein, C., Boireau, P. & Pagès, J.-C. Benefits and limitations of emerging techniques for mosquito vector control. Comptes Rendus Biol. 342, 270–272 (2019).Article 

Google Scholar 
Maïga, H., Gilles, J. R. L., Lees, R. S., Yamada, H. & Bouyer, J. Demonstration of resistance to satyrization behavior in Aedes aegypti from La Réunion island. Parasite 27, 22 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Zeileis, A., Kleiber, C. & Jackman, S. Regression models for count data in R. J. Stat. Soft. https://doi.org/10.18637/jss.v027.i08 (2008).Article 

Google Scholar 
Fawaz, E. Y., Allan, S. A., Bernier, U. R., Obenauer, P. J. & Diclaro, J. W. Swarming mechanisms in the yellow fever mosquito: Aggregation pheromones are involved in the mating behavior of Aedes aegypti. J. Vector Ecol. 39, 347–354 (2014).Article 
PubMed 

Google Scholar 
Guthery, F. S., Burnham, K. P. & Anderson, D. R. Model selection and multimodel inference: A practical information-theoretic approach. J. Wildl. Manag. 67, 655 (2003).Article 

Google Scholar 
Manly, B. F. J. Randomization, Bootstrap and Monte Carlo Methods in Biology 399 (CRC Press/Chapman & Hall, 2006). https://doi.org/10.1201/9781315273075.Book 
MATH 

Google Scholar 
R Core Team. R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, 2022).Barton, K. MuMIn: Multi-Model Inference. (R-Forge, 2022).
Google Scholar 
Burnham, K. P. & Anderson, D. R. Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach 496 (Springer-Verlag, 2002).MATH 

Google Scholar 
Xie, Y., Dervieux, C. & Riederer, E. R Markdown Cookbook (Chapman; Hall/CRC, 2020). https://doi.org/10.1201/9781003097471.Book 

Google Scholar  More

Sket, B. Can we agree on an ecological classification of subterranean animals?. J. Nat. Hist. 42, 1549–1563. https://doi.org/10.1080/00222930801995762 (2008).Article 

Google Scholar 
Mammola, S. et al. Scientists’ warning on the conservation of subterranean ecosystems. Bioscience 69, 641–650. https://doi.org/10.1093/biosci/biz064 (2019).Article 

Google Scholar 
Boulton, A. J., Fenwick, G. D., Hancock, P. J. & Harvey, M. S. Biodiversity, functional roles and ecosystem services of groundwater invertebrates. Invertebr. Syst. 22, 103–116. https://doi.org/10.1071/IS07024 (2008).Article 

Google Scholar 
Danielopol, D. L. & Griebler, C. Changing paradigms in groundwater ecology—From the ‘living fossils’ tradition to the ‘new groundwater ecology’. Int. Rev. Hydrobiol. 93, 565–577. https://doi.org/10.1002/iroh.200711045 (2008).Article 

Google Scholar 
Griebler, C., Malard, F. & Lefébure, T. Current developments in groundwater ecology—From biodiversity to ecosystem function and services. Curr. Opin. Biotechnol. 27, 159–167. https://doi.org/10.1016/j.copbio.2014.01.018 (2014).Article 
PubMed 

Google Scholar 
Fišer, C. Niphargus—A model system for evolution and ecology. In Encyclopedia of Caves (eds Culver, D. C. et al.) 746–755 (Academic Press, 2019).Chapter 

Google Scholar 
Riddle, M. R. et al. Insulin resistance in cavefish as an adaptation to a nutrient-limited environment. Nature 555, 647–651. https://doi.org/10.1038/nature26136 (2018).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Gibert, J. et al. Assessing and conserving groundwater biodiversity: Synthesis and perspectives. Freshw. Biol. 54, 930–941. https://doi.org/10.1111/j.1365-2427.2009.02201.x (2009).Article 

Google Scholar 
Trontelj, P. et al. A molecular test for cryptic diversity in ground water: How large are the ranges of macro stygobionts?. Freshw. Biol. 54, 727–744. https://doi.org/10.1111/j.1365-2427.2007.01877.x (2009).Article 

Google Scholar 
Cooper, J. E. Ecological and Behavioral Studies in Shelta Cave, Alabama, with Emphasis on Decapod Crustaceans (University of Kentucky, 1975).
Google Scholar 
Voituron, Y., de Fraipont, M., Issartel, J., Guillaume, O. & Clobert, J. Extreme lifespan of the human fish (Proteus anguinus): A challenge for ageing mechanisms. Biol. Lett. 7, 105–107. https://doi.org/10.1098/rsbl.2010.0539 (2011).Article 
PubMed 

Google Scholar 
Poulson, T. L. Cave adaptation in amblyopsid fishes. Am. Midl. Nat. 70, 257–290. https://doi.org/10.2307/2423056 (1963).Article 

Google Scholar 
Venarsky, M. P., Huryn, A. D. & Benstead, J. P. Re-examining extreme longevity of the cave crayfish Orconectes australis using new mark–recapture data: A lesson on the limitations of iterative size-at-age models. Freshw. Biol. 57, 1471–1481. https://doi.org/10.1111/j.1365-2427.2012.02812.x (2012).Article 

Google Scholar 
Culver, D. C., Kane, T. C. & Fong, D. W. Adaptation and Natural Selection in Caves: The Evolution of Gammarus minus (Harvard University Press, 1995).Book 

Google Scholar 
Niemiller, M. L. & Poulson, T. L. Subterranean fishes of North America: Amblyopsidae. In Biology of Subterranean Fishes (eds Trajano, E. et al.) 169–280 (CRC Press, 2010).Chapter 

Google Scholar 
Fišer, C., Zagmajster, M. & Zakšek, V. Coevolution of life history traits and morphology in female subterranean amphipods. Oikos 122, 770–778. https://doi.org/10.1111/j.1600-0706.2012.20644.x (2013).Article 

Google Scholar 
Purvis, A., Gittleman, J. L., Cowlishaw, G. & Mace, G. M. Predicting extinction risk in declining species. Proc. Biol. Sci. 267, 1947–1952. https://doi.org/10.1098/rspb.2000.1234 (2000).Article 
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. https://doi.org/10.1038/nclimate2113 (2014).Article 
ADS 

Google Scholar 
Niemiller, M. L., Bichuette, E. & Taylor, S. J. Conservation of cave fauna in Europe and the Americas. In Ecological Studies: Cave Ecology (eds Moldovan, O. T. et al.) 451–478 (Springer, 2018).Chapter 

Google Scholar 
Niemiller, M. L. & Taylor, S. J. Protecting cave life. In Encyclopedia of Caves (eds Culver, D. C. et al.) 822–829 (Academic Press, 2019).Chapter 

Google Scholar 
Niemiller, M. L., Taylor, S. J., Slay, M. E. & Hobbs, H. H. III. Biodiversity in the United States and Canada. In Encyclopedia of Caves (eds Culver, D. C. et al.) 163–176 (Academic Press, 2019).Chapter 

Google Scholar 
Hortal, J. et al. Seven shortfalls that beset large-scale knowledge of biodiversity. Annu. Rev. Ecol. Evol. Syst. 46, 523–529. https://doi.org/10.1146/annurev-ecolsys-112414-054400 (2015).Article 

Google Scholar 
MacKenzie, D. I. et al. Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence (Academic Press, 2018).MATH 

Google Scholar 
Roberto, P. & Pietro, B. Species rediscovery or lucky endemic? Looking for the supposed missing species Leistus punctatissimus through a biogeographer’s eye (Coleoptera, Carabidae). ZooKeys 740, 97–108. https://doi.org/10.3897/zookeys.740.23495 (2018).Article 

Google Scholar 
Chu, C., Mandrak, N. E. & Minns, C. K. Potential impacts of climate change on the distributions of several common and rare freshwater fishes in Canada. Divers. Distrib. 11, 299–310. https://doi.org/10.1111/j.1366-9516.2005.00153.x (2005).Article 

Google Scholar 
Larson, E. R. & Olden, J. D. Latent extinction and invasion risk of crayfishes in the southeastern United States. Conserv. Biol. 24, 1099–1110. https://doi.org/10.1111/j.1523-1739.2010.01462.x (2010).Article 
PubMed 

Google Scholar 
Filipe, A. F. et al. Selection of priority areas for fish conservation in Guadiana River Basin, Iberian Peninsula. Conserv. Biol. 18, 189–200. https://doi.org/10.1111/j.1523-1739.2004.00620.x (2004).Article 

Google Scholar 
Mammola, S. et al. Fundamental research questions in subterranean biology. Biol. Rev. 95, 1855–1872. https://doi.org/10.1111/brv.12642 (2020).Article 
PubMed 

Google Scholar 
Domínguez-Domínguez, O., Martínez-Meyer, E., Zombrano, L. & de León, G. P. Using ecological-niche modeling as a conservation tool for freshwater species: Live-bearing fishes in central Mexico. Conserv. Biol. 20, 1730–1739. https://doi.org/10.1111/j.1523-1739.2006.00588.x (2006).Article 
PubMed 

Google Scholar 
Mammola, S. & Leroy, B. Applying species distribution models to caves and other subterranean habitats. Ecography 41, 1194–1208. https://doi.org/10.1111/ecog.03464 (2018).Article 

Google Scholar 
Castellarini, F., Malard, F., Dole-Olivier, M. & Gibert, J. Modelling the distribution of stygobionts in the Jura Mountains (eastern France). Implications for the protection of ground waters. Divers. Distrib. 13, 213–224. https://doi.org/10.1111/j.1472-4642.2006.00317.x (2007).Article 

Google Scholar 
Foulquier, A., Malard, F., Lefébure, T., Douady, C. J. & Gibert, J. The imprint of Quaternary glaciers on the present-day distribution of the obligate groundwater amphipod Niphargus virei (Niphargidae). J. Biogeogr. 35, 552–564. https://doi.org/10.1111/j.1365-2699.2007.01795.x (2008).Article 

Google Scholar 
Johns, T. et al. Regional-scale drivers of groundwater faunal distributions. Freshw. Sci. 34, 316–328. https://doi.org/10.1086/678460 (2015).Article 

Google Scholar 
Camp, C. D., Wooten, J. A., Jensen, J. B. & Bartek, D. F. Role of temperature in determining relative abundance in cave twilight zones by two species of lungless salamander (family Plethodontidae). Can. J. Zool. 92, 119–127. https://doi.org/10.1139/cjz-2013-0178 (2014).Article 

Google Scholar 
Korbel, K. L., Hancock, P. J., Serov, P., Lim, R. P. & Hose, G. C. Groundwater ecosystems vary with land use across a mixed agricultural landscape. J. Environ. Qual. 42, 380–390. https://doi.org/10.2134/jeq2012.0018 (2013).Article 
PubMed 

Google Scholar 
Español, C. et al. Does land use impact on groundwater invertebrate diversity and functionality in floodplains?. Ecol. Eng. 103, 394–403. https://doi.org/10.1016/j.ecoleng.2016.11.061 (2017).Article 

Google Scholar 
Christman, M. C. et al. Predicting the occurrence of cave-inhabiting fauna based on features of the earth surface environment. PLoS One 11, e0160408. https://doi.org/10.1371/journal.pone.0160408 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Zagmajster, M. et al. Geographic variation in range size and beta diversity of groundwater crustaceans: Insights from habitats with low thermal seasonality. Glob. Ecol. Biogeogr. 23, 1135–1145. https://doi.org/10.1111/geb.12200 (2014).Article 

Google Scholar 
Poff, N. L. Landscape filters and species traits: Towards mechanistic understanding and prediction in stream ecology. J. North Am. Benthol. Soc. 16, 391–409. https://doi.org/10.2307/1468026 (1997).Article 

Google Scholar 
Stevenson, R. J. Scale-dependent determinants and consequences of benthic algal heterogeneity. J. North Am. Benthol. Soc. 16, 248–262. https://doi.org/10.2307/1468255 (1997).Article 
ADS 

Google Scholar 
U.S. Geological Survey. NLCD 2011 land cover. Multi-Resolution Land Characteristics. https://www.mrlc.gov/data/nlcd-2011-land-cover-conus (2011).Adamski, J. C. Geochemistry of the Springfield Plateau Aquifer of the Ozark Plateaus Province in Arkansas, Kansas, Missouri and Oklahoma, USA. Hydrol. Process. 14, 849–866. https://doi.org/10.1002/(SICI)1099-1085(20000415)14:5%3c849::AID-HYP973%3e3.0.CO;2-7 (2000).Article 
ADS 

Google Scholar 
Woods, A. J. et al. Ecoregions of Oklahoma (Color Poster with Map, Descriptive Text, Summary Tables, and Photographs) (U.S. Geological Survey, 2005).
Google Scholar 
Unklesbay, A. G. & Vineyard, J. D. Missouri Geology: Three Billion Years of Volcanoes, Seas, Sediments, and Erosion (University of Missouri Press, 1992).
Google Scholar 
Eigenmann, C. H. A new blind fish. In Proceedings of the Indiana Academy of Science 1897 (ed Waldo, C. A.) 231 (1898).Graening, G. O., Fenolio, D. B., Niemiller, M. L., Brown, A. V. & Beard, J. B. The 30-year recovery effort for the Ozark cavefish (Amblyopsis rosae): Analysis of current distribution, population trends, and conservation status of this threatened species. Environ. Biol. Fish. 87, 55–88. https://doi.org/10.1007/s10641-009-9568-2 (2010).Article 

Google Scholar 
Niemiller, M. L., Near, T. J. & Fitzpatrick, B. M. Delimiting species using multilocus data: Diagnosing cryptic diversity in the southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae). Evolution 66, 846–866. https://doi.org/10.1111/j.1558-5646.2011.01480.x (2012).Article 
PubMed 

Google Scholar 
Hobbs, H. H. Jr. & Brown, A. V. A new troglobitic crayfish from northwestern Arkansas (Decapoda: Cambaridae). Proc. Biol. Soc. Wash. 100, 1040–1048 (1987).
Google Scholar 
Graening, G. O., Slay, M. E., Brown, A. V. & Koppelman, J. B. Status and distribution of the endangered Benton cave crayfish, Cambarus aculabrum (Decapoda: Cambaridae). Southwest. Nat. 51, 376–381. https://doi.org/10.1894/0038-4909(2006)51[376:SADOTE]2.0.CO;2 (2006).Article 

Google Scholar 
Faxon, W. Cave animals from southwestern Missouri. Bull. Mus. Comp. Zool. 17, 225–240 (1889).
Google Scholar 
Graening, G. O., Hobbs, H. H. III., Slay, M. E., Elliott, W. R. & Brown, A. V. Status update for bristly cave crayfish, Cambarus setosus (Decapoda: Cambaridae), and range extension into Arkansas. Southwest. Nat. 51, 382–392. https://doi.org/10.1894/0038-4909(2006)51[382:SUFBCC]2.0.CO;2 (2006).Article 

Google Scholar 
Hobbs, H. H. III. Cambarus (Jugicambarus) subterraneus, a new cave crayfish (Decapoda: Cambaridae) from northeastern Oklahoma, with a key to the troglobitic members of the subgenus Jugicambarus. Proc. Biol. Soc. Wash. 106, 719–727 (1993).
Google Scholar 
Graening, G. O. & Fenolio, D. B. Status update of the Delaware County cave crayfish, Cambarus subterraneus (Decapoda: Cambaridae). Proc. Okla. Acad. Sci. 85, 85–89 (2005).
Google Scholar 
Hobbs, H. H. Jr. & Cooper, M. R. A new troglobitic crayfish from Oklahoma (Decapoda: Astacidae). Proc. Biol. Soc. Wash. 85, 49–56 (1972).
Google Scholar 
Graening, G. O. et al. Range extension and status update for the Oklahoma cave crayfish, Cambarus tartarus (Decapoda: Cambaridae). Southwest. Nat. 51, 94–99 (2006).Article 

Google Scholar 
Hobbs, H. H. III. A new cave crayfish of the genus Orconectes, subgenus Orconectes, from southcentral Missouri, USA, with a key to the stygobitic species of the genus (Decapoda, Cambaridae). Crustaceana 74, 635–646. https://doi.org/10.1163/156854001750377911 (2001).Article 

Google Scholar 
Miller, B. V. The Hydrology of the Carroll Cave-Toronto Springs System: Identifying and Examining Source Mixing Through Dye Tracing, Geochemical Monitoring, Seepage Runs, and Statistical Methods (Western Kentucky University, 2010).
Google Scholar 
Mouser, J. B., Brewer, S. K., Niemiller, M. L., Mollenhauer, R. & Van Den Bussche, R. Comparing visual and environmental DNA surveys for detection of stygobionts. Subterr. Biol. 39, 79–105. https://doi.org/10.3897/subtbiol.39.64279 (2021).Article 

Google Scholar 
Longmire, J. L., Maltbie, M. & Baker, R. J. Use of “Lysis Buffer” in DNA Isolation and Its Implication for Museum Collections (Museum of Texas Tech University, 1997).Book 

Google Scholar 
Mouser, J. B., Mollenhauer, R. & Brewer, S. K. Relationships between landscape constraints and a crayfish assemblage with consideration of competitor presence. Divers. Distrib. 25, 61–73. https://doi.org/10.1111/ddi.12840 (2019).Article 

Google Scholar 
U.S. Geological Survey. 1 Arc-second digital elevation models (DEMs)—USGS national map 3DEP downloadable data collection. https://data.usgs.gov/datacatalog/data/USGS:35f9c4d4-b113-4c8d-8691-47c428c29a5b (U.S. Geological Survey, 2017).Oak Ridge National Laboratory Distributed Active Archive Center. MODIS and VIIRS land products global subsetting and visualization tool. Oak Ridge National Laboratory Distributed Active Archive Center. https://doi.org/10.3334/ORNLDAAC/1379 (2018).Horton, J. D., San Juan, C. A. & Stoeser, D. B. The state geologic map compilation (SGMC) geodatabase of the conterminous United States. U.S. Geol. Surv. https://doi.org/10.3133/ds1052 (2017).Article 

Google Scholar 
MacKenzie, D. I. et al. Estimating site occupancy rates when detection probabilities are less than one. Ecology 83, 2248–2255. https://doi.org/10.1890/0012-9658(2002)083[2248:ESORWD]2.0.CO;2 (2002).Article 

Google Scholar 
Tyre, A. J. et al. Improving precision and reducing bias in biological surveys: Estimating false negative error rates. Ecol. Appl. 13, 1790–1801. https://doi.org/10.1890/02-5078 (2003).Article 

Google Scholar 
Gelman, A. & Hill, J. Data Analysis Using Regression and Multilevel Hierarchical Models (Cambridge University Press, 2007).
Google Scholar 
Kéry, M. & Royle, J. A. Applied Hierarchical Modeling in Ecology: Analysis of Distribution, Abundance and Species Richness in R and BUGS (Academic Press, 2016).MATH 

Google Scholar 
Plummer, M. JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling. In Proceedings of the 3rd International Workshop on Distributed Statistical Computing (eds Hornik, K. et al.) 1–10 (Austrian Science Foundation, 2003).
Google Scholar 
R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2020).
Google Scholar 
Kellner, J. jagsUI: A wrapper around ‘rjags’ to streamline ‘JAGS’ analyses. https://CRAN.R-project.org/package=jagsUI (R-project, 2019).Brooks, S. P. & Gelman, A. General methods for monitoring convergence of iterative simulations. J. Comput. Graph. Stat. 7, 434–455. https://doi.org/10.1080/10618600.1998.10474787 (1998).Article 
MathSciNet 

Google Scholar 
Kruschke, J. K. Doing Bayesian Data Analysis: A Tutorial with R, JAGS, and Stan (Academic Press, 2015).MATH 

Google Scholar 
Hobbs, N. T. & Hooten, M. B. Bayesian Models (Princeton University Press, 2015). https://doi.org/10.1515/9781400866557.Book 

Google Scholar 
Conn, P. B., Johnson, D. S., Williams, P. J., Melin, S. R. & Hooten, M. B. A guide to Bayesian model checking for ecologists. Ecol. Monogr. 88, 526–542. https://doi.org/10.1002/ecm.1314 (2018).Article 

Google Scholar 
Allan, J. D. Landscapes and riverscapes: The influence of land use on stream ecosystems. Annu. Rev. Ecol. Evol. Syst. 35, 257–284. https://doi.org/10.1146/annurev.ecolsys.35.120202.110122 (2004).Article 

Google Scholar 
Paul, M. J. & Meyer, J. L. Streams in the urban landscape. Annu. Rev. Ecol. Evol. Syst. 32, 333–365. https://doi.org/10.1146/annurev.ecolsys.32.081501.114040 (2001).Article 

Google Scholar 
Wicks, C., Kelley, C. & Peterson, E. Estrogen in a karstic aquifer. Groundwater 42, 384–389. https://doi.org/10.1111/j.1745-6584.2004.tb02686.x (2004).Article 

Google Scholar 
Buřič, M., Kouba, A., Máchová, J., Mahovská, I. & Kozák, P. Toxicity of the organophosphate pesticide diazinon to crayfish of differing age. Int. J. Environ. Sci. Technol. 10, 607–610. https://doi.org/10.1007/s13762-013-0185-4 (2013).Article 

Google Scholar 
Sohn, L., Brodie, R. J., Couldwell, G., Demmons, E. & Sturve, J. Exposure to a nicotinoid pesticide reduces defensive behaviors in a non-target organism, the rusty crayfish Orconectes rusticus. Ecotoxicology 27, 900–907. https://doi.org/10.1007/s10646-018-1950-4 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Noltie, D. B. & Wicks, C. M. How hydrogeology has shaped the ecology of Missouri’s Ozark cavefish, Amblyopsis rosae, and southern cavefish, Typhlichthys subterraneus: Insights on the sightless from understanding the underground. Environ. Biol. Fish. 62, 171–194. https://doi.org/10.1023/A:1011815806589 (2001).Article 

Google Scholar 
Kuhajda, B. R. & Mayden, R. L. Status of the federally endangered Alabama cavefish, Speoplatyrhinus poulsoni (Amblyopsidae), in Key Cave and surrounding caves, Alabama. Environ. Biol. Fish. 62, 215–222. https://doi.org/10.1023/A:1011817023749 (2001).Article 

Google Scholar 
Hutchins, B. T. The conservation status of Texas groundwater invertebrates. Biodivers. Conserv. 27, 475–501. https://doi.org/10.1007/s10531-017-1447-0 (2018).Article 

Google Scholar 
Niemiller, M. L. et al. Discovery of a new population of the federally endangered Alabama cave shrimp, Palaemonias alabamae Smalley, 1961, in northern Alabama. Subterr. Biol. 32, 43–59. https://doi.org/10.3897/subtbiol.32.38280 (2019).Article 

Google Scholar 
Abell, R., Allan, J. D. & Lehner, B. Unlocking the potential of protected areas for freshwaters. Biol. Conserv. 134, 48–63. https://doi.org/10.1016/j.biocon.2006.08.017 (2007).Article 

Google Scholar 
Liu, Y. et al. A review on effectiveness of best management practices in improving hydrology and water quality: Needs and opportunities. Sci. Total Environ. 601–602, 580–593. https://doi.org/10.1016/j.scitotenv.2017.05.212 (2017).Article 
ADS 
PubMed 

Google Scholar  More