Ecology

Rutz, C. Predator fitness increases with selectivity for odd prey. Curr. Biol. 22, 820–824 (2012).CAS 
PubMed 

Google Scholar 
Santos, C. D. et al. Personality and morphological traits affect pigeon survival from raptor attacks. Sci. Rep. 5, 1–8 (2015).
Google Scholar 
Brown, M. B. & Wells, E. Skeletal dysplasia-like syndromes in wild giraffe. BMC Res. Notes 13, 569 (2020).PubMed 
PubMed Central 

Google Scholar 
van Grouw, H. What colour is that bird? The causes and recognition of common colour aberrations in birds. Br. Birds 106, 17–29 (2013).
Google Scholar 
Slagsvold, T., Rofstad, G. & Sandvik, J. Partial albinism and natural selection in the hooded crow Corvus corone cornix. J. Zool. 214, 157–166 (1988).
Google Scholar 
Stevens, M. et al. Revealed by conspicuousness: distractive markings reduce camouflage. Behav. Ecol. 24, 213–222 (2013).
Google Scholar 
van Grouw, H. What’s in a name? Nomenclature for colour aberrations in birds reviewed. Bull. Br. Ornithol. Club 141, 276–299 (2021).
Google Scholar 
Parsons, G. J. & Bonderup-Nielsen, S. Partial albinism in an island population of Meadow Voles, Microtus pennsylvanicus, from Nova Scotia. Can. Field-Nat. 109, 263–264 (1995).
Google Scholar 
Reis, A. da S., Zampaulo, R. de A. & Talamoni, S. A. Frequency of leucism in a colony of Anoura geoffroyi (Chiroptera: Phyllostomidae) roosting in a ferruginous cave in Brazil. Biota Neotropica 19(3): e20180676. https://doi.org/10.1590/1676-0611-BN-2018-0676 (2019).Jehl, J. R. Leucism in Eared Grebes in western north America. Condor 87, 439–441 (1985).
Google Scholar 
Forrest, S. & Naveen, R. Prevalence of leucism in Pygoscelid penguins of the Antarctic peninsula. Waterbirds 23, 283–285 (2000).
Google Scholar 
González-Ortegón, E., Drake, P., Quigley, D. T. G. & Cuesta, J. A. Leucism in the European sardine Sardina pilchardus (Clupeidae). Ecol. Indic. 117, 106544 (2020).
Google Scholar 
David, B. Z. First report of partial leucism in the poison frog Epipedobates anthonyi (Anura: Dendrobatidae) in El Oro, Ecuador. Neotrop. Biodivers. 7, 1–4 (2021).
Google Scholar 
Krecsák, L. Albinism and leucism among European Viperinae: a review. Russ. J. Herpetol. 15, 97–102 (2008).
Google Scholar 
Ritland, K., Newton, C. & Marshall, H. D. Inheritance and population structure of the white-phased “Kermode” black bear. Curr. Biol. 11, 1468–1472 (2001).CAS 
PubMed 

Google Scholar 
Galván, I., Bijlsma, R. G., Negro, J. J., Jarén, M. & Garrido-Fernández, J. Environmental constraints for plumage melanization in the northern goshawk Accipiter gentilis. J. Avian Biol. 41, 523–531 (2010).
Google Scholar 
Pijpe, A., Gardien, K. L. M., Meijeren-Hoogendoorn, R. E. van, Middelkoop, E. & Zuijlen, P. P. M. van. Scar Symptoms: Pigmentation Disorders in Textbook On Scar Management (eds. Téot, L., Mustoe, T. A., Middelkoop, E. & Gauglitz, G. G.) 109–115 (Springer, 2020).Edelaar, P. et al. Apparent selective advantage of leucism in a coastal population of Southern caracaras (Falconidae). Evol. Ecol. Res. 13, 187–196 (2011).
Google Scholar 
Ellegren, H., Lindgren, G., Primmer, C. R. & Møller, A. P. Fitness loss and germline mutations in barn swallows breeding in Chernobyl. Nature 389, 593–596 (1997).ADS 
CAS 
PubMed 

Google Scholar 
Benítez-López, A. & García-Egea, I. First record of an aberrantly colored Pin-tailed Sandgrouse (Pterocles alchata). Wilson J. Ornithol. 127, 755–759 (2015).
Google Scholar 
Zbyryt, A., Mikula, P., Ciach, M., Morelli, F. & Tryjanowski, P. A large-scale survey of bird plumage colour aberrations reveals a collection bias in Internet-mined photographs. Ibis 163, 566–578 (2020).
Google Scholar 
Bensch, S., Hansson, B., Hasselquist, D. & Nielsen, B. Partial albinism in a semi-isolated population of Great Reed Warblers. Hereditas 133, 167–170 (2000).CAS 
PubMed 

Google Scholar 
Izquierdo, L. et al. Factors associated with leucism in the common blackbird Turdus merula. J. Avian Biol. 49, e01778 (2018).
Google Scholar 
Møller, A. P. & Mousseau, T. A. Albinism and phenotype of barn swallows (Hirundo rustica) from Chernobyl. Evolution 55, 2097–2104 (2001).PubMed 

Google Scholar 
Troscianko, J., Wilson-Aggarwal, J., Stevens, M. & Spottiswoode, C. N. Camouflage predicts survival in ground-nesting birds. Sci. Rep. 6, 1–8 (2016).
Google Scholar 
Aragonés, J., Arias de Reyna, L. & Recuerda, P. Visual communication and sexual selection in a nocturnal bird species, Caprimulgus ruficollis, a balance between crypsis and conspicuousness. Wilson Bull. 111, 340–345 (1999).
Google Scholar 
Negro, J. J., Bortolotti, G. R. & Sarasola, J. H. Deceptive plumage signals in birds: manipulation of predators or prey? Biol. J. Linn. Soc. 90, 467–477 (2007).
Google Scholar 
Brooke, M. de L. Unexplained recurrent features of the plumage of birds. Ibis 152, 845–847 (2010).Forero, M. G., Tella, J. L. & García, L. Age related evolution of sexual dimorphism in the Red-necked Nightjar Caprimulgus ruficollis. J. Ornithol. 136, 447–451 (1995).
Google Scholar 
Camacho, C. Early age at first breeding and high natal philopatry in the Red-necked Nightjar Caprimulgus ruficollis. Ibis 156, 442–445 (2014).
Google Scholar 
Camacho, C. et al. The road to opportunities: landscape change promotes body-size divergence in a highly mobile species. Curr. Zool. 62, 7–14 (2016).PubMed 
PubMed Central 

Google Scholar 
Forero, M. G., Tella, J. L. & Oro, D. Annual survival rates of adult Red-necked Nightjars Caprimulgus ruficollis. Ibis 143, 273–277 (2001).
Google Scholar 
Henner, J. et al. Genetic mapping of the (G)-locus responsible for the coat color phenotype “Progressive Greying with Age” in horses (Equus caballus). Mamm. Genome 13, 535–537 (2002).CAS 
PubMed 

Google Scholar 
Edson, J. M. An epidemic of albinism. Auk 45, 377–378 (1928).
Google Scholar 
Camacho, C., Palacios, S., Sáez, P., Sánchez, S. & Potti, J. Human-induced changes in landscape configuration influence individual movement routines: lessons from a versatile, highly mobile species. PLoS ONE 9, e104974 (2014).ADS 
PubMed 
PubMed Central 

Google Scholar 
Enders, F. & Post, W. White-spotting in the genus Ammospiza and other grassland sparrows. Bird-Band. 42, 210–219 (1971).
Google Scholar 
Sage, B. L. Albinism and melanism in birds. Br. Birds 55, 201–225 (1962).
Google Scholar 
O’Sullivan, J. D. B. et al. The biology of human hair greying. Biol. Rev. 96, 107–128 (2021).PubMed 

Google Scholar 
Nichols, J. D., Hines, J. E. & Blums, P. Tests for senescent decline in annual survival probabilities of common pochards, Aythya ferina. Ecology 78, 1009–1018 (1997).
Google Scholar 
Owen, M. & Skimmings, P. The occurrence and performance of leucistic Barnacle Geese Branta leucopsis. Ibis 134, 22–26 (1992).
Google Scholar 
Mulder, T., Campbell, C. J. & Ruxton, G. D. Evaluation of disruptive camouflage of avian cup-nests. Ibis 163, 150–158 (2021).
Google Scholar 
Holyoak, D. Variable albinism of the flight feathers as an adaptation for recognition of individual birds in some Polynesian populations of Acrocephalus warblers. Ardea 66, 112–117 (1978).
Google Scholar 
Griffith, S. C., Parker, T. H. & Olson, V. A. Melanin- versus carotenoid-based sexual signals: is the difference really so black and red? Anim. Behav. 71, 749–763 (2006).
Google Scholar 
Galván, I., Jorge, A., Nielsen, J. T. & Møller, A. P. Pheomelanin synthesis varies with protein food abundance in developing goshawks. J. Comp. Physiol. B 189, 441–450 (2019).PubMed 

Google Scholar 
Zaragoza-Trello, C., Vilà, M., Botías, C. & Bartomeus, I. Interactions among global change pressures act in a non-additive way on bumblebee individuals and colonies. Funct. Ecol. 35, 420–434 (2021).
Google Scholar 
Rollin, N. A note on abnormally marked Song Thrushes and Blackbirds. Trans. Nat. Hist. Soc. Northumberl. Durh. Newctle upon Tyne 10, 183–184 (1953).Guerrero-Bosagna, C. et al. Transgenerational epigenetic inheritance in birds. Environ. Epigenet. 4, dvy008 (2018).Camacho, C., Negro, J. J., Redondo, I., Palacios, S. & Sáez-Gómez, P. Correlates of individual variation in the porphyrin-based fluorescence of red-necked nightjars (Caprimulgus ruficollis). Sci. Rep. 9, 1–9 (2019).
Google Scholar 
Camacho, C. Tropical phenology in temperate regions: extended breeding season in a long-distance migrant. Condor 115, 830–837 (2013).
Google Scholar 
Cleere, N. Nightjars: a guide to nightjars and related birds (A&C Black, London, 2010).
Google Scholar 
Gargallo, G. Flight feather moult in the red-necked nightjar Caprimulgus ruficollis. J. Avian Biol. 25, 119–124 (1994).
Google Scholar 
Jackson, H. D. A field survey to investigate why nightjars frequent roads at night. Ostrich 74, 97–101 (2003).
Google Scholar 
Jackson, H. D. Finding and trapping nightjars. Bokmakierie 36, 86–89 (1984).
Google Scholar 
Sénar, J. C. & Pascual, J. Keel and tarsus length may provide a good predictor of avian body size. Ardea 85, 269–274 (1997).
Google Scholar 
Svensson, L. Identification Guide To European Passerines (Lars Svensson, Cleveland, 1992).
Google Scholar 
van de Pol, M. & Wright, J. A simple method for distinguishing within-versus between-subject effects using mixed models. Anim. Behav. 77, 753–758 (2009).
Google Scholar 
Schielzeth, H. & Forstmeier, W. Conclusions beyond support: overconfident estimates in mixed models. Behav. Ecol. 20, 416–420 (2009).PubMed 

Google Scholar 
Rising, J. D. & Somers, K. M. The measurement of overall body size in birds. Auk 106, 666–674 (1989).
Google Scholar 
Magnusson, A. et al. Package “glmmTMB”. R Package Version 0.2.0. (2017).Hartig, F. DHARMa: residual diagnostics for hierarchical (multi-level/mixed) regression models. R package version 0.2, 4. (2019).Nakagawa, S. & Schielzeth, H. A general and simple method for obtaining R2 from generalized linear mixed-effects models. Methods Ecol. Evol. 4, 133–142 (2013).
Google Scholar 
Barton, K. MuMIn: Multi-Model inference. Model selection and model averaging based on information criteria (AICc and alike). R package version 1.43.17. (2020). More

Boutaiba, S., Hacene, H., Bidle, K. A. & Maupin-Furlow, J. A. Microbial diversity of the hypersaline Sidi Ameur and Himalatt Salt Lakes of the Algerian Sahara. J. Arid Environ. 75, 909–916. https://doi.org/10.1016/j.jaridenv.2011.04.010 (2011).ADS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Ventosa, A. Unusual micro-organisms from unusual habitats: hypersaline environments. Symposia Society for General Microbiology (2006).Fukuchi, S., Yoshimune, K., Wakayama, M., Moriguchi, M. & Nishikawa, K. Unique amino acid composition of proteins in halophilic bacteria. J. Mol. Biol. 327, 347–357 (2003).CAS 
Article 

Google Scholar 
Pillai, S. D., Nakatsu, C. H., Miller, R. V. & Yates, M. V. Manual of environmental microbiology. Life High-Salinity Environ. https://doi.org/10.1128/9781555818821 (2015).Article 

Google Scholar 
Poli, A. et al. Microbial diversity in extreme marine habitats and their biomolecules. Microorganisms 5, 25. https://doi.org/10.3390/microorganisms5020025 (2017).CAS 
Article 
PubMed Central 

Google Scholar 
Azpiazu-Muniozguren, M., Martinez-Ballesteros, I., Gamboa, J., Seoane, S. & Bikandi, J. Altererythrobacter muriae sp. nov., isolated from hypersaline Aana Salt Valley spring water, a continental thalassohaline-type solar saltern. Int. J. Syst. Evol. Microbiol. 71, 3 (2021).
Google Scholar 
Zhang, J. et al. Bacterial diversity in Bohai Bay Solar Saltworks, China. Curr. Microbiol. 72, 55–63 (2016).CAS 
Article 

Google Scholar 
Highfield, A., Ward, A., Pipe, R. & Schroeder, D. C. Molecular and phylogenetic analysis reveals new diversity of Dunaliella salina from hypersaline environments. J. Mar. Biol. Assoc. UK 101, 27–37. https://doi.org/10.1017/s0025315420001319 (2021).CAS 
Article 

Google Scholar 
Cycil, L. M. et al. Metagenomic insights into the diversity of halophilic microorganisms indigenous to the Karak Salt Mine, Pakistan. Front. Microbiol. https://doi.org/10.3389/fmicb.2020.01567 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Jacob, J. H., Hussein, E. I., Shakhatreh, M. A. K. & Cornelison, C. T. Microbial community analysis of the hypersaline water of the Dead Sea using high-throughput amplicon sequencing. Microbiol. Open 6, e00500. https://doi.org/10.1002/mbo3.500 (2017).CAS 
Article 

Google Scholar 
Ben Abdallah, M. et al. Abundance and diversity of prokaryotes in ephemeral hypersaline lake Chott El Jerid using Illumina Miseq sequencing, DGGE and qPCR assay. Extremophiles 22, 811–823. https://doi.org/10.1007/s00792-018-1040-9 (2018).CAS 
Article 
PubMed 

Google Scholar 
Tazi, L., Breakwell, D. P., Harker, A. R. & Crandall, K. A. Life in extreme environments: Microbial diversity in Great Salt Lake, Utah. Extremophiles 18, 525–535. https://doi.org/10.1007/s00792-014-0637-x (2014).Article 
PubMed 

Google Scholar 
Kashi, F. J., Owlia, P., Amoozegar, M. A. & Kazemi, B. Halophilic prokaryotes in Urmia Salt Lake, a hypersaline environment in Iran. Curr. Microbiol. 78(8), 3230–3238 (2021).Article 

Google Scholar 
Sorokin, D. Y., Roman, P. & Kolganova, T. V. Halo(natrono)archaea from hypersaline lakes can utilize sulfoxides other than DMSO as electron acceptors for anaerobic respiration. Extremophiles 25, 173–180 (2021).CAS 
Article 

Google Scholar 
Hwang, K., Choe, H. & Kim, K. M. Complete genome of Nocardioides aquaticus KCTC 9944T isolated from meromictic and hypersaline Ekho Lake, Antarctica. Mar. Genom. 1, 100889 (2021).Article 

Google Scholar 
Didari, M. et al. Diversity of halophilic and halotolerant bacteria in the largest seasonal hypersaline lake (Aran-Bidgol-Iran). J. Environ. Health Sci. Eng. 18, 961–971. https://doi.org/10.1007/s40201-020-00519-3 (2020).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Oren, A. Diversity of halophilic microorganisms: Environments, phylogeny, physiology, and applications. J. Ind. Microbiol. Biotechnol. 28, 56–63 (2002).CAS 
Article 

Google Scholar 
Mutlu, M. B. et al. Prokaryotic diversity in Tuz Lake, a hypersaline environment in Inland Turkey. FEMS Microbiol. Ecol. 65, 474–483. https://doi.org/10.1111/j.1574-6941.2008.00510.x (2008).CAS 
Article 
PubMed 

Google Scholar 
Antón, J. et al. Distribution, abundance and diversity of the extremely halophilic bacterium Salinibacter ruber. Saline Syst. 4, 15. https://doi.org/10.1186/1746-1448-4-15 (2008).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Oren, A. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Syst. 4, 2. https://doi.org/10.1186/1746-1448-4-2 (2008).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Abdeljabbar, H., Badiaa, E., Jean-Luc, C., Marie-Laure, F. & Najla, S. Prokaryotic biodiversity of halophilic microorganisms isolated from Sehline Sebkha Salt Lake (Tunisia). Afr. J. Microbiol. Res. 8, 355–367. https://doi.org/10.5897/ajmr12.1087 (2014).Article 

Google Scholar 
Najjari, A., Elshahed, M. S., Cherif, A., Youssef, N. H. & Löffler, F. E. Patterns and determinants of halophilic archaea (Class Halobacteria) diversity in Tunisian endorheic salt lakes and Sebkhet systems. Appl. Environ. Microbiol. 81, 4432–4441. https://doi.org/10.1128/aem.01097-15 (2015).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Aharon, O. The ecology of the extremely halophilic archaea. FEMS Microbiol. Rev. 1, 415–440 (1994).
Google Scholar 
Oren, A. Halophilic Archaea. FEMS Microbiol. Rev. https://doi.org/10.1016/b978-0-12-809633-8.20800-5 (2019).Article 

Google Scholar 
Feng, Y. et al. The evolutionary origins of extreme halophilic archaeal lineages. Genome Biol. Evol. 13, 8. https://doi.org/10.1093/gbe/evab166 (2021).CAS 
Article 

Google Scholar 
Ventosa, A., Nieto, J. J. & Oren, A. Biology of moderately halophilic aerobic bacteria. Microbiol. Mol. Biol. Rev. 62, 504–544 (1998).CAS 
Article 

Google Scholar 
Kushner, D. J. Halophilic bacteria. Adv. Appl. Microbiol. 10, 73–99 (1968).CAS 
Article 

Google Scholar 
Ghozlan, H., Deif, H., Kandil, R. A. & Sabry, S. Biodiversity of moderately halophilic bacteria in hypersaline habitats in Egypt. J. Gen. Appl. Microbiol. 52, 63–72 (2006).CAS 
Article 

Google Scholar 
Ali, I., Prasongsuk, S., Akbar, A., Aslam, M. & Rakshit, S. K. Hypersaline habitats and halophilic microorganisms. Maejo Int. J. Sci. Technol. 10, 330–345 (2016).CAS 

Google Scholar 
Margesin, R. & Schinner, F. Biodegradation and bioremediation of hydrocarbons in extreme environments. Appl. Microbiol. Biotechnol. 56, 650–663. https://doi.org/10.1007/s002530100701 (2001).CAS 
Article 
PubMed 

Google Scholar 
Poosarla, V. G. & Ts, C. Xylanase production by halophilic bacterium Gracilibacillus sp. TSCPVG under solid state fermentation. Res. J. Biotechnol. 16, 92–100 (2021).Article 

Google Scholar 
Foti, M. et al. Diversity, activity, and abundance of sulfate-reducing bacteria in saline and hypersaline soda lakes. Appl. Environ. Microbiol. 73, 2093–2100. https://doi.org/10.1128/aem.02622-06 (2007).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Boujelben, I. et al. Spatial and seasonal prokaryotic community dynamics in ponds of increasing salinity of Sfax solar saltern in Tunisia. Antonie Van Leeuwenhoek 101, 845–857. https://doi.org/10.1007/s10482-012-9701-7 (2012).CAS 
Article 
PubMed 

Google Scholar 
García-Maldonado, J. Q., Bebout, B. M., Everroad, R. C. & López-Cortés, A. Evidence of novel phylogenetic lineages of methanogenic archaea from hypersaline microbial mats. Microb. Ecol. 69, 106–117. https://doi.org/10.1007/s00248-014-0473-7 (2014).CAS 
Article 
PubMed 

Google Scholar 
Abed, R. M. M., de Beer, D. & Stief, P. Functional-structural analysis of nitrogen-cycle bacteria in a hypersaline mat from the omani desert. Geomicrobiol. J. 32, 119–129. https://doi.org/10.1080/01490451.2014.932033 (2014).CAS 
Article 

Google Scholar 
Coban, O., Rasigraf, O., Jong, A., Spott, O. & Bebout, B. M. Quantifying potential N turnover rates in hypersaline microbial mats by 15 N tracer techniques. Appl. Environ. Microbiol. 87, 8 (2021).Article 

Google Scholar 
Rodriguez-Valera, F. Introduction to Saline Environments (Springer, 1993).
Google Scholar 
Wei, H. C., Qi-Shun, F., Fu-Yuan, A., Fa-Shou, S. & Qin, Z. J. Chemical elements in core sediments of the qarhan salt lake and palaeoclimate evolution during 94–9 ka. Acta Geosci. Sin. (2016).Yu, S., Liu, X., Tan, H. & Cao, G. Sustainable Utilization of Qarhan Salt Lake Resources 27–265 (Science Press, 2009).
Google Scholar 
Zhu, D. et al. An evaluation of the core bacterial communities associated with hypersaline environments in the Qaidam Basin, China. Arch. Microbiol. 202, 2093–2103. https://doi.org/10.1007/s00203-020-01927-7 (2020).CAS 
Article 
PubMed 

Google Scholar 
Liu, W., Jiang, H., Yang, J. & Wu, G. Gammaproteobacterial diversity and carbon utilization in response to salinity in the lakes on the qinghai-tibetan plateau. Geomicrobiol. J. 35, 392–403. https://doi.org/10.1080/01490451.2017.1378951 (2018).CAS 
Article 

Google Scholar 
Zhong, Z.-P. et al. Prokaryotic community structure driven by salinity and ionic concentrations in plateau lakes of the tibetan plateau. Appl. Environ. Microbiol. 82, 1846–1858. https://doi.org/10.1128/aem.03332-15 (2016).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
He, C. et al. Synergistic effect of magnetite and zero-valent iron on anaerobic degradation and methanogenesis of phenol. Biores. Technol. 291, 121874. https://doi.org/10.1016/j.biortech.2019.121874 (2019).CAS 
Article 

Google Scholar 
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336. https://doi.org/10.1038/nmeth.f.303 (2010).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. Embnet J. 17, 10–12 (2011).Article 

Google Scholar 
Zhang, J., Kassian, K., Tomáš, F. & Alexandros, S. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30, 614 (2014).CAS 
Article 

Google Scholar 
Schmieder, R. & Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863–864 (2011).CAS 
Article 

Google Scholar 
Edgar, R. C. UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996–1000 (2013).CAS 
Article 

Google Scholar 
Schloss, P. D. et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537 (2009).ADS 
CAS 
Article 

Google Scholar 
Chen, H. & Boutros, P. C. VennDiagram: A package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinform. 12, 35. https://doi.org/10.1186/1471-2105-12-35 (2011).Article 

Google Scholar 
McArdle, B. H. et al. Fitting multivariate models to community data: A comment on distance-based redundancy analysis. Ecology 82, 290–290 (2001).Article 

Google Scholar 
Langille, M. G. I. et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31, 814–821. https://doi.org/10.1038/nbt.2676 (2013).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Louca, S. & Doebeli, M. Efficient comparative phylogenetics on large trees. Bioinformatics 34, 1–3 (2017).
Google Scholar 
Louca, S., Parfrey, L. W. & Doebeli, M. Decoupling function and taxonomy in the global ocean microbiome. Science 353, 1272 (2016).ADS 
CAS 
Article 

Google Scholar 
Junker, B. H. & Schreiber, F. Analysis of Biological Networks 283–304 (Analysis of biological networks, 2008).Book 

Google Scholar 
Faust, K. & Raes, J. Microbial interactions: From networks to models. Nat. Rev. Microbiol. 10, 538–550. https://doi.org/10.1038/nrmicro2832 (2012).CAS 
Article 
PubMed 

Google Scholar 
Behzad, H., Ibarra, M. A., Mineta, K. & Gojobori, T. Metagenomic studies of the Red Sea. Gene 576, 717–723. https://doi.org/10.1016/j.gene.2015.10.034 (2016).CAS 
Article 
PubMed 

Google Scholar 
Naghoni, A. et al. Microbial diversity in the hypersaline Lake Meyghan, Iran. Sci. Rep. https://doi.org/10.1038/s41598-017-11585-3 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Kambura, A. K. et al. Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya. BMC Microbiol. https://doi.org/10.1186/s12866-016-0748-x (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Paul, D. et al. Exploration of microbial diversity and community structure of Lonar lake: The only hypersaline meteorite crater lake within basalt rock. Front. Microbiol. https://doi.org/10.3389/fmicb.2015.01553 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Ventosa, A., de la Haba, R. R., Sánchez-Porro, C. & Papke, R. T. Microbial diversity of hypersaline environments: A metagenomic approach. Curr. Opin. Microbiol. 25, 80–87. https://doi.org/10.1016/j.mib.2015.05.002 (2015).CAS 
Article 
PubMed 

Google Scholar 
Liu, F. H. et al. Bacterial and archaeal assemblages in sediments of a large shallow freshwater lake, Lake Taihu, as revealed by denaturing gradient gel electrophoresis. J. Appl. Microbiol. 106, 1022–1032. https://doi.org/10.1111/j.1365-2672.2008.04069.x (2009).CAS 
Article 
PubMed 

Google Scholar 
Song, H., Li, Z., Du, B., Wang, G. & Ding, Y. Bacterial communities in sediments of the shallow Lake Dongping in China. J. Appl. Microbiol. 112, 79–89. https://doi.org/10.1111/j.1365-2672.2011.05187.x (2012).CAS 
Article 
PubMed 

Google Scholar 
Wu, Q. L., Zwart, G., Schauer, M., Agterveld, K. V. & Hahn, M. W. Bacterioplankton community composition along a salinity gradient of sixteen high-mountain lakes located on the Tibetan Plateau, China. Appl. Environ. Microbiol. 72, 5478–5485 (2006).ADS 
CAS 
Article 

Google Scholar 
Xing, P., Hahn, M. W. & Wu, Q. L. Low taxon richness of bacterioplankton in high-altitude lakes of the Eastern Tibetan Plateau, with a predominance of bacteroidetes and Synechococcus spp. Appl. Environ. Microbiol. 75, 7017–7025. https://doi.org/10.1128/aem.01544-09 (2009).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Liu, Y. et al. Bacterial diversity of freshwater Alpine Lake Puma Yumco on the Tibetan Plateau. Geomicrobiol. J. 26, 131–145. https://doi.org/10.1080/01490450802660201 (2009).CAS 
Article 

Google Scholar 
MounÃc, S., Caumette, P., Matheron, R. & Willison, J. C. Molecular sequence analysis of prokaryotic diversity in the anoxic sediments underlying cyanobacterial mats of two hypersaline ponds in Mediterranean salterns. FEMS Microbiol. Ecol. 44, 117–130. https://doi.org/10.1016/s0168-6496(03)00017-5 (2003).Article 

Google Scholar 
Valenzuela-Encinas, C. et al. Changes in the bacterial populations of the highly alkaline saline soil of the former lake Texcoco (Mexico) following flooding. Extremophiles 13, 609–621. https://doi.org/10.1007/s00792-009-0244-4 (2009).Article 
PubMed 

Google Scholar 
Kim, T. J., Lee, E. Y., Kim, Y. J., Cho, K.-S. & Ryu, H. W. Degradation of polyaromatic hydrocarbons by Burkholderia cepacia 2A–12. World J. Microbiol. Biotechnol. 19, 411–417. https://doi.org/10.1023/A:1023998719787 (2003).CAS 
Article 

Google Scholar 
Gales, G. et al. Preservation of ancestral Cretaceous microflora recovered from a hypersaline oil reservoir. Sci. Rep. https://doi.org/10.1038/srep22960 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Kleinsteuber, S., Riis, V., Fetzer, I., Harms, H. & Müller, S. Population dynamics within a microbial consortium during growth on diesel fuel in saline environments. Appl. Environ. Microbiol. 72, 3531–3542. https://doi.org/10.1128/aem.72.5.3531-3542.2006 (2006).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Valenzuela-Encinas, C. et al. The archaeal diversity and population in a drained alkaline saline soil of the former lake Texcoco (Mexico). Geomicrobiol. J. 29, 18–22. https://doi.org/10.1080/01490451.2010.520075 (2012).Article 

Google Scholar 
He, S., Tan, J., Hu, W. & Mo, C. Diversity of archaea and its correlation with environmental factors in the Ebinur Lake Wetland. Curr. Microbiol. 76, 1417–1424. https://doi.org/10.1007/s00284-019-01768-8 (2019).CAS 
Article 
PubMed 

Google Scholar 
Sandaa, R. A., Enger, O. & Torsvik, V. Abundance and diversity of Archaea in heavy-metal-contaminated soils. Appl. Environ. Microbiol. 65, 3293–3297 (1999).ADS 
CAS 
Article 

Google Scholar 
Dave, B. P. & Soni, A. Diversity of halophilic archaea at salt pans around Bhavnagar Coast, Gujarat. Proc. Natl. Acad. Sci. India B 83, 225–232. https://doi.org/10.1007/s40011-012-0124-z (2012).Article 

Google Scholar 
Zafrilla, B., Martínez-Espinosa, R., Alonso, M. A. & Bonete, M. J. Biodiversity of Archaea and floral of two inland saltern ecosystems in the Alto Vinalopó Valley, Spain. Saline Syst. 6, 10 (2010).Article 

Google Scholar 
Costa, M., Santos, H. & Galinski, E. A. An overview of the role and diversity of compatible solutes in Bacteria and Archaea. Adv. Biochem. Eng. Biotechnol. 61, 117 (1998).PubMed 

Google Scholar 
Williams, R. J., Howe, A. & Hofmockel, K. S. Demonstrating microbial co-occurrence pattern analyses within and between ecosystems. Front. Microbiol. https://doi.org/10.3389/fmicb.2014.00358 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Schmidt, T. S. B., MatiasRodrigues, J. F. & von Mering, C. A family of interaction-adjusted indices of community similarity. ISME J. 11, 791–807. https://doi.org/10.1038/ismej.2016.139 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Oyewusi, H. A. et al. Functional profiling of bacterial communities in Lake Tuz using 16S rRNA gene sequences. Biotechnol. Biotechnol. Equip. 35, 1–10. https://doi.org/10.1080/13102818.2020.1840437 (2020).CAS 
Article 

Google Scholar  More

Taylor, M. W., Radax, R., Steger, D. & Wagner, M. Sponge-associated microorganisms: Evolution, ecology, and biotechnological potential. Microbiol. Mol. Biol. Rev. 71, 295–347 (2007).CAS 
PubMed 
PubMed Central 

Google Scholar 
Thomas, T. et al. Diversity, structure and convergent evolution of the global sponge microbiome. Nat. Commun. 7, 11870 (2016).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Webster, N. S. et al. Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts. Environ. Microbiol. 12, 2070–2082 (2010).CAS 
PubMed 
PubMed Central 

Google Scholar 
Sipkema, D. et al. Similar sponge-associated bacteria can be acquired via both vertical and horizontal transmission: Microbial transmission in Petrosia ficiformis. Environ. Microbiol. 17, 3807–3821 (2015).CAS 
PubMed 

Google Scholar 
Cleary, D. F. R. et al. The sponge microbiome within the greater coral reef microbial metacommunity. Nat. Commun. 10, 1644 (2019).Björk, J. R., Díez-Vives, C., Astudillo-García, C., Archie, E. A. & Montoya, J. M. Vertical transmission of sponge microbiota is inconsistent and unfaithful. Nat. Ecol. Evol. 3, 1172–1183 (2019).PubMed 
PubMed Central 

Google Scholar 
Webster, N. S. & Taylor, M. W. Marine sponges and their microbial symbionts: Love and other relationships. Environ. Microbiol. 14, 335–346 (2012).CAS 
PubMed 

Google Scholar 
Kennedy, J. et al. Evidence of a putative deep sea specific microbiome in marine sponges. PLoS ONE 9, e91092 (2014).ADS 
PubMed 
PubMed Central 

Google Scholar 
Steinert, G. et al. Compositional and quantitative insights into bacterial and archaeal communities of south pacific deep-sea sponges (Demospongiae and Hexactinellida). Front. Microbiol. 11, 716 (2020).Busch, K. et al. On giant shoulders: How a seamount affects the microbial community composition of seawater and sponges. Biogeosciences 17, 3471–3486 (2020).ADS 
CAS 

Google Scholar 
Olson, J. B. & Gao, X. Characterizing the bacterial associates of three Caribbean sponges along a gradient from shallow to mesophotic depths. FEMS Microbiol. Ecol. 85, 74–84 (2013).PubMed 

Google Scholar 
Steinert, G. et al. In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity. PeerJ 4, e1936 (2016).PubMed 
PubMed Central 

Google Scholar 
Morrow, K. M., Fiore, C. L. & Lesser, M. P. Environmental drivers of microbial community shifts in the giant barrel sponge, Xestospongia muta, over a shallow to mesophotic depth gradient. Environ. Microbiol. 18, 2025–2038 (2016).CAS 
PubMed 

Google Scholar 
Ebada, S. S. & Proksch, P. The chemistry of marine sponges. In Handbook of Marine Natural Products (eds Fattorusso, E. et al.) 191–293 (Springer, 2012). https://doi.org/10.1007/978-90-481-3834-0_4.Chapter 

Google Scholar 
Kornprobst, J.-M. Porifera (Sponges). Encyclopedia of Marine Natural Products (Wiley, 2014).
Google Scholar 
Leal, M. C., Puga, J., Serôdio, J., Gomes, N. C. M. & Calado, R. Trends in the discovery of new marine natural products from invertebrates over the last two decades—Where and what are we bioprospecting?. PLoS ONE 7, e30580 (2012).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Blunt, J. W., Copp, B. R., Keyzers, R. A., Munro, M. H. G. & Prinsep, M. R. Marine natural products. Nat. Prod. Rep. 34, 235–294 (2017).CAS 
PubMed 

Google Scholar 
Unson, M. D., Holland, N. D. & Faulkner, D. J. A brominated secondary metabolite synthesized by the cyanobacterial symbiont of a marine sponge and accumulation of the crystalline metabolite in the sponge tissue. Mar. Biol. 119, 1–11 (1994).CAS 

Google Scholar 
Bewley, C. A., Holland, N. D. & Faulkner, D. J. Two classes of metabolites from Theonella swinhoei are localized in distinct populations of bacterial symbionts. Experientia 52, 716–722 (1996).CAS 
PubMed 

Google Scholar 
Wilson, M. C. et al. An environmental bacterial taxon with a large and distinct metabolic repertoire. Nature 506, 58–62 (2014).ADS 
CAS 
PubMed 

Google Scholar 
Tianero, M. D., Balaich, J. N. & Donia, M. S. Localized production of defence chemicals by intracellular symbionts of Haliclona sponges. Nat. Microbiol. 4, 1149–1159 (2019).CAS 
PubMed 

Google Scholar 
Ivanišević, J., Thomas, O. P., Lejeusne, C., Chevaldonné, P. & Pérez, T. Metabolic fingerprinting as an indicator of biodiversity: Towards understanding inter-specific relationships among Homoscleromorpha sponges. Metabolomics 7, 289–304 (2011).
Google Scholar 
Pérez, T. et al. Oscarella balibaloi, a new sponge species (Homoscleromorpha: Plakinidae) from the Western Mediterranean Sea: Cytological description, reproductive cycle and ecology: O. balibaloi: Description, reproductive cycle and ecology. Mar. Ecol. (Berl.) 32, 174–187 (2011).ADS 

Google Scholar 
Reveillaud, J. et al. Relevance of an integrative approach for taxonomic revision in sponge taxa: Case study of the shallow-water Atlanto-Mediterranean Hexadella species (Porifera: Ianthellidae: Verongida). Invertebr. Syst. 26, 230–248 (2012).
Google Scholar 
Olsen, E. K. et al. Marine AChE inhibitors isolated from Geodia barretti: Natural compounds and their synthetic analogs. Org. Biomol. Chem. 14, 1629–1640 (2016).CAS 
PubMed 

Google Scholar 
Reverter, M., Perez, T., Ereskovsky, A. V. & Banaigs, B. Secondary metabolome variability and inducible chemical defenses in the Mediterranean Sponge Aplysina cavernicola. J. Chem. Ecol. 42, 60–70 (2016).CAS 
PubMed 

Google Scholar 
Reverter, M., Tribalat, M.-A., Pérez, T. & Thomas, O. P. Metabolome variability for two Mediterranean sponge species of the genus Haliclona: Specificity, time, and space. Metabolomics 14, 114 (2018).Villegas-Plazas, M. et al. Variations in microbial diversity and metabolite profiles of the tropical marine sponge Xestospongia muta with season and depth. Microb. Ecol. 78, 243–256 (2019).CAS 
PubMed 

Google Scholar 
Mohanty, I. et al. Multi-omic profiling of Melophlus sponges reveals diverse metabolomic and microbiome architectures that are non-overlapping with ecological neighbors. Mar. Drugs 18, 124 (2020).CAS 
PubMed Central 

Google Scholar 
Bowerbank, J. S. On the anatomy and physiology of the Spongiadae. Part I. On the spicula. Philos. Trans. R. Soc. Lond. 148, 279–332 (1858).ADS 

Google Scholar 
Vosmaer, G. C. J. The sponges of the ‘Willem Barents’ expedition 1880 and 1881. Bijdragen tot de Dierkunde 12, 1–47 (1885).
Google Scholar 
Radax, R. et al. Metatranscriptomics of the marine sponge Geodia barretti: Tackling phylogeny and function of its microbial community. Environ. Microbiol. 14, 1308–1324 (2012).CAS 
PubMed 

Google Scholar 
Topsent, E. Spongiaires provenant des campagnes scientifiques de la ‘Princesse Alice’ dans les Mers du Nord (1898–1899—1906–1907). Résultats des campagnes scientifiques accomplies par le Prince Albert I. Monaco 45, 1–67 (1913).
Google Scholar 
Yashayaev, I. & Loder, J. W. Further intensification of deep convection in the Labrador Sea in 2016. Geophys. Res. Lett. 44, 1429–1438 (2017).ADS 

Google Scholar 
Gutleben, J. et al. Diversity of tryptophan halogenases in sponges of the genus Aplysina. FEMS Microbiol. Ecol. 95, fiz108 (2019).CAS 
PubMed 
PubMed Central 

Google Scholar 
Indraningrat, A. et al. Cultivation of sponge-associated bacteria from Agelas sventres and Xestospongia muta collected from different depths. Mar. Drugs 17, 578 (2019).CAS 
PubMed Central 

Google Scholar 
Ramiro-Garcia, J. et al. NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes. F1000 Res. 5, 1791 (2018).
Google Scholar 
Yilmaz, P. et al. The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucl. Acids Res. 42, D643–D648 (2014).CAS 
PubMed 

Google Scholar 
Erngren, I., Smit, E., Pettersson, C., Cárdenas, P. & Hedeland, M. The effects of sampling and storage conditions on the metabolite profile of the marine sponge Geodia barretti. Front. Chem. 9:662659 (2021)Smith, C. A., Want, E. J., O’Maille, G., Abagyan, R. & Siuzdak, G. XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem. 78, 779–787 (2006).CAS 
PubMed 

Google Scholar 
Kuhl, C., Tautenhahn, R., Böttcher, C., Larson, T. R. & Neumann, S. CAMERA: An integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Anal. Chem. 84, 283–289 (2012).CAS 
PubMed 

Google Scholar 
Oksanen, J. et al. vegan: Community Ecology Package (2017).Dat, T. T. H., Steinert, G., Thi Kim Cuc, N., Smidt, H. & Sipkema, D. Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam. PeerJ 6, e4970 (2018).PubMed 
PubMed Central 

Google Scholar 
Miller, M. A., Pfeiffer, W. & Schwartz, T. Creating the CIPRES science gateway for inference of large phylogenetic trees. In 2010 Gateway Computing Environments Workshop (GCE) 1–8 (IEEE, 2010). https://doi.org/10.1109/GCE.2010.5676129.Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v4: Recent updates and new developments. Nucl. Acids Res. 47, W256–W259 (2019).CAS 
PubMed 
PubMed Central 

Google Scholar 
Thévenot, E. A., Roux, A., Xu, Y., Ezan, E. & Junot, C. Analysis of the human adult urinary metabolome variations with age, body mass index, and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. J. Proteome Res. 14, 3322–3335 (2015).PubMed 

Google Scholar 
Weiss, S. et al. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J. 10, 1669–1681 (2016).CAS 
PubMed 
PubMed Central 

Google Scholar 
Deng, Y. et al. Molecular ecological network analyses. BMC Bioinform. 13, 113 (2012).
Google Scholar 
Friedman, J. & Alm, E. J. Inferring correlation networks from genomic survey data. PLoS Comput. Biol. 8, e1002687 (2012).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Durno, W. E., Hanson, N. W., Konwar, K. M. & Hallam, S. J. Expanding the boundaries of local similarity analysis. BMC Genom. 14, S3 (2013).
Google Scholar 
Reshef, D. N. et al. Detecting novel associations in large data sets. Science 334, 1518–1524 (2011).ADS 
CAS 
PubMed 
PubMed Central 
MATH 

Google Scholar 
Hall, M. M., Torres, D. J. & Yashayaev, I. Absolute velocity along the AR7W section in the Labrador Sea. Deep Sea Res. Part 1 Oceanogr. Res. Pap. 72, 72–87 (2013).
Google Scholar 
Reveillaud, J. et al. Host-specificity among abundant and rare taxa in the sponge microbiome. ISME J. 8, 1198–1209 (2014).CAS 
PubMed 
PubMed Central 

Google Scholar 
Moitinho-Silva, L. et al. Predicting the HMA-LMA status in marine sponges by machine learning. Front. Microbiol. 8, 752 (2017).Lidgren, G., Bohlin, L. & Bergman, J. Studies of Swedish marine organisms VII. A novel biologically active indole alkaloid from the sponge Geodia barretti. Tetrahedron Lett. 27, 3283–3284 (1986).CAS 

Google Scholar 
Sjögren, M. et al. Antifouling activity of brominated cyclopeptides from the marine sponge Geodia barretti. J. Nat. Prod. 67, 368–372 (2004).PubMed 

Google Scholar 
Sölter, S. Identifizierung und Synthese von Naturstoffen aus Borealen Schwämmen (Universität Hamburg, 2004).
Google Scholar 
Di, X. et al. 6-Bromoindole derivatives from the Icelandic marine sponge Geodia barretti: Isolation and anti-inflammatory activity. Mar. Drugs 16, 437 (2018).CAS 
PubMed Central 

Google Scholar 
Carstens, B. B. et al. Isolation, characterization, and synthesis of the barrettides: Disulfide-containing peptides from the marine sponge Geodia barretti. J. Nat. Prod. 78, 1886–1893 (2015).CAS 
PubMed 

Google Scholar 
Hedner, E. et al. Brominated cyclodipeptides from the marine sponge Geodia barretti as selective 5-HT ligands. J. Nat. Prod. 69, 1421–1424 (2006).CAS 
PubMed 

Google Scholar 
Hedner, E. et al. Antifouling activity of a dibrominated cyclopeptide from the marine sponge Geodia barretti. J. Nat. Prod. 71, 330–333 (2008).CAS 
PubMed 

Google Scholar 
Erwin, P. M., Pita, L., López-Legentil, S. & Turon, X. Stability of sponge-associated bacteria over large seasonal shifts in temperature and irradiance. Appl. Environ. Microbiol. 78, 7358–7368 (2012).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Cárdenas, C. A., Bell, J. J., Davy, S. K., Hoggard, M. & Taylor, M. W. Influence of environmental variation on symbiotic bacterial communities of two temperate sponges. FEMS Microbiol. Ecol. 88, 516–527 (2014).PubMed 

Google Scholar 
Glasl, B., Smith, C. E., Bourne, D. G. & Webster, N. S. Exploring the diversity-stability paradigm using sponge microbial communities. Sci. Rep. 8, 8425 (2018).Schöttner, S. et al. Relationships between host phylogeny, host type and bacterial community diversity in cold-water coral reef sponges. PLoS ONE 8, e55505 (2013).ADS 
PubMed 
PubMed Central 

Google Scholar 
Lurgi, M., Thomas, T., Wemheuer, B., Webster, N. S. & Montoya, J. M. Modularity and predicted functions of the global sponge-microbiome network. Nat. Commun. 10, 992 (2019).ADS 
PubMed 
PubMed Central 

Google Scholar 
Luter, H. M. et al. Microbiome analysis of a disease affecting the deep-sea sponge Geodia barretti. FEMS Microbiol. Ecol. 93, fix074 (2017).Thistle, D. Ecosystems of the Deep Oceans (Elsevier, 2003).
Google Scholar 
Pita, L., Erwin, P. M., Turon, X. & López-Legentil, S. Till death do us part: Stable sponge-bacteria associations under thermal and food shortage stresses. PLoS ONE 8, e80307 (2013).ADS 
PubMed 
PubMed Central 

Google Scholar 
Webster, N. S., Cobb, R. E. & Negri, A. P. Temperature thresholds for bacterial symbiosis with a sponge. ISME J. 2, 830–842 (2008).CAS 
PubMed 

Google Scholar 
Gerringer, M. E., Drazen, J. C. & Yancey, P. H. Metabolic enzyme activities of abyssal and hadal fishes: Pressure effects and a re-evaluation of depth-related changes. Deep Sea Res. Part 1 Oceanogr. Res. Pap. 125, 135–146 (2017).CAS 

Google Scholar 
Yashayaev, I. Hydrographic changes in the Labrador Sea, 1960–2005. Prog. Oceanogr. 73, 242–276 (2007).ADS 

Google Scholar 
Rhein, M., Steinfeldt, R., Kieke, D., Stendardo, I. & Yashayaev, I. Ventilation variability of Labrador Sea Water and its impact on oxygen and anthropogenic carbon: A review. Philos. Trans. A Math. Phys. Eng. Sci. 375, 20160321 (2017).ADS 
PubMed 
PubMed Central 

Google Scholar 
Galand, P. E., Potvin, M., Casamayor, E. O. & Lovejoy, C. Hydrography shapes bacterial biogeography of the deep Arctic Ocean. ISME J. 4, 564–576 (2010).PubMed 

Google Scholar 
Frank, A. H., Garcia, J. A. L., Herndl, G. J. & Reinthaler, T. Connectivity between surface and deep waters determines prokaryotic diversity in the North Atlantic Deep Water: North Atlantic dark ocean prokaryotic biogeography. Environ. Microbiol. 18, 2052–2063 (2016).PubMed 
PubMed Central 

Google Scholar 
Agogué, H., Lamy, D., Neal, P. R., Sogin, M. L. & Herndl, G. J. Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing. Mol. Ecol. 20, 258–274 (2011).PubMed 

Google Scholar 
Djurhuus, A., Boersch-Supan, P. H., Mikalsen, S.-O. & Rogers, A. D. Microbe biogeography tracks water masses in a dynamic oceanic frontal system. R. Soc. Open Sci. 4, 170033 (2017).ADS 
PubMed 
PubMed Central 

Google Scholar 
Müller, O. et al. Spatiotemporal dynamics of ammonia-oxidizing Thaumarchaeota in distinct Arctic water masses. Front. Microbiol. 9, 1–13 (2018).ADS 

Google Scholar 
Kraemer, S., Ramachandran, A., Colatriano, D., Lovejoy, C. & Walsh, D. A. Diversity and biogeography of SAR11 bacteria from the Arctic Ocean. ISME J. https://doi.org/10.1038/s41396-019-0499-4 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Monier, A. et al. Upper Arctic Ocean water masses harbor distinct communities of heterotrophic flagellates. Biogeosciences 10, 4273–4286 (2013).ADS 

Google Scholar 
Monier, A. et al. Oceanographic structure drives the assembly processes of microbial eukaryotic communities. ISME J. 9, 990–1002 (2015).CAS 
PubMed 

Google Scholar 
Corrège, T. The relationship between water masses and benthic ostracod assemblages in the western Coral Sea, Southwest Pacific. Palaeogeogr. Palaeoclimatol. Palaeoecol. 105, 245–266 (1993).
Google Scholar 
Muhling, B. A., Beckley, L. E., Koslow, J. A. & Pearce, A. F. Larval fish assemblages and water mass structure off the oligotrophic south-western Australian coast: SW Australian larval fish assemblages. Fish. Oceanogr. 17, 16–31 (2007).
Google Scholar 
Eerkes-Medrano, D. et al. A community assessment of the demersal fish and benthic invertebrates of the Rosemary Bank Seamount Marine Protected Area (NE Atlantic). Deep Sea Res. Part 1 Oceanogr. Res. Pap. https://doi.org/10.1016/j.dsr.2019.103180 (2019).Article 

Google Scholar 
Puerta, P. et al. Influence of water masses on the biodiversity and biogeography of deep-sea benthic ecosystems in the North Atlantic. Front. Mar. Sci. 7, 239 (2020).Roberts, E. et al. Water masses constrain the distribution of deep-sea sponges in the North Atlantic Ocean and Nordic Seas. Mar. Ecol. Prog. Ser. 659, 75–96 (2021).ADS 

Google Scholar 
Kenchington, E. et al. Connectivity modelling of areas closed to protect vulnerable marine ecosystems in the northwest Atlantic. Deep Sea Res. Part 1 Oceanogr. Res. Pap. 143, 85–103 (2019).
Google Scholar 
Louca, S. et al. Function and functional redundancy in microbial systems. Nat. Ecol. Evol. 2, 936–943 (2018).PubMed 

Google Scholar 
McCauley, M., Chiarello, M., Atkinson, C. L. & Jackson, C. R. Gut microbiomes of freshwater mussels (Unionidae) are taxonomically and phylogenetically variable across years but remain functionally stable. Microorganisms 9, 411 (2021).CAS 
PubMed 
PubMed Central 

Google Scholar 
Page, M., West, L., Northcote, P., Battershill, C. & Kelly, M. Spatial and temporal variability of cytotoxic metabolites in populations of the New Zealand Sponge Mycale hentscheli. J. Chem. Ecol. 31, 1161–1174 (2005).CAS 
PubMed 

Google Scholar 
Ternon, E., Perino, E., Manconi, R., Pronzato, R. & Thomas, O. P. How environmental factors affect the production of guanidine alkaloids by the Mediterranean sponge Crambe crambe. Mar. Drugs 15, 181 (2017).PubMed Central 

Google Scholar 
Sacristán-Soriano, O., Banaigs, B. & Becerro, M. A. Temporal trends in the secondary metabolite production of the sponge Aplysina aerophoba. Mar. Drugs 10, 677–693 (2012).PubMed 
PubMed Central 

Google Scholar 
Ivanisevic, J. et al. Biochemical trade-offs: Evidence for ecologically linked secondary metabolism of the sponge Oscarella balibaloi. PLoS ONE 6, e28059 (2011).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Burg, M. B. & Ferraris, J. D. Intracellular organic osmolytes: Function and regulation. J. Biol. Chem. 283, 7309–7313 (2008).CAS 
PubMed 
PubMed Central 

Google Scholar 
Nau-Wagner, G., Boch, J., Le Good, J. A. & Bremer, E. High-affinity transport of choline-O-sulfate and its use as a compatible solute in Bacillus subtilis. Appl. Environ. Microbiol. 65, 560–568 (1999).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Popowich, A., Zhang, Q. & Le, X. C. Arsenobetaine: The ongoing mystery. Natl. Sci. Rev. 3, 451–458 (2016).CAS 

Google Scholar 
Connor, K. M. & Gracey, A. Y. High-resolution analysis of metabolic cycles in the intertidal mussel Mytilus californianus. Am. J. Physiol. Regul. Integr. Comp. Physiol. 302, R103–R111 (2012).CAS 
PubMed 

Google Scholar 
Cárdenas, P. Who produces Ianthelline? The Arctic sponge Stryphnus fortis or its sponge Epibiont Hexadella dedritifera: A probable case of sponge–sponge contamination. J. Chem. Ecol. 42, 339–347 (2016).PubMed 

Google Scholar 
Steffen, K. et al. Barrettides: A peptide family specifically produced by the deep-sea sponge Geodia barretti. J. Nat. Prod. 84, 3138–3146 (2021).CAS 
PubMed 
PubMed Central 

Google Scholar 
Abbamondi, G. R., De Rosa, S., Iodice, C. & Tommonaro, G. Cyclic dipeptides produced by marine sponge-associated bacteria as quorum sensing signals. Nat. Prod. Commun. 9, 229–232 (2014).CAS 
PubMed 

Google Scholar 
Kasheverov, I. et al. 6-Bromohypaphorine from Marine Nudibranch Mollusk Hermissenda crassicornis is an agonist of human α7 nicotinic acetylcholine receptor. Mar. Drugs 13, 1255–1266 (2015).CAS 
PubMed 
PubMed Central 

Google Scholar 
Moitinho-Silva, L. et al. The sponge microbiome project. Gigascience 6, 1–7 (2017).CAS 
PubMed 

Google Scholar 
Kielak, A. M., Barreto, C. C., Kowalchuk, G. A., van Veen, J. A. & Kuramae, E. E. The ecology of acidobacteria: Moving beyond genes and genomes. Front. Microbiol. 7, 744 (2016).Crits-Christoph, A., Diamond, S., Butterfield, C. N., Thomas, B. C. & Banfield, J. F. Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis. Nature 558, 440–444 (2018).ADS 
CAS 
PubMed 

Google Scholar  More

To our knowledge, this study provides the first recorded information on the active swimming of Japanese eels and on their transport by currents in the open ocean. Specifically, the strong flow of the KC largely dominated the movements of the eels and transported them northeastward while they swam mainly southward, and active swimming contributed a little to their travel trajectories. In contrast, the swimming of eels made a relatively higher contribution to their travel trajectories in the TS area.Our in situ estimates of the mean swimming speeds of Japanese eels (26–41 cm/s) were similar or slightly lower than those of European eels. In the acoustic tracking experiment of European eels considering environmental current vectors, their swimming speeds were 35–58 cm/s in the coastal midwater26. In a laboratory experiment using stamina tunnels with stable temperatures, the optimal swimming speeds of European eels were estimated to be 61–68 cm/s (0.74–1.02 BL/s)56, which were higher than the in situ estimates. The minimum swimming speed of European eels is considered to be 40 cm/s if they will arrive at their spawning area in the Sargasso Sea (distance of 5500 km) in 6 months, and their optimal swimming speeds were sufficient to migrate over the long distance in time for the near-spawning period after escape from their growth habitats56. However, field studies using PSAT tagging also reported that in situ migration speeds (including transport by currents) were less than the optimal swimming speeds and suggested that some European eels could reach their spawning area within the near-spawning periods and that others only arrive in time for the following spawning season19.Our estimated effective swimming speed of Japanese eels, all day and all night over the tracking periods, ranged from 3 to 30 cm/s with individual variations. These estimates were consistent with the swimming speeds (excluding transport by currents) of 2.2–15.1 km/day (2–18 cm/s) estimated in the PSAT study of Japanese eels14. Silver-phase Japanese eels start migrating from their coastal growth habitats in Japan primarily in October to December57, 58, and spawning near the West Mariana Ridge occurs in April to August33, 35. Numerical models assuming that migrating eels use true navigation (readjusted compass) or a constant compass heading (fixed compass from the departure place to the spawning site) indicate that the minimal swimming speed required to arrive at the spawning area within 8 months is 10–12 cm/s37. Our estimated effective swimming speeds of five out of ten eels during the day and eight out of ten eels during the night were similar or higher than these minimal speeds. The low effective swimming speeds frequently observed during the day might be due to the relatively low values observed in the swimming speed at 10 min intervals and the swimming directions often varying during the day. When eels swim with stable orientation, as observed in three of the eels (WE2999_TS, WE3001_TS, and WE3002_TS) during the night, the effective swimming speeds exceeded 25 cm/s. If such a stable orientation is maintained and compensate the low speeds during the day, the eels that leave during autumn and winter will be able to arrive at the spawning area during the next spring to summer.It should also be noted that the swimming speeds in body length per second were significantly higher in shallow water during the night than in deep water during the day. In the open ocean, anguillid species exhibit DVMs during oceanic migration, swimming at depth during the day and in the shallows during the night9,10,11,12,13,14,15,16,17,18,19,20,21,22. These DVMs are likely related to the possible avoidance from visual predators under light conditions19 or maturation control59. Essentially, through the DVMs, the eels encounter low temperatures ( 20 °C) during the same day. Generally, the swimming speeds of fishes are restricted by the ambient water temperature60, and the water temperature encountered through DVMs might influence the horizontal-swimming speeds of Japanese eels.Other factors besides swimming speed are important for the success of eel migrations, such as adapting to mesopelagic zones that silver eels undergo during their spawning migrations. The most important and obvious morphological adaptation in mesopelagic fish is their well-developed eyes, and migrating eels also seem to use this strategy. These fish often have relatively large pupils61, high photosensitive structures, such as tubular eyes62, a pure rod multibank retina63, and maximum rhodopsin absorption to adapt to the blue-green light in the deep sea64. The eyes of catadromous eels displayed enlargement during their transformation into migrating silver-phase eels65, 66 and potentially increase their retinal surface area, which results in the possibility of increased photon capture. In addition, the rhodopsins in the eyes change from a freshwater type with a maximum absorption of ~ 500 nm to a deep-sea type with a maximum absorption of ~ 480 nm67,68,69. Their extreme sensitivity to light is evident through their DVM in mesopelagic water, where the timing of a large descent and ascent in the DVM demonstrated by migrating catadromous eels is precisely synchronized with sunrise and sunset. Furthermore, eels alter their swimming depth in response to the phase of the Moon9, 15, 20, 21, appearing to be capable of perceiving extremely low-intensity moonlight.This study showed that three eels released in the TS area (mainly 300–400-m depth) and one eel in the KC area (near surface) were found to change their swimming direction around the time of the solar culmination when the Sun’s bearing changed. The clockwise and counterclockwise trajectories of these eels corresponded to whether the Sun moved from the east to west in the southern and northern sky, suggesting that they demonstrated horizontal negative phototaxis swimming to avoid sunlight. They might move to avoid high-intensity sunlight horizontally, not vertically, as they gradually increase the swimming depths possibly due to acclimation to cold deep water after release. The daytime swimming depths of the eels became deeper day-by-day after their release (Fig. 4); a similar phenomenon was observed in European eels12, American eels17, and long fin eels13. Recently, Higuchi et al.20 observed that the daytime swimming depths of Japanese eels released in the TS area gradually became deeper until 13 days after their release. These facts indicate that they gradually acclimate to the cold water at the deep depths after release. Since this tracking study was conducted 2–8 days after their release, the daytime swimming depth of eels would not have reached a steady state yet. The relatively high intensity from sunlight at the shallow depths where eels swam immediately after release in the TS area might cause horizontal avoidance behavior from the light.In other cases, many eels, especially those released in the KC area, did not demonstrate the rotational behavior. The eels in the KC area mostly stayed deeper (500–800 m) during the day than the eels in the TS area (stayed at depths of 300–600 m) even during the periods shortly after their release. This is possibly due to higher water temperatures even at the deeper depths in the KC area (Fig. 4). The eels in the TS area did not demonstrate clear rotational behavior at depths of more than 400 m. The PSAT studies have reported that the steady swimming depths during the day were 500–800 m14, 20. Therefore, it was assumed that the rotational behavior observed in some eels was not a regular behavior during their migration. However, the rotational behavior observed in this study suggests that they surely perceive the horizontal direction of Sun’s bearing at 400 m depths at least. Generally, they exhibit DVM precisely synchronizing with sunrise and sunset and surely perceive the change in sunlight intensity at deeper depths9,10,11,12,13,14,15,16,17,18,19,20,21,22. Even though the rotational behavior were not observed below 400 m, it remains unknown whether the eels could not perceive the Sun’s bearing from the light penetrated at depth; thus, further investigation of response to underwater light is required in future.While possible negative phototaxis behaviors were observed in some eels after release around the time of solar culmination, the trajectories of ten eels during the entire period of tracking experiments implied that each eel tended to swim meridionally toward the bearing of the Sun at culmination. We observed that eels released at middle (20°–34° N) and low (12°–13°N) latitudes tended to swim southward and northward in the meridional direction, respectively (Fig. 6A, B). The tendency to move in a north–south swimming direction corresponded to whether the Sun culminated to the north or south: eels swam southward if the culmination occurred in the southern sky, but they swam northward if it occurred in the northern sky (Fig. 6). In the KC area (33°–35° N), the Sun rose in the southeast, passed celestial meridian in the southern sky, and set in the southwest (Fig. 6C). At 20° N in the summer time when the tracking study was conducted, the Sun also passed a celestial meridian in the southern sky, but rose in the northeast and set in the northwest (Fig. 6C). When Sun culmination occurred in the southern sky, the meridional swimming directions tended to be southward (Fig. 6A). However, at 12° to 13° N in the summer time, the Sun rose in the northeast, passed the celestial meridian in the northern sky, and set in the northwest (Fig. 6D). When the Sun at culmination appeared in the northern sky, the meridional swimming directions tended to be northward (Fig. 6B). Furthermore, the swimming behavior by one eel (WE4264_TS) that was released slightly south (14° 15′ N) from the latitude with the Sun passing through the zenith was also indicative of the meridional swimming traits. This eel moved in a northerly direction on the first day, but then it lost its north–south bias in swimming around 14° 30′ N, where the Sun nearly passed through the zenith (Figs. 1 and 6D). These observations imply that the eels might move toward the latitude with the Sun passing through the zenith.Figure 6Swimming trajectories of eels and solar paths in the celestial sphere viewed from east during each tracking period. Swimming trajectories of eels released at (A) 20°N in the tropical–subtropical area and the Kuroshio Current area, and (B) 12°–14°15′N in the tropical–subtropical area. Solar paths through the north (N)–south (S) axis and the zenith at the time of tracking in (C) 20°N in the tropical–subtropical area and the Kuroshio Current area, and (D) 12°–14°15′N in the tropical–subtropical area.Full size imageTheoretically, it is possible for mesopelagic animals to use solar cues for navigation at depths shallower than the asymptotic depth, below which penetrating light rays are symmetrical around the vertical axis and the polarization plane becomes horizontal. For example, the Sargasso Sea, where the two Atlantic catadromous eels spawn1, 3, has extremely transparent water70, and the major axis of radiance distribution still remains tilted in the mesopelagic zone. The angle of maximum radiance of sunlight at 475 nm was 13° at depths of 400 m when the Sun’s elevation was 60° (Fig. 7)52, 53. In highly transparent water, the asymptotic depth could be as high as 1000–1200 m, and the depths below this cannot be utilized for compass use53. Currently, it is not possible to verify whether the Sun culminating to north or south caused the meridional swimming tendencies of eels in this study. Potentially, these meridional swimming tendencies could be due to other orientation clues, such as the geomagnetic field, as discussed for temperate anguillid eels17, 45. Nevertheless, in future studies, it would be worthwhile considering solar cues as a possible candidate factor in the orientation of eels, even when under faint underwater light conditions.Figure 7Optical features of underwater sunlight. (A) Schematic diagram of sunlight penetrating the deep ocean at 90° to the solar bearing. The line of arrows indicates the major axis of the incident beam in a vertical plane perpendicular to the Sun’s bearing. Blue light (around 475 nm) reaches the lowest depths. With increasing depth, the light field alters its character into a less directed distribution and a lower energetic level through scattering and absorption processes. Penetrating light rays are symmetrical around the region below the asymptotic depth. (B) An example of spectral radiance distribution (e. g. 475 nm) at a certain depth. The radiance distribution is shown by an ellipsoid and the major axis is drawn by a line with arrow. The refracted angular deviation (a) of the major axis of underwater radiance distribution from the vertical axis equals the tilt of the electric vector (ee bar) from the horizontal axis53. When the Sun’ s elevation was 60° in the Sargasso Sea, the radiance distributions were measured at three different depths and the tilt of the electric vector were estimated to be 24° at depths of 100 m and 200 m and 13° at depth of 400 m52, 53.Full size imageGiven that eels might be able to use the Sun’s bearing at culmination to orient their meridional swimming direction, this orientation scheme could support a clockwise eel migration route following a partial subtropical gyre2, 37. Japanese eels that departed from the nursery area first transported northeastward via the strong KC. Maintaining southward swimming in the current, they eventually crossed the current and shifted to the southward migration course. When they enter the KC, movement to the left of the bearing of the Sun at culmination (i.e., south) is the typical pattern for the early migration of eels from Japan. The movements of eels observed in the KC were consistent with the expected route; however, eels released at low latitudes of the TS area often swam northward but also westward, which resulted in their traveling an unreasonable distance from the spawning area. This might be due to their behavior during early migration. In this study, eels were transported from Japan and released into the open ocean at low latitudes. They might have swum toward the expected bearing of the Sun at culmination as if they were in the north and moved to the left of the Sun’s bearing along with the North Equatorial Current, which would mimic the early migration of eels leaving Japan and moving along the KC.Among the eels tracked in this study were individuals with impaired swim bladders, yellow-phase eels in the process of hormone-treatment maturation, and silver-phase eels collected from different rivers in different years. Despite these variations, the swimming characteristics of the eels did not differ in terms of their DVM behavior16 and swimming speed. Nevertheless, confirmation of our results using samples with a uniform status in future research would be highly desirable. In this study, the tracked eel position was assumed to be identical to that of the tracking ship and the errors between these two positions could not be evaluated; thus, the positioning of tracked fish also may need to be improved in future studies. Experimental studies, such as tracking of blind, magnetically disturbed, or olfactory-blocked eels, could help obtain or eliminate alternative candidate clues and enhance our understanding of the navigational system of anguillid eels. Controlled laboratory experiments are required to directly quantify the ability of eels to perceive radiance distribution or polarization, along with any associated behaviors. In addition, the internal clock of eels required to perform celestial navigation should be investigated. Meanwhile, the results obtained from this study can enhance our knowledge of the mechanisms underlying the migratory behaviors of eels in the open ocean. More

Hutchinson, G. E. An Introduction to Population Ecology (Yale University, 1978).MATH 

Google Scholar 
Erb, J., Boyce, M. S. & Stenseth, N. C. Population dynamics of large and small mammals. Oikos 92, 3–12 (2001).
Google Scholar 
Gaillard, J. M., Festa-Bianchet, M. & Yoccoz, N. G. Population dynamics of large herbivores: Variable recruitment with constant adult survival. Trends Ecol. Evol. 13, 58–63 (1998).CAS 
PubMed 

Google Scholar 
Dennis, B., Ponciano, J. M., Lele, S. R., Taper, M. L. & Staples, D. F. Estimating density dependence, process noise, and observation error. Ecol. Monogr. 76, 323–341 (2006).
Google Scholar 
Rockwood, L. L. Introduction to Population Ecology (Wiley, 2015).
Google Scholar 
Caughley, G. Directions in conservation biology. J. Anim. Ecol. 63, 215–244 (1994).
Google Scholar 
Hoffmann, M. et al. The impact of conservation on the status of the world’s vertebrates. Science 330, 1503–1509 (2010).ADS 
CAS 
PubMed 

Google Scholar 
Ripple, W. J. et al. Collapse of the world’s largest herbivores. Sci. Adv. 1, e1400103 (2015).ADS 
PubMed 
PubMed Central 

Google Scholar 
Dickinson, A. B. A History of Sealing in the Falkland Island and Dependencies, 1764–1972. Doctoral dissertation, Scott Polar Research Institute, University of Cambridge. (1987).Clapham, P. J. & Baker, C. S. Whaling, modern. In Encyclopedia of Marine Mammals (eds Perrin, W. F. et al.) 1070–1074 (Academic Press, 2018).
Google Scholar 
Reeves, R. R. The origins and character of ‘aboriginal subsistence’ whaling: a global review. Mamm. Rev. 32, 71–106 (2002).
Google Scholar 
Reeves, R. R. Hunting of marine mammals. In Encyclopedia of Marine Mammals (eds Perrin, W. F. et al.) 585–588 (Academic Press, 2009).
Google Scholar 
Magera, A. M., Flemming, J. E. M., Kaschner, K., Christensen, L. B. & Lotze, H. K. Recovery trends in marine mammal populations. PLoS One 8, e77908 (2013).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Tulloch, V. J., Plagányi, É. E., Matear, R., Brown, C. J. & Richardson, A. J. Ecosystem modelling to quantify the impact of historical whaling on Southern Hemisphere baleen whales. Fish Fish. 19, 117–137 (2017).
Google Scholar 
Best, P. B. Increase rates in severely depleted stocks of baleen whales. ICES J. Mar. Sci. 50, 169–186 (1993).
Google Scholar 
Townsend, C. H. The distribution of certain whales as shown by logbook records of American whaleships. Zool. Sci. Contr. New York Zool. Soc. 19, 1–50 (1935).MathSciNet 

Google Scholar 
Du Pasquier, J. T. Les baleiniers français au XIXe siècle, 1814–1868 (Terre et mer, 1982).Richards, R. Into the South Seas: The Southern Whale Fishery Comes of Age on the Brazil Banks 1765 to 1812 (The Paramatta Press, 1993).
Google Scholar 
International Whaling Commission. Report of the workshop on the comprehensive assessment of right whales: A worldwide comparison. J. Cetacean Res. Manag. (Special Issue) 2, 1–60 (2001).
Google Scholar 
Jackson, J., Patenaude, N., Carroll, E. & Baker, C. S. How few whales were there after whaling? Inference from contemporary mtDNA diversity. Mol. Ecol. 17, 236–251 (2008).CAS 
PubMed 

Google Scholar 
Tormosov, D. D. et al. Soviet catches of southern right whales Eubalaena australis, 1951–1971. Biological data and conservation implications. Biol. Conserv. 86, 185–197 (1998).
Google Scholar 
International Whaling Commission. Report of the IWC workshop on the assessment of Southern Right whales. J. Cetacean Res. Manag. (Supp) 14, 439–462 (2013).
Google Scholar 
Carroll, E. L. et al. Accounting for female reproductive cycles in a superpopulation capture–recapture framework. Ecol. Appl. 23, 1677–1690 (2013).CAS 
PubMed 

Google Scholar 
Brandão, A., Vermeulen, E., Ross-Gillespie, A., Findlay, K. & Butterworth, D. Updated application of a photo-identification based assessment model to southern right whales in South African waters, focussing on inferences to be drawn from a series of appreciably lower counts of calving females over 2015 to 2017. IWC SC/67b/SH/22 (2018).Bannister, J. L. Project A7- Monitoring Population Dynamics of ‘Western’ Right Whales off Southern Australia 2015–2018. Final report to National Environment Science Program, Australian Commonwealth Government. (2017).Stamation, K., Watson, M., Moloney, P., Charlton, C. & Bannister, J. L. Population estimate and rate of increase of Southern Right whales Eubalaena australis in Southeastern Australia. Endanger. Species Res. 41, 373–383 (2020).
Google Scholar 
Baker, C. S., Patenaude, N. J., Bannister, J. L., Robins, J. & Kato, H. Distribution and diversity of mtDNA lineages among southern right whales (Eubalaena australis) from Australia and New Zealand. Mar. Biol. 134, 1–7 (1999).CAS 

Google Scholar 
Patenaude, N. J. et al. Mitochondrial DNA diversity and population structure among southern right whales (Eubalaena australis). J. Hered. 98, 147–157 (2007).CAS 
PubMed 

Google Scholar 
Carroll, E. L. et al. Population structure and individual movement of southern right whales around New Zealand and Australia. Mar. Ecol. Prog. Ser. 432, 257–268 (2011).ADS 
CAS 

Google Scholar 
Cooke, J. G., Rowntree, V. J. & Payne, R. Estimates of demographic parameters for southern right whales (Eubalaena australis) observed off Península Valdés, Argentina. J. Cetacean Res. Manag. (Special Issue) 2, 125–132 (2001).
Google Scholar 
Cooke, J., Rowntree, V. & Sironi, M. Southwest Atlantic right whales: interim updated population assessment from photo-id collected at Península Valdéz, Argentina. IWC SC/66a/BRG/23 (2015).Crespo, E. A. et al. The southwestern Atlantic southern right whale, Eubalaena australis, population is growing but at a decelerated rate. Mar. Mamm. Sci. 35, 93–107 (2019).
Google Scholar 
Groch, K. R., Palazzo, J. T. Jr., Flores, P. A. C., Adler, F. R. & Fabian, M. E. Recent rapid increases in the right whale (Eubalaena australis) population off southern Brazil. LAJAM 4, 41–47 (2005).
Google Scholar 
Danilewicz, D., Moreno, I. B., Tavares, M. & Sucunza, F. Southern right whales (Eubalaena australis) off Torres, Brazil: group characteristics, movements, and insights into the role of the Brazilian-Uruguayan wintering ground. Mammalia 81, 225–234 (2017).
Google Scholar 
Costa, P., Praderi, R., Piedra, M. & Franco-Fraguas, P. Sightings of southern right whales, Eubalaena australis, off Uruguay. LAJAM 4, 157–161 (2005).
Google Scholar 
Lodi, L. & Tardelli, R. M. Southern right whale on the coast of Rio de Janeiro State, Brazil: Conflict between conservation and human activity. J. Mar. Biol. Ass. UK 87, 105–107 (2007).
Google Scholar 
Belgrano, J., Iñíguez, M., Gibbons, J., García, C. & Olavarría, C. South-west Atlantic right whales Eubalaena australis (Desmoulins, 1822) distribution nearby the Magellan Strait. Anales Instituto Patagonia (Chile) 36, 69–74 (2008).
Google Scholar 
Belgrano, J., Kröhling, F., Arcucci, D., Melcón, M. & Iñíguez, M. First Southern right whale aerial surveys in Golfo San Jorge, Santa Cruz, Argentina. IWC SC/63/BRG11 (2011).Arias, M. et al. Southern right whale Eubalaena australis in Golfo San Matías (Patagonia, Argentina): Evidence of recolonisation. PloS One 13(12), e0207524 (2018).CAS 
PubMed 
PubMed Central 

Google Scholar 
Mandiola, M. A. et al. Half a century of sightings data of southern right whales in Mar del Plata (Buenos Aires, Argentina). J. Mar. Biol. Ass. UK 100, 165–171 (2020).
Google Scholar 
Weir, C. R. & Stanworth, A. The Falkland Islands (Malvinas) as sub-Antarctic foraging, migratory and wintering habitat for southern right whales. J. Mar. Biol. Ass. UK 100, 153–163 (2020).
Google Scholar 
Du Pasquier, T. Catch history of French right whaling mainly in the South Atlantic. Right whales: Past and present status. Rep. Int. Whaling Commission (Special Issue) 10, 269–274 (1986).
Google Scholar 
Best, P. B. Estimates of the landed catch of right (and other whalebone) whales in the American fishery, 1805–1909. Fish. Bull. 85, 403–418 (1987).
Google Scholar 
Rowntree, V., Groch, K. R., Vilches, F. & Sironi, M. Sighting Histories of 124 Southern Right Whales Recorded off Both Southern Brazil and Península Valdés, Argentina, between 1971 and 2017. IWC SC/68B/CMP/20 (2020).Zerbini, A. N., et al. Satellite tracking of Southern right whales (Eubalaena australis) from Golfo San Matias, Rio Negro Province, Argentina. IWC SC/67b/CMP/17 (2018).Rowntree, V. J., Valenzuela, L. O., Fraguas, P. F. & Seger, J. Foraging behaviour of Southern Right Whales (Eubalaena australis) inferred from variation of carbon stable isotope ratios in their baleen. IWC SC/60/BRG23 (2008).Vighi, M. A. et al. Stable isotopes indicate population structuring in the Southwest Atlantic population of right whales (Eubalaena australis). PLoS One 9, e90489 (2014).ADS 
PubMed 
PubMed Central 

Google Scholar 
Valenzuela, L. O., Rowntree, V. J., Sironi, M. & Seger, J. Stable isotopes (d15N, d13C, d34S) in skin reveal diverse food sources used by southern right whales Eubalaena australis. Mar. Ecol. Prog. Ser. 603, 243–255 (2018).ADS 
CAS 

Google Scholar 
Ott, P. H., Flores, P. A. C., Freitas, T. R. O. & White, B. N. Genetic diversity and population structure of southern right whales, Eubalaena australis, from the Atlantic coast of South America. IWC SC/S11/RW25 (2011).Carroll, E. L. et al. Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile-Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground. J. Hered. 111, 263–276 (2020).PubMed 
PubMed Central 

Google Scholar 
Smith, T. D., Reeves, R. R., Josephson, E. A. & Lund, J. N. Spatial and seasonal distribution of American whaling and whales in the age of sail. PLoS One 7, e34905 (2012).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
International Whaling Commission. Report of the Scientific Committee of the International Whaling Commission. J. Cetacean Res. Manage. 20 (Suppl.), 675 (2019).Peterson, B. W. South Atlantic whaling: 1603–1830. Ph.D. thesis, University of California. (1948).Palazzo, J. T. Jr., Groch, K. R. & Silveira, H. A. Projeto Baleia Franca: 25 anos de pesquisa e conservação, 1982–2007 (2007).Reeves, R. R. & Smith, T. D. A taxonomy of world whaling. In Whales, Whaling, and Ocean Ecosystems (eds Estes, J. A. et al.) 82–101 (University of California Press, 2006).
Google Scholar 
Richards, R. Past and present distributions of southern right whales (Eubalaena australis). N. Z. J. Zool. 36, 447–459 (2009).
Google Scholar 
Harcourt, R., Van Der Hoop, J., Kraus, S. & Carroll, E. L. Future directions in Eubalaena spp.: comparative research to inform conservation. Front. Mar. Sci. 5, 530 (2019).Cooke, J. G. & Zerbini, A. N. Eubalaena australis. IUCN Red List of Threatened Species 2018: e. T8153A50354147 (2018).Ellis, M. Aspectos da pesca da baleia no Brasil colonial. Rev. Hist. Sao Paulo 14, 1–126 (1958).
Google Scholar 
Ellis, M. A baleia no Brasil colonial (Melhoramentos, 1969).Palazzo, J. T., Jr. & Carter, L. A. A caça de baleias no Brasil (AGAPAN, 1983).Furniss, H. W. Whaling in Brazil. Bull. Int. Union Am. Republ. 2, 1048–1054 (1909).
Google Scholar 
Acosta y Lara, E. F. Un ballenero inglés en la Cisplatina. Hoy es Historia 24, 82–88 (1987).Moore, M. J. et al. Relative abundance of large whales around South Georgia (1979–1998). Mar. Mamm. Sci. 15, 1287–1302 (1999).
Google Scholar 
Comerlato, F. A baleia como recurso energético no Brasil. Simpósio Internacional de História Ambiental e Migrações 1119–1138 (2010).Comerlato, F. As armações baleeiras na configuração da costa catarinense em tempos coloniais. Tempos Históricos 15, 481–501 (2011).
Google Scholar 
de Morais, I. O. B. et al. From the southern right whale hunting decline to the humpback whaling expansion: A review of whale catch records in the tropical western South Atlantic Ocean. Mammal Rev. 47, 11–23 (2017).
Google Scholar 
American Whaling Logbook Data: A Database, by New Bedford Whaling Museum and Mystic Seaport Museum, Inc. Compilers Judith Lund and Tim Smith. Hosted at whalinghistory.org. (2020).BSWF Databases. 2020. Compilers–A. G. E. Jones; Dale Chatwin; Rhys Richards. Contributors–Jane Clayton; Mark Howard. Hosted at whalinghistory.orgFrench Offshore Whaling Voyages: A Database, https://whalinghistory.org/fv/, Mystic Seaport Museum, Inc. and New Bedford Whaling Museum.Allison, C. IWC summary catch database Version 6.1. (2016).Vighi, M. et al. The missing whales: relevance of “struck and lost” rates for the impact assessment of historical whaling in the southwestern Atlantic Ocean. ICES J. Mar. Sci. 78, 14–24 (2021).
Google Scholar 
McCullagh, P. & Nelder, J. Generalized Linear Models Monographs on Statistics and Applied Probability (Chapman and Hall, 1989).MATH 

Google Scholar 
Zuur, A. F., Ieno, E. N., Walker, N. J., Saveliev, A. A. & Smith, G. M. Mixed Effects Model and Extension in Ecology with R (Springer, 2009).MATH 

Google Scholar 
Ward, E., Zerbini, A., Kinas, P. G., Engel, M. H. & Adriolo, A. Estimates of growth rates of humpback whales (Megaptera novaeangliae) in the wintering grounds off the coast of Brazil (Breeding Stock A). J. Cetacean Res. Manag. (Special Issue) 3, 145–149 (2011).
Google Scholar 
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria (2019).Rowntree, V., Payne, R. & Schell, D. M. Changing patterns of habitat use by southern right whales (Eubalaena australis) on their nursery ground at Península Valdés, Argentina, and in their long-range movements. J. Cetacean Res. Manag. (Special Issue) 2, 133–143 (2001).
Google Scholar 
de Valpine, P. & Hastings, A. Fitting population models incorporating process noise and observation error. Ecol. Monogr. 72, 57–76 (2002).
Google Scholar 
Pella, J. J. & Tomlinson, P. K. A generalised stock production model. Int.-Am. Trop. Tuna Commun. Bull. 13, 421–496 (1969).
Google Scholar 
Zerbini, A. N. et al. Assessing the recovery of an Antarctic predator from historical exploitation. R. Soc. Open Sci. 6, 190368 (2019).ADS 
PubMed 
PubMed Central 

Google Scholar 
Halley, J. & Inchausti, P. Lognormality in ecological time series. Oikos 99, 518–530 (2002).
Google Scholar 
Best, J. K. & Punt, A. E. Parameterizations for Bayesian state-space surplus production models. Fish. Res. 222, 105411 (2020).
Google Scholar 
Walters, C. & Ludwig, D. Calculation of Bayes posterior probability distributions for key population parameters. Can. J. Fish. Aquat. Sci. 51, 713–722 (1994).
Google Scholar 
International Whaling Commission. Annex I: report of the sub-committee on stock definition. J. Cetacean Res. Manag. 13(Supp.), 233–241 (2012).Butterworth, D. S. & Punt, A. E. On the Bayesian approach suggested for the assessment of the Bering-Chukchi-Beaufort Seas stock of bowhead whales. Rep. Int. Whaling Commun. 45, 303–311 (1995).
Google Scholar 
McAllister, M. K., Pikitch, E. K., Punt, A. E. & Hilborn, R. Bayesian approach to stock assessment and harvest decisions using the sampling/importance resampling algorithm. Can. J. Fish. Aquat. Sci. 12, 2673–2687 (1999).
Google Scholar 
Best, P., Brandao, A. & Butterworth, D. Demographic parameters of southern right whales off South Africa. J. Cetacean Res. Manag. (Special Issue) 2, 161–169 (2001).
Google Scholar 
Punt, A. E. et al. Robustness of potential biological removal to monitoring, environmental, and management uncertainties. ICES J. Mar. Sci. 77, 2491–2507 (2020).
Google Scholar 
Pace, R. M., Corkeron, P. J. & Kraus, S. D. State-space mark-recapture estimates reveal a recent decline in abundance of North Atlantic right whales. Ecol. Evol. 7, 8730–8741 (2017).PubMed 
PubMed Central 

Google Scholar 
Sueyro, N., Crespo, E. A., Arias, M. & Coscarella, M. A. Density-dependent changes in the distribution of Southern right whales (Eubalaena australis) in the breeding ground Peninsula Valdés. PeerJ 6, e5957 (2018).PubMed 
PubMed Central 

Google Scholar 
Wilberg, M. J., Thorson, J. T., Linton, B. C. & Berkson, J. Incorporating time-varying catchability into population dynamic stock assessment models. Rev. Fish. Sci. 18, 7–24 (2010).
Google Scholar 
Kass, R. E. & Raftery, A. E. Bayes factors. J. Am. Stat. Assoc. 90, 773–795 (1995).MathSciNet 
MATH 

Google Scholar 
Chang, Y. J. et al. Model selection and multi-model inference for Bayesian surplus production models: a case study for Pacific blue and striped marlin. Fish. Res. 166, 129–139 (2015).CAS 

Google Scholar 
Barker, D. & Sibly, R. M. The effects of environmental perturbation and measurement error on estimates of the shape parameter in the theta-logistic model of population regulation. Ecol. Model. 219, 170–177 (2008).
Google Scholar 
Dennis, B., Ponciano, J. M. & Taper, M. L. Replicated sampling increases efficiency in monitoring biological populations. Ecology 91, 610–620 (2010).PubMed 

Google Scholar 
Punt, A. E. Review of contemporary cetacean stock assessment models. J. Cetacean Res. Manag. 17, 35–56 (2017).
Google Scholar 
Punt, A. E., Butterworth, D. S., de Moor, C. L., De Oliveira, J. A. & Haddon, M. Management strategy evaluation: best practices. Fish Fish. 17, 303–334 (2016).
Google Scholar 
Baker, C. S. & Clapham, P. J. Modelling the past and future of whales and whaling. Trends Ecol. Evol. 19, 365–371 (2004).
Google Scholar 
Lotze, H. K. & Worm, B. Historical baselines for large marine animals. Trends Ecol. Evol. 24, 254–262 (2009).PubMed 

Google Scholar 
Foley, C. M. & Lynch, H. J. A method to estimate pre-exploitation population size. Conserv. Biol. 34, 256–265 (2020).PubMed 

Google Scholar 
Collins, A. C., Böhm, M. & Collen, B. Choice of baseline affects historical population trends in hunted mammals of North America. Biol. Conserv. 242, 108421 (2020).
Google Scholar 
Jackson, J. A. et al. An integrated approach to historical population assessment of the great whales: Case of the New Zealand southern right whale. R. Soc. Open Sci. 3, 150669 (2016).ADS 
PubMed 
PubMed Central 

Google Scholar 
Richards, R. & Du Pasquier, T. Bay whaling off southern Africa, c. 1785–1805. S. Afr. J. Mar. Sci. 8, 231–250 (1989).
Google Scholar 
Brandão, A., Best, P. B. & Butterworth, D. S. Estimates of demographic parameters for southern right whales off South Africa from survey data from 1979 to 2006. IWC SC/62/BRG30 (2010).Rowntree, V. J. et al. Unexplained recurring high mortality of southern right whale Eubalaena australis calves at Península Valdés, Argentina. Mar. Ecol. Progr. Ser. 493, 275–289 (2013).ADS 

Google Scholar 
Valenzuela, L. O., Sironi, M., Rowntree, V. J. & Seger, J. Isotopic and genetic evidence for culturally inherited site fidelity to feeding grounds in southern right whales (Eubalaena australis). Mol. Ecol. 18, 782–791 (2009).CAS 
PubMed 

Google Scholar 
Clapham, P. J., Aguilar, A. & Hatch, L. T. Determining spatial and temporal scales for management: lessons from whaling. Mar. Mamm. Sci. 24, 183–201 (2008).
Google Scholar 
Baker, C. S. et al. Strong maternal fidelity and natal philopatry shape genetic structure in North Pacific humpback whales. Mar. Ecol. Prog. Ser. 494, 291–306 (2013).ADS 

Google Scholar 
González, C. V., Piola, A., O’Brien, T. D., Tormosov, D. D. & Acha, E. M. Circumpolar frontal systems as potential feeding grounds of Southern Right whales. Prog. Oceanogr. 176, 102123 (2019).
Google Scholar 
Leaper, R. et al. Global climate drives southern right whale (Eubalaena australis) population dynamics. Biol. Lett. 2, 289–292 (2006).PubMed 
PubMed Central 

Google Scholar 
Seyboth, E. et al. Southern right whale (Eubalaena australis) reproductive success is influenced by krill (Euphausia superba) density and climate. Sci. Rep. 6, 28205 (2016).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Punt, A. E. Extending production models to include process error in the population dynamics. Can. J. Fish. Aquat. Sci. 60, 1217–1228 (2003).
Google Scholar 
Tulloch, V. J., Plagányi, É. E., Brown, C., Richardson, A. J. & Matear, R. Future recovery of baleen whales is imperiled by climate change. Glob. Change Biol. 25, 1263–1281 (2019).ADS 

Google Scholar 
Witting, L. Selection-delayed population dynamics in baleen whales and beyond. Popul. Ecol. 55, 377–401 (2013).
Google Scholar 
Pante, E. & Benoit, S.-B. marmap: A package for importing, plotting and analyzing bathymetric and topographic data in R. PLoS ONE 8, e73051 (2013).ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).MATH 

Google Scholar  More

Müller, K. Investigations on the organic drift in north Swedish streams. Rep. Inst. Freshw. Res. Drottningholm 35, 133–148 (1954).
Google Scholar 
Müller, K. Stream drift as a chronobiological phenomenon in running water ecosystems. Annu. Rev. Ecol. Syst. 5, 309–323 (1974).Article 

Google Scholar 
Waters, T. F. Interpretation of invertebrate drift in streams. Ecology 46, 327–334. https://doi.org/10.2307/1936336 (1965).Article 

Google Scholar 
Waters, T. F. The drift of stream insects. Annu. Rev. Entomol. 17, 253–272 (1972).Article 

Google Scholar 
Thiesmeier, B. Der Feuersalamander (Laurenti, 2004).
Google Scholar 
Hughes, D. A. Some factors affecting drift and upstream movements of Gammarus pulex. Ecology 51, 301–305. https://doi.org/10.2307/1933668 (1970).Article 

Google Scholar 
Humphries, S. & Ruxton, G. D. Is there really a drift paradox?. J. Anim. Ecol. 71, 151–154 (2002).Article 

Google Scholar 
Altig, R. & McDiarmid, R. W. In Tadpoles: The Biology of Anuran Larvae (eds McDiarmid, R. W. & Altig, R.) 24–51 (University of Chicago Press, 2000).
Google Scholar 
Sherratt, E., Vidal-García, M., Anstis, M. & Keogh, J. S. Adult frogs and tadpoles have different macroevolutionary patterns across the Australian continent. Nat. Ecol. Evol. 1, 1385–1391. https://doi.org/10.1038/s41559-017-0268-6 (2017).Article 
PubMed 

Google Scholar 
Griffiths, R. A. Newts and Salamanders of Europe (Poyser Natural History, 1996).
Google Scholar 
Cecala, K. K., Price, S. J. & Dorcas, M. E. Evaluating existing movement hypotheses in linear systems using larval stream salamanders. Can. J. Zool. 87, 292–298. https://doi.org/10.1139/z09-013 (2009).Article 

Google Scholar 
Grant, E. H. C., Nichols, J. D., Lowe, W. H. & Fagan, W. F. Use of multiple dispersal pathways facilitates amphibian persistence in stream networks. Proc. Natl. Acad. Sci. USA 107, 6936–6940. https://doi.org/10.1073/pnas.1000266107 (2010).ADS 
Article 

Google Scholar 
Lowe, W. H. Linking dispersal to local population dynamics: A case study using a headwater salamander system. Ecology 84, 2145–2154. https://doi.org/10.1890/0012-9658(2003)084[2145:LDTLPD]2.0.CO;2 (2003).Article 

Google Scholar 
Bruce, R. C. Upstream and downstream movements of Eurycea bislineata and other salamanders in a southern appalachian stream. Herpetologica 42, 149–155 (1986).
Google Scholar 
Thiesmeier, B. Untersuchungen zur Phänologie und Populationsdynamik des Feuersalamanders (Salamandra salamandra terrestris Lacépède, 1788) im Niederbergische Land (BRD). Zool. Jahrbücher Abteilung für Systematik Ökologie Geographie der Tiere 117, 331–353 (1990).
Google Scholar 
Thiesmeier, B. & Schuhmacher, H. Causes of larval drift of the fire salamander, Salamandra salamandra terrestris, and its effects on population dynamics. Oecologia 82, 259–263. https://doi.org/10.1007/BF00323543 (1990).ADS 
Article 
PubMed 

Google Scholar 
Reinhardt, T., Baldauf, L., Ilic, M. & Fink, P. Cast away: Drift as the main determinant for larval survival in western fire salamanders (Salamandra salamandra) in headwater streams. J. Zool. 306, 171–179 (2018).Article 

Google Scholar 
Baumgartner, N., Waringer, A. & Waringer, J. Hydraulic microdistribution patterns of larval fire salamanders (Salamandra salamandra salamandra) in the Weidlingbach near Vienna, Austria. Freshw. Biol. 41, 31–41. https://doi.org/10.1046/j.1365-2427.1999.00378.x (1999).Article 

Google Scholar 
Krause, E. T., Steinfartz, S. & Caspers, B. A. Poor nutritional conditions during the early larval stage reduce risk-taking activities of fire salamander larvae (Salamandra salamandra). Ethology 117, 416–421. https://doi.org/10.1111/j.1439-0310.2011.01886.x (2011).Article 

Google Scholar 
Veith, M. et al. Drift compensation in larval European fire salamanders, Salamandra salamandra (Amphibia: Urodela)?. Hydrobiologia 828, 315–325. https://doi.org/10.1007/s10750-018-3820-8 (2019).Article 

Google Scholar 
Arnold, A. Zur Verbreitung des Feuersalamanders im Tal der Zwickauer Mulde. Veröffentlichungen aus dem Museum für Naturkunde Karl-Marx-Stadt 71–79 (1983).Thiesmeier, B. Ökologie des Feuersalamanders (Westarp Wissenschaften, 1992).
Google Scholar 
Thiesmeier-Hornberg, B. Zur Ökologie und Populationsdynamik des Feuersalamanders (Salamandra salamandra terrestris Lacépède, 1788) im niederbergischen Land unter besonderer Berücksichtigung der Larvalphase. PhD thesis, Universität-Gesamthochschule Essen (1988).Thiesmeier, B. & Grossenbacher, K. Salamandra salamandra (Linnaeus, 1758)—Feuersalamander. In Die Amphibien und Reptilien Europas. Schwanzlurche IIB (eds Thiesmeier, B. & Grossenbacher, K.) 1059–1132 (Aula, 2004).
Google Scholar 
Reques, R. & Tejedo, M. Intraspecific aggressive behaviour in fire salamander larvae (Salamandra salamandra): The effects of density and body size. Herpetol. J. 6, 15–19 (1996).
Google Scholar 
Thiesmeier, B. & Günther, R. Feuersalamander: Salamandra salamandra (Linnaeus, 1758). In Die Amphibien und Reptilien Deutschlands (ed. Günther, R.) 82–104 (Fischer, 1996).
Google Scholar 
Wagner, N., Pfrommer, J. & Veith, M. Comparison of different methods to estimate abundances of larval fire salamanders (Salamandra salamandra) in first-order creeks. Salamandra 56, 265–274 (2020).
Google Scholar 
Peig, J. & Green, A. J. New perspectives for estimating body condition from mass/length data: The scaled mass index as an alternative method. Oikos 118, 1883–1891. https://doi.org/10.1111/j.1600-0706.2009.17643.x (2009).Article 

Google Scholar 
White, G. C. & Burnham, K. P. Program MARK: Survival estimation from populations of marked animals. Bird Study 46, S120–S139 (1999).Article 

Google Scholar 
Otis, D. L., Burnham, K. P., White, G. C. & Anderson, D. R. Statistical inference from capture data on closed animal populations. Wildl. Monogr. 62, 3–135 (1978).MATH 

Google Scholar 
Schwarz, C. J. & Arnason, A. N. A general methodology for the analysis of capture-recapture experiments in open populations. Biometrics 52, 860–873 (1996).MathSciNet 
Article 

Google Scholar 
Seber, G. A. A note on the multiple-recapture census. Biometrika 52, 249–259 (1965).MathSciNet 
CAS 
Article 

Google Scholar 
Jolly, G. M. Explicit estimates from capture-recapture data with both death and immigration-stochastic model. Biometrika 52, 225–247 (1965).MathSciNet 
CAS 
Article 

Google Scholar 
Cormack, R. Estimates of survival from the sighting of marked animals. Biometrika 51, 429–438 (1964).Article 

Google Scholar 
Razali, N. M. & Wah, Y. B. Power comparisons of Shapiro-Wilk, Kolmogorov-Smirnov, Lilliefors and Anderson-Darling tests. J. Stat. Model. Anal. 2, 21–33 (2011).
Google Scholar 
Bates, D., Mächler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48. https://doi.org/10.18637/jss.v067.i01 (2015).Article 

Google Scholar 
R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2017).
Google Scholar 
Segev, O. & Blaustein, L. Influence of water velocity and predation risk on fire salamander (Salamandra infraimmaculata) larval drift among temporary pools in ephemeral streams. Freshw. Sci. 33, 950–957. https://doi.org/10.1086/676634 (2014).Article 

Google Scholar 
Montori, A., Llorente, G. & Richter-Boix, À. Habitat features affecting the small-scale distribution and longitudinal migration patterns of Calotriton asper in a Pre-Pyrenean population. Amphibia-Reptilia 29, 371–381. https://doi.org/10.1163/156853808785112048 (2008).Article 

Google Scholar 
Zakrzewski, M. Effect of definite temperature ranges on development metamorphosis and procreation of the spotted salamander larvae, Salamandra salamandra (L.). Acta Biol. Crac. Ser. Zool. 29, 77–83 (1987).
Google Scholar 
Degani, G., Goldenberg, S. & Warburg, M. R. Cannibalistic phenomena in Salamandra salamandra larvae in certain water bodies and under experimental conditions. Hydrobiologia 75, 123–128. https://doi.org/10.1007/BF00007425 (1980).Article 

Google Scholar 
Manenti, R., Ficetola, G. F. & De Bernardi, F. Water, stream morphology and landscape: Complex habitat determinants for the fire salamander Salamandra salamandra. Amphibia-Reptilia 30, 7–15. https://doi.org/10.1163/156853809787392766 (2009).Article 

Google Scholar 
Klewen, R. Landsalamander Europa: Teil1. Die Gattungen Salamandra und Mertensiella 2nd edn. (Ziemsen-Verlag, 1991).
Google Scholar 
Orth, R., Zscheischler, J. & Seneviratne, S. I. Record dry summer in 2015 challenges precipitation projections in Central Europe. Sci. Rep. 6, 1–8 (2016).Article 

Google Scholar 
Degani, G. Temperature selection in Salamandra salamandra (L.) larvae and juveniles from different habitats. Biol. Behav. 9, 175–183 (1984).
Google Scholar  More

Wilson, A. D. M. et al. Social networks in changing environments. Behav. Ecol. Sociobiol. 69, 1617–1629 (2015).
Google Scholar 
Ward, A. J. W. et al. Association patterns and shoal fidelity in the three–spined stickleback. Proc. R. Soc. Lond. Ser. B Biol. Sci. 269, 2451–2455 (2002).
Google Scholar 
Croft, D. P. et al. Assortative interactions and social networks in fish. Oecologia 143, 211–219 (2005).CAS 
PubMed 

Google Scholar 
Helfman, G. S. & Schultz, E. T. Social transmission of behavioural traditions in a coral reef fish. Anim. Behav. 32, 379–384 (1984).
Google Scholar 
Wong, M. Y. L., Buston, P. M., Munday, P. L. & Jones, G. P. The threat of punishment enforces peaceful cooperation and stabilizes queues in a coral-reef fish. Proc. R. Soc. B Biol. Sci. 274, 1093–1099 (2007).
Google Scholar 
King, A. J., Fehlmann, G., Biro, D., Ward, A. J. & Fürtbauer, I. Re-wilding collective behaviour: an ecological perspective. Trends Ecol. Evol. 33, 347–357 (2018).PubMed 

Google Scholar 
Bro-Jørgensen, J., Franks, D. W. & Meise, K. Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation. Philos. Trans. R. Soc. B Biol. Sci. 374, 20190008 (2019).
Google Scholar 
Rose, G. A. Cod spawning on a migration highway in the north-west Atlantic. Nature 366, 458 (1993).
Google Scholar 
Wilson, A. D. M., Croft, D. P. & Krause, J. Social networks in elasmobranchs and teleost fishes. Fish Fish. 15, 676–689 (2014). This study reviewed the state of knowledge of the mechanisms and functions underpinning social network structure in fishes, including a discussion on methodological issues and developments in this area of research.Taborsky, M. & Wong, M. In Comparative Social Evolution (eds. Rubenstein, D. R., Abbot, P.) 354–389 (Cambridge University Press, 2017).Lusseau, D. Evidence for social role in a dolphin social network. Evol. Ecol. 21, 357–366 (2007).
Google Scholar 
Krause, J., James, R., Franks, D. W. & Croft, D. P. Animal social networks. (Oxford University Press, 2015).Smith, J. E. & Pinter‐Wollman, N. Observing the unwatchable: Integrating automated sensing, naturalistic observations and animal social network analysis in the age of big data. J. Anim. Ecol. 90, 62–75 (2021).PubMed 

Google Scholar 
Webber, Q. M. R. & Vander Wal, E. Trends and perspectives on the use of animal social network analysis in behavioural ecology: a bibliometric approach. Anim. Behav. 149, 77–87 (2019).
Google Scholar 
Aspillaga, E., Arlinghaus, R., Martorell-Barceló, M., Barcelo-Serra, M. & Alós, J. High-throughput tracking of social networks in marine fish populations. Front. Mar. Sci. 8, 794 (2021). This original and pioneering study demonstrated the use of high-resolution tracking to infer social behaviour and social structure in the marine environment.Silk, M. J., Jackson, A. L., Croft, D. P., Colhoun, K. & Bearhop, S. The consequences of unidentifiable individuals for the analysis of an animal social network. Anim. Behav. 104, 1–11 (2015).
Google Scholar 
Hughey, L. F., Hein, A. M., Strandburg-Peshkin, A. & Jensen, F. H. Challenges and solutions for studying collective animal behaviour in the wild. Philos. Trans. R. Soc. B Biol. Sci. 373, 20170005 (2018).
Google Scholar 
Hussey, N. E. et al. Aquatic animal telemetry: a panoramic window into the underwater world. Science 348, 1255642 (2015).PubMed 

Google Scholar 
Barkley, A. N. et al. A framework to estimate the likelihood of species interactions and behavioural responses using animal-borne acoustic telemetry transceivers and accelerometers. J. Anim. Ecol. 89, 146–160 (2020).PubMed 

Google Scholar 
Baktoft, H., Gjelland, K. Ø., Økland, F. & Thygesen, U. H. Positioning of aquatic animals based on time-of-arrival and random walk models using YAPS (Yet Another Positioning Solver). Sci. Rep. 7, 14294 (2017).PubMed 
PubMed Central 

Google Scholar 
Aspillaga, E. et al. Performance of a novel system for high-resolution tracking of marine fish societies. Anim. Biotelemetry 9, 1 (2021).
Google Scholar 
Jacoby, D. M. P., Papastamatiou, Y. P. & Freeman, R. Inferring animal social networks and leadership: applications for passive monitoring arrays. J. R. Soc. Interface 13, 20160676 (2016).PubMed 
PubMed Central 

Google Scholar 
Papastamatiou, Y. P., Meyer, C. G., Watanabe, Y. & Heithaus, M. in Shark Research: Emerging Technologies and Applications for the Field and Laboratory, (eds. Carrier, J. C., Heithaus, M. R., Simpfendorfer, C. A.) 83–119 (C. R. C. Press, 2018).Butcher, P. A. et al. The drone revolution of shark. Sci. A Rev. Drones 5, 8 (2021).
Google Scholar 
Hamede, R. K., Bashford, J., McCallum, H. & Jones, M. Contact networks in a wild Tasmanian devil (Sarcophilus harrisii) population: using social network analysis to reveal seasonal variability in social behaviour and its implications for transmission of devil facial tumour disease. Ecol. Lett. 12, 1147–1157 (2009).PubMed 

Google Scholar 
Sih, A., Spiegel, O., Godfrey, S., Leu, S. & Bull, C. M. Integrating social networks, animal personalities, movement ecology and parasites: a framework with examples from a lizard. Anim. Behav. 136, 195–205 (2018).
Google Scholar 
Carne, C., Semple, S., Morrogh-Bernard, H., Zuberbühler, K. & Lehmann, J. Predicting the vulnerability of great apes to disease: the role of superspreaders and their potential vaccination. PLoS ONE 8, e84642 (2013).PubMed 
PubMed Central 

Google Scholar 
Fielding, H. R. et al. Spatial and temporal variation in proximity networks of commercial dairy cattle in Great Britain. Prev. Vet. Med. 194, 105443 (2021).PubMed 
PubMed Central 

Google Scholar 
Haulsee, D. E. et al. Social network analysis reveals potential fission-fusion behavior in a shark. Sci. Rep. 6, 34087 (2016).CAS 
PubMed 
PubMed Central 

Google Scholar 
Merrick, M. J. & Koprowski, J. L. Should we consider individual behavior differences in applied wildlife conservation studies? Biol. Conserv. 209, 34–44 (2017).
Google Scholar 
Kressler, M. M., Gerlam, A., Spence-Jones, H. & Webster, M. M. Passive traps and sampling bias: Social effects and personality affect trap entry by sticklebacks. Ethology 127, 446–452 (2021).
Google Scholar 
Blumstein, D. T. In Social Behaviour (eds. Szekely, T., Moore, A. J., Komdeur, J.) 520–534 (Cambridge University Press, 2010).Berger-Tal, O. et al. A systematic survey of the integration of animal behavior into conservation. Conserv. Biol. 30, 744–753 (2016).PubMed 

Google Scholar 
Mucientes, G. R., Queiroz, N., Sousa, L. L., Tarroso, P. & Sims, D. W. Sexual segregation of pelagic sharks and the potential threat from fisheries. Biol. Lett. 5, 156–159 (2009).PubMed 
PubMed Central 

Google Scholar 
Mourier, J., Vercelloni, J. & Planes, S. Evidence of social communities in a spatially structured network of a free-ranging shark species. Anim. Behav. 83, 389–401 (2012).
Google Scholar 
Perryman, R. J. Y. et al. Social preferences and network structure in a population of reef manta rays. Behav. Ecol. Sociobiol. 73, 114 (2019).
Google Scholar 
He, P., Maldonado-Chaparro, A. A. & Farine, D. R. The role of habitat configuration in shaping social structure: a gap in studies of animal social complexity. Behav. Ecol. Sociobiol. 73, 9 (2019).
Google Scholar 
Mourier, J., Lédée, E. J. I. & Jacoby, D. M. P. A multilayer perspective for inferring spatial and social functioning in animal movement networks. bioRxiv https://www.biorxiv.org/content/10.1101/749085v1.full (2019).Snijders, L., Blumstein, D. T., Stanley, C. R. & Franks, D. W. Animal social network theory can help wildlife conservation. Trends Ecol. Evol. 32, 567–577 (2017). This review paper outlines how understanding of direct and indirect relationships between animals can be profitably applied by wildlife managers and conservationists.Beyer, K., Gozlan, R. E. & Copp, G. H. Social network properties within a fish assemblage invaded by non-native sunbleak Leucaspius delineatus. Ecol. Modell. 221, 2118–2122 (2010).
Google Scholar 
Hasenjager, M. J., Leadbeater, E. & Hoppitt, W. Detecting and quantifying social transmission using network-based diffusion analysis. J. Anim. Ecol. 90, 8–26 (2021).PubMed 

Google Scholar 
Fritzsche McKay, A. & Hoye, B. J. Are migratory animals superspreaders of infection? Integr. Comp. Biol. 56, 260–267 (2016).PubMed 

Google Scholar 
Albery, G. F., Kirkpatrick, L., Firth, J. A. & Bansal, S. Unifying spatial and social network analysis in disease ecology. J. Anim. Ecol. 90, 45–61 (2021).PubMed 

Google Scholar 
Salvanes, A. & Braithwaite, V. The need to understand the behaviour of fish reared for mariculture or restocking. ICES J. Mar. Sci. 63, 345–354 (2006).
Google Scholar 
Andrew, J. E., Holm, J., Kadri, S. & Huntingford, F. A. The effect of competition on the feeding efficiency and feed handling behaviour in gilthead sea bream (Sparus aurata L.) held in tanks. Aquaculture 232, 317–331 (2004).
Google Scholar 
Muñoz, L., Aspillaga, E., Palmer, M., Saraiva, J. L. & Arechavala-Lopez, P. Acoustic telemetry: a tool to monitor fish swimming behavior in sea-cage aquaculture. Front. Mar. Sci. 7, 645 (2020).
Google Scholar 
Macaulay, G., Bui, S., Oppedal, F. & Dempster, T. Challenges and benefits of applying fish behaviour to improve production and welfare in industrial aquaculture. Rev. Aquac. 13, 934–948 (2021).
Google Scholar 
Jacoby, D. M. P. et al. Social network analysis reveals the subtle impacts of tourist provisioning on the social behavior of a generalist marine apex predator. Front. Mar. Sci. 8, 1202 (2021).
Google Scholar 
Shizuka, D. & Johnson, A. E. How demographic processes shape animal social networks. Behav. Ecol. 31, 1–11 (2020).
Google Scholar 
Guerra, A. S., Kao, A. B., McCauley, D. J. & Berdahl, A. M. Fisheries-induced selection against schooling behaviour in marine fishes. Proc. R. Soc. B Biol. Sci. 287, 20201752 (2020).
Google Scholar 
Frisch, A. Sex-change and gonadal steroids in sequentially-hermaphroditic teleost fish. Rev. Fish. Biol. Fish. 14, 481–499 (2004).
Google Scholar 
Webber, Q. M. R. & Vander Wal, E. An evolutionary framework outlining the integration of individual social and spatial ecology. J. Anim. Ecol. 87, 113–127 (2018).PubMed 

Google Scholar 
Staveley, T. A. B. et al. Sea surface temperature dictates movement and habitat connectivity of Atlantic cod in a coastal fjord system. Ecol. Evol. 9, 9076–9086 (2019).PubMed 
PubMed Central 

Google Scholar 
Sosa, S., Jacoby, D. M. P., Lihoreau, M. & Sueur, C. Animal social networks: towards an integrative framework embedding social interactions, space and time. Methods Ecol. Evol. 12, 4–9 (2021).
Google Scholar 
Albery, G. F. et al. Multiple spatial behaviours govern social network positions in a wild ungulate. Ecol. Lett. 24, 676–686 (2021).PubMed 

Google Scholar 
Ellis, S. et al. Mortality risk and social network position in resident killer whales: sex differences and the importance of resource abundance. Proc. R. Soc. B Biol. Sci. 284, 20171313 (2017).
Google Scholar 
Ellis, S., Snyder-Mackler, N., Ruiz-Lambides, A., Platt, M. L. & Brent, L. J. N. Deconstructing sociality: the types of social connections that predict longevity in a group-living primate. Proc. R. Soc. B Biol. Sci. 286, 20191991 (2019).
Google Scholar 
Kohn, G. M. Friends give benefits: autumn social familiarity preferences predict reproductive output. Anim. Behav. 132, 201–208 (2017).
Google Scholar 
Villegas-Ríos, D., Freitas, C., Moland, E., Thorbjørnsen, S. H. & Olsen, E. M. Inferring individual fate from aquatic acoustic telemetry data. Methods Ecol. Evol. 11, 1186–1198 (2020).
Google Scholar 
Mourier, J., Bass, N. C., Guttridge, T. L., Day, J. & Brown, C. Does detection range matter for inferring social networks in a benthic shark using acoustic telemetry? R. Soc. open Sci. 4, 170485 (2017).PubMed 
PubMed Central 

Google Scholar 
Vanovac, S., Howard, D., Monk, C. T., Arlinghaus, R. & Giabbanelli, P. J. Network analysis of intra- and interspecific freshwater fish interactions using year-around tracking. J. R. Soc. Interface 18, 20210445 (2021).PubMed 

Google Scholar 
Dahl, K. A., Patterson, W. F. & Snyder, R. A. Experimental assessment of lionfish removals to mitigate reef fish community shifts on northern Gulf of Mexico artificial reefs. Mar. Ecol. Prog. Ser. 558, 207–221 (2016).
Google Scholar 
Fitzpatrick, J. L. et al. Female-mediated causes and consequences of status change in a social fish. Proc. R. Soc. B Biol. Sci. 275, 929–936 (2008).CAS 

Google Scholar 
Mourier, J., Brown, C. & Planes, S. Learning and robustness to catch-and-release fishing in a shark social network. Biol. Lett. 13, 20160824 (2017).PubMed 
PubMed Central 

Google Scholar 
Rutledge, L. Y. et al. Protection from harvesting restores the natural social structure of eastern wolf packs. Biol. Conserv. 143, 332–339 (2010).
Google Scholar 
Jacoby, D. M. P. et al. Synergistic patterns of threat and the challenges facing global anguillid eel conservation. Glob. Ecol. Conserv 4, 321–333 (2015).
Google Scholar 
Geffroy, B., Bru, N., Dossou-Gbété, S., Tentelier, C. & Bardonnet, A. The link between social network density and rank-order consistency of aggressiveness in juvenile eels. Behav. Ecol. Sociobiol. 68, 1073–1083 (2014).
Google Scholar  More

Lombard, M. et al. South African and Lesotho Stone Age sequence updated. S. Afr. Archaeol. Bull. 67, 120–144 (2012).
Google Scholar 
Kandel, A. W. et al. Increasing behavioral flexibility? An integrative macro-scale approach to understanding the Middle Stone Age of southern Africa. J. Archaeol. Method Theory 23, 623–628 (2015).
Google Scholar 
Porraz, G. et al. Experimentation preceding innovation in a MIS5 Pre-Still Bay layer from Diepkloof Rock Shelter (South Africa): emerging technologies and symbols. Preprint at EcoEvoRxiv https://ecoevorxiv.org/ch53r/ (2020).Texier, P. J. et al. A Howiesons Poort tradition of engraving ostrich eggshell containers dated to 60,000 years ago at Diepkloof Rock Shelter, South Africa. Proc. Natl Acad. Sci. USA 107, 6180–6185 (2010).CAS 
PubMed 
PubMed Central 

Google Scholar 
Henshilwood, C. S. et al. Klipdrift Shelter, southern Cape, South Africa: preliminary report on the Howiesons Poort layers. J. Archaeol. Sci. 45, 284–303 (2014).
Google Scholar 
Powell, A., Shennan, S. & Thomas, M. G. Late Pleistocene demography and the appearance of modern human behavior. Science 324, 1298–1301 (2009).CAS 
PubMed 

Google Scholar 
Marean, C. W. The transition to foraging for dense and predictable resources and its impact on the evolution of modern humans. Phil. Trans. R. Soc. B 371, 20150239 (2016).PubMed 
PubMed Central 

Google Scholar 
Mackay, A., Stewart, B. A. & Chase, B. M. Coalescence and fragmentation in the late Pleistocene archaeology of southernmost Africa. J. Hum. Evol. 72, 26–51 (2014).PubMed 

Google Scholar 
Wilkins, J. et al. Innovative Homo sapiens behaviours 105,000 years ago in a wetter Kalahari. Nature 592, 248–252 (2021).CAS 
PubMed 

Google Scholar 
Dewar, G. & Stewart, B. A. Preliminary results of excavations at Spitzkloof Rockshelter, Richtersveld, South Africa. Quat. Int. 270, 30–39 (2012).
Google Scholar 
Cowling, R. M. & Pierce, S. Namaqualand: A Succulent Desert (Fernwood Press, 1999).Hijmans, R. J., Cameron, S. E., Parra, J. L., Jones, P. G. & Jarvis, A. Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 25, 1965–1978 (2005).
Google Scholar 
Mucina, L. et al. in The Vegetation of South Africa, Lesotho and Swaziland (eds Mucina, L. & Rutherford, M. C.) 221–299 (SANBI, 2006).Rebelo, A. G., Boucher, C., Helme, N., Mucina, L. & Rutherford, M. C. in The Vegetation of South Africa, Lesotho and Swaziland (eds Mucina, L. & Rutherford, M. C.) 53–219 (SANBI, 2006).Marean, C. W. et al. in Fynbos: Ecology, Evolution, and Conservation of a Megadiverse Region (eds Allsopp, N. et al.) 164–199 (Oxford Univ. Press, 2014).Carr, A. S., Chase, B. M. & Mackay, A. in Africa from MIS 6-2: Population Dynamics and Paleoenvironments (eds Jones, S. & Stewart, B. A.) 23–47 (Springer, 2016).Chase, B. M. & Meadows, M. E. Late Quaternary dynamics of southern Africa’s winter rainfall zone. Earth Sci. Rev. 84, 103–138 (2007).
Google Scholar 
Steele, T. E. et al. Varsche Rivier 003: a Middle and Later Stone Age site with Still Bay and Howiesons Poort assemblages in southern Namaqualand, South Africa. Paleoanthropology 2016, 100–163 (2016).
Google Scholar 
Sharp, W. D. et al. 230Th/U burial dating of ostrich eggshell. Quat. Sci. Rev. 219, 263–276 (2019).
Google Scholar 
Chase, B. M. et al. South African speleothems reveal influence of high- and low-latitude forcing over the last 113.5 kyr. Geology 49, 1353–1357 (2021).CAS 

Google Scholar 
Chase, B. M. et al. Influence of tropical easterlies in southern Africa’s winter rainfall zone during the Holocene. Quat. Sci. Rev. 107, 138–148 (2015).
Google Scholar 
Manning, J. Namaqualand (Briza, 2008).Skinner, J. D. & Chimimba, C. T. The Mammals of the Southern African Subregion 3rd edn (Cambridge Univ. Press, 2005).Skead, C. J. Historical Mammal Incidence in the Cape Province Vol 1: The Western and Northern Cape (Cape Town Department of Nature and Environmental Conservation, 1980).Churcher, C. S. Distribution and history of the Cape zebra (Equus capensis) in the Quaternary of Africa. Trans. R. Soc. S. Afr. 61, 89–95 (2006).
Google Scholar 
Spratt, R. M. & Lisiecki, L. E. A Late Pleistocene sea level stack. Climate 12, 1079–1092 (2016).
Google Scholar 
De Wet, W. Bathymetry of the South African Continental Shelf. MSc thesis, Univ. Cape Town (2013).Jerardino, A. & Marean, C. W. Shellfish gathering, marine paleoecology and modern human behavior: perspectives from Cave PP13B, Pinnacle Point, South Africa. J. Hum. Evol. 59, 412–424 (2010).PubMed 

Google Scholar 
Marean, C. W. Pinnacle Point Cave 13B (Western Cape Province, South Africa) in context: the Cape Floral kingdom, shellfish, and modern human origins. J. Hum. Evol. 59, 425–443 (2010).PubMed 

Google Scholar 
Kandel, A. W. Modification of ostrich eggs by carnivores and its bearing on the interpretation of archaeological and paleontological find. J. Archaeol. Sci. 31, 377–391 (2004).
Google Scholar 
Steele, T. E. & Klein, R. G. The Middle and Later Stone Age faunal remains from Diepkloof Rock Shelter, Western Cape, South Africa. J. Archaeol. Sci. 40, 3453–3462 (2013).
Google Scholar 
Klein, R. G. et al. The Ysterfontein 1 Middle Stone Age site, South Africa, and early human exploitation of coastal resources. Proc. Natl Acad. Sci. USA 101, 5708–5715 (2004).CAS 
PubMed 
PubMed Central 

Google Scholar 
Vogelsang, R. et al. New excavations of Middle Stone Age deposits at Apollo 11 Rockshelter, Namibia: stratigraphy, archaeology, chronology and past environments. J. Afr. Archaeol. 8, 185–218 (2010).Marean, C. W. et al. Early human use of marine resources and pigment in South Africa during the Middle Pleistocene. Nature 449, 905–908 (2007).CAS 
PubMed 

Google Scholar 
Schmidt, I. et al. New investigations at the Middle Stone Age site of Pockenbank Rockshelter, Namibia. Antiquity 90, e2 (2016).
Google Scholar 
Vogelsang, R. Middle Stone Age Fundstellen in Südwest-Namibia, Africa (Heinrich-Barth-Institut, 1998).Plug, I. Aquatic animals and their associates from the Middle Stone Age levels at Sibudu. South. Afr. Humanit. 18, 289–299 (2006).
Google Scholar 
Wurz, S. Technological trends in the Middle Stone Age of South Africa between MIS 7 and MIS 3. Curr. Anthropol. 54, S305–S319 (2013).
Google Scholar 
Volman, T. P. The Middle Stone Age in the Southern Cape. PhD thesis, Univ. Chicago (1981).Schmidt, P. & Mackay, A. Why was silcrete heat-treated in the Middle Stone Age? An early transformative technology in the context of raw material use at Mertenhof Rock Shelter, South Africa. PloS ONE 11, e0149243 (2016).PubMed 
PubMed Central 

Google Scholar 
Porraz, G. et al. Technological successions in the Middle Stone Age sequence of Diepkloof Rock Shelter, Western Cape, South Africa. J. Archaeol. Sci. 40, 3376–3400 (2013).
Google Scholar 
Schmid, V., Conard, N. J., Parkington, J., Texier, P. J. & Porraz, G. The ‘MSA 1’ of Elands Bay Cave (South Africa) in the context of the southern African early MSA technologies. South. Afr. Humanit. 29, 153–201 (2016).
Google Scholar 
Evans, U. Hollow Rock Shelter, a Middle Stone Age site in the Cederberg. South. Afr. Field Archaeol. 3, 63–73 (1994).
Google Scholar 
Mackay, A., Jacobs, Z. & Steele, T. E. Pleistocene archaeology and chronology of Putslaagte 8 (PL8) rockshelter, Western Cape, South Africa. J. Afr. Archaeol. 13, 71–98 (2015).
Google Scholar 
Thompson, J. C. et al. Ecological risk, demography and technological complexity in the Late Pleistocene of northern Malawi: implications for geographical patterning in the Middle Stone Age. J. Quat. Sci. 33, 261–284 (2018).
Google Scholar 
Vaesen, K. & Houkes, W. Is human culture cumulative? Curr. Anthropol. 62, 218–238 (2021).
Google Scholar 
Boyd, R., Richerson, P. J. & Henrich, J. The cultural niche: why social learning is essential for human adaptation. Proc. Natl Acad. Sci. USA 108, 10918–10925 (2011).CAS 
PubMed 
PubMed Central 

Google Scholar 
Sterelny, K. From hominins to humans: how sapiens became behaviourally modern. Phil. Trans. R. Soc. B 366, 809–822 (2011).PubMed 
PubMed Central 

Google Scholar 
Gärdenfors, P. & Högberg, A. The archaeology of teaching and the evolution of Homo docens. Curr. Anthropol. 58, 188–208 (2017).
Google Scholar 
Marwick, B. Pleistocene exchange networks as evidence for the evolution of language. Camb. Archaeol. J. 13, 67–81 (2003).
Google Scholar 
Blegen, N. The earliest long-distance obsidian transport: evidence from the ∼200 ka Middle Stone Age Sibilo School Road Site, Baringo, Kenya. J. Hum. Evol. 103, 1–19 (2017).PubMed 

Google Scholar 
McBrearty, S. & Brooks, A. S. The revolution that wasn’t: a new interpretation of the origin of modern human behavior. J. Hum. Evol. 39, 453–563 (2000).CAS 
PubMed 

Google Scholar 
Klein, R. G. Archeology and the evolution of human behavior. Evol. Anthropol. 9, 17–36 (2000).
Google Scholar 
Wynn, T. & Coolidge, F. L. Archeological insights into hominin cognitive evolution. Evol. Anthropol. 25, 200–213 (2016).PubMed 

Google Scholar 
Derex, M. & Mesoudi, A. Cumulative cultural evolution within evolving population structures. Trends Cogn. Sci. 24, 654–667 (2020).PubMed 

Google Scholar 
Sterelny, K. Adaptable individuals and innovative lineages. Phil. Trans. R. Soc. B 371, 20150196 (2016).PubMed 
PubMed Central 

Google Scholar 
Henshilwood, C. S. & Marean, C. W. The origin of modern human behavior: critique of the models and their test implications. Curr. Anthropol. 44, 627–651 (2003).PubMed 

Google Scholar 
Stoops, G., Marcelino, V. & Mees, F. (eds) Interpretation of Micromorphological Features of Soils and Regoliths (Elsevier, 2010).Stoops, G. Guidelines for Analysis and Description of Soil and Regolith Thin Sections (Soil Science Society of America, 2003).McPherron, S. P. Additional statistical and graphical methods for analyzing site formation processes using artifact orientations. PLoS ONE 13, e0190195 (2018).PubMed 
PubMed Central 

Google Scholar 
Thomsen, K. J., Murray, A. S., Jain, M. & Bøtter-Jensen, L. Laboratory fading rates of various luminescence signals from feldspar-rich sediment extracts. Radiat. Meas. 43, 1474–1486 (2008).CAS 

Google Scholar 
Armitage, S. J. & Bailey, R. M. The measured dependence of laboratory beta dose rates on sample grain size. Radiat. Meas. 39, 123–127 (2005).CAS 

Google Scholar 
Huntley, D. J. & Lamothe, M. Ubiquity of anomalous fading in K-feldspars and the measurement and correction for it in optical dating. Can. J. Earth Sci. 38, 1093–1106 (2001).CAS 

Google Scholar 
Jaffey, A. H., Flynn, K. F., Glendenin, L. E. & Essling, A. M. Precision measurement of half-lives and specific activities of 235U and 238U. Phys. Rev. C 4, 1889–1906 (1971).
Google Scholar 
Cheng, H. et al. Improvements in 230Th dating, 230Th and 234U half-life values, and U–Th isotopic measurements by multi-collector inductively coupled plasma mass spectrometry. Earth Planet. Sci. Lett. 371–372, 82–91 (2013).
Google Scholar 
Holden, N. E. Total half-lives for selected nuclides. Pure Appl. Chem. 62, 941–958 (1990).CAS 

Google Scholar 
Ludwig, K. R. Isoplot/Ex Version 3.75: A Geochronological Toolkit for Microsoft Excel (Berkeley Geochronology Center Special Publication, 2010).Collins, B. & Steele, T. E. An often overlooked resource: ostrich (Struthio spp.) eggshell in the archaeological record. J. Archaeol. Sci. Rep. 13, 121–131 (2017).
Google Scholar 
Schmidt, P. How reliable is the visual identification of heat treatment on silcrete? A quantitative verification with a new method. Archaeol. Anthropol. Sci. 11, 713–726 (2017).
Google Scholar 
Roberts, D. L. Age, Genesis and Significance of South African Coastal Belt Silcretes (Council for Geoscience, South Africa, 2003).Schmidt, P. et al. A previously undescribed organic residue sheds light on heat treatment in the Middle Stone Age. J. Hum. Evol. 85, 22–34 (2015).PubMed 

Google Scholar 
Trabucco, A. & Zomer, R. Global Aridity Index and Potential Evapotranspiration (ET0) Climate Database v2 (figshare, 2019); https://doi.org/10.6084/m9.figshare.7504448.v3World Atlas of Desertification 2nd edn (UNEP, 1997).Mucina, L. & Rutherford, M. C. The Vegetation of South Africa, Lesotho and Swaziland (South African National Biodiversity Institute, 2006).Cordova, C. E. C3 Poaceae and Restionaceae phytoliths as potential proxies for reconstructing winter rainfall in South Africa. Quat. Int. 287, 121–140 (2013).
Google Scholar 
Esteban, I. et al. Modern soil phytolith assemblages used as proxies for paleoscape reconstruction on the south coast of South Africa. Quat. Int. 434, 160–179 (2017).
Google Scholar 
Laskar, J. et al. A long-term numerical solution for the insolation quantities of the Earth. Astron. Astrophys. 428, 261–285 (2004).
Google Scholar 
Chase, B. M. et al. Orbital controls on Namib Desert hydroclimate over the past 50,000 years. Geology 47, 867–871 (2019).
Google Scholar 
Farmer, E. C., deMenocal, P. B. & Marchitto, T. M. Holocene and deglacial ocean temperature variability in the Benguela upwelling region: implications for low‐latitude atmospheric circulation. Paleoceanography 20, PA2018 (2005).
Google Scholar 
Pichevin, L., Cremer, M., Giraudeau, J. & Bertrand, P. A 190 kyr record of lithogenic grain size on the Namibian slope: forging a tight link between past wind‐strength and coastal upwelling dynamics. Mar. Geol. 218, 81–96 (2005).
Google Scholar 
Little, M. G. et al. Trade wind forcing of upwelling, seasonality, and Heinrich events as a response to sub‐Milankovitch climate variability. Paleoceanography 12, 568–576 (2005).
Google Scholar 
Stuut, J.-B. et al. A 300‐kyr record of aridity and wind strength in southwestern Africa: inferences from grain‐size distributions of sediments on Walvis Ridge, SE Atlantic. Mar. Geol. 180, 221–233 (2002).
Google Scholar 
Kandel, A. W. & Conard, N. J. Production sequences of ostrich eggshell beads and settlement dynamics in the Geelbek Dunes of the Western Cape, South Africa. J. Archaeol. Sci. 32, 1711–1721 (2005).
Google Scholar  More