Philippa Kaur

Worden AZ, Follows MJ, Giovannoni SJ, Wilken S, Zimmerman AE, Keeling PJ. Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes. Science. 2015;347:1257594–1257594.PubMed 
Article 
CAS 

Google Scholar 
Guillou L, Viprey M, Chambouvet A, Welsh RM, Kirkham AR, Massana R, et al. Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environ Microbiol. 2008;10:3349–65.CAS 
PubMed 
Article 

Google Scholar 
Jephcott TG, Alves-de-Souza C, Gleason FH, van Ogtrop FF, Sime-Ngando T, Karpov SA, et al. Ecological impacts of parasitic chytrids, syndiniales and perkinsids on populations of marine photosynthetic dinoflagellates. Fungal Ecol. 2016;19:47–58.Article 

Google Scholar 
Alacid E, Reñé A, Garcés E. New Insights into the Parasitoid Parvilucifera sinerae Life Cycle: The Development and Kinetics of Infection of a Bloom-forming Dinoflagellate Host. Protist. 2015;166:677–99.PubMed 
Article 

Google Scholar 
Not F, Gausling R, Azam F, Heidelberg JF, Worden AZ. Vertical distribution of picoeukaryotic diversity in the Sargasso Sea. Environ Microbiol. 2007;9:1233–52.CAS 
PubMed 
Article 

Google Scholar 
Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, et al. Determinants of community structure in the global plankton interactome. Science 2015;348:1262073.de Vargas C, Audic S, Henry N, Decelle J, Mahe F, Logares R, et al. Eukaryotic plankton diversity in the sunlit ocean. Science. 2015;348:1261605.PubMed 
Article 
CAS 

Google Scholar 
Siano R, Alves-De-Souza C, Foulon E, Bendif M, Simon E, Guillou NL. et al. Distribution and host diversity of Amoebophryidae parasites across oligotrophic waters of the Mediterranean Sea. Biogeosciences. 2011;8:267–78.Article 

Google Scholar 
Coats DW. Parasitic life styles of marine dinoflagellates. J Eukaryot Microbiol. 1999;46:402–9.Article 

Google Scholar 
Farhat S, Le P, Kayal E, Noel B, Bigeard E, Corre E, et al. Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp. BMC Biol. 2021;19:1–21.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Gornik SG, Febrimarsa, Cassin AM, MacRae JI, Ramaprasad A, Rchiad Z, et al. Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate. Proc Natl Acad Sci USA. 2015;112:5767–72.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
John U, Lu Y, Wohlrab S, Groth M, Janouškovec J, Kohli GS, et al. An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome. Sci Adv. 2019;5:1–12.Article 
CAS 

Google Scholar 
McFadden GI, Reith ME, Munholland J, Lang-Unnasch N. Plastid in human parasites. Nature. 1996;381:482.CAS 
PubMed 
Article 

Google Scholar 
Sibbald SJ, Archibald JM. Genomic Insights into Plastid Evolution. Genome Biol Evol. 2020;12:978–90.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Not F, Probert I, Ribeiro CG, Crenn K, Guillou L, Jeanthon C, et al. Photosymbiosis in Marine Pelagic Environments. In: M. S. Cretoiu (ed). The Marine Microbiome. 2016. New York, NY: Springer International Publishing, pp 305–32.Cai R, Kayal E, Alves-de-Souza C, Bigeard E, Corre E, Jeanthon C, et al. Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach. Sci Rep. 2020;10:1–11.Article 
CAS 

Google Scholar 
Coats DW, Park MG. Parasitism of photosynthetic dinoflagellates by three strains of Amoebophrya (Dinophyta): Parasite survival, infectivity, generation time, and host specificity. J Phycol. 2002;38:520–8.Article 

Google Scholar 
Kayal E, Alves-de-Souza C, Farhat S, Velo-Suarez L, Monjol J, Szymczak J, et al. Dinoflagellate Host Chloroplasts and Mitochondria Remain Functional During Amoebophrya Infection. Front Microbiol. 2020;11:1–11.Article 

Google Scholar 
Miller JJ, Delwiche CF, Coats DW. Ultrastructure of Amoebophrya sp. and its Changes during the Course of Infection. Protist. 2012;163:720–45.PubMed 
Article 

Google Scholar 
Decelle J, Stryhanyuk H, Gallet B, Veronesi G, Schmidt M, Balzano S, et al. Algal Remodeling in a Ubiquitous Planktonic Photosymbiosis. Curr Biol. 2019;29:968–978.e4.CAS 
PubMed 
Article 

Google Scholar 
Uwizeye C, Mars Brisbin M, Gallet B, Chevalier F, LeKieffre C, Schieber NL, et al. Cytoklepty in the plankton: A host strategy to optimize the bioenergetic machinery of endosymbiotic algae. Proc Natl Acad Sci USA 2021;118.Uwizeye C, Decelle J, Jouneau P, Flori S, Gallet B, Keck J, et al. Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging. Nat Commun. 2021;12:1049.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Lowe DG. Distinctive Image Features from Scale-Invariant Keypoints. Int J Comput Vis. 2004;60:91–110.Article 

Google Scholar 
Hennies J, Lleti JMS, Schieber NL, Templin RM, Steyer AM, Schwab Y. AMST: alignment to median smoothed template for focused ion beam scanning electron microscopy image stacks. Sci Rep. 2020;10:1–10.Article 
CAS 

Google Scholar 
Kikinis R, Pieper SD, Vosburgh KG. 3D Slicer: A Platform for Subject-Specific Image Analysis, Visualization, and Clinical Support. Intraoperative Imaging and Image-Guided Therapy. 2014. Springer New York, New York, NY, pp 277–89.Polerecky L, Adam B, Milucka J, Musat N, Vagner T, Kuypers MMM. Look@NanoSIMS – a tool for the analysis of nanoSIMS data in environmental microbiology. Environ Microbiol. 2012;14:1009–23.CAS 
PubMed 
Article 

Google Scholar 
Jia B, Zhu XF, Pu ZJ, Duan YX, Hao LJ, Zhang J, et al. Integrative view of the diversity and evolution of SWEET and semiSWEET sugar transporters. Front Plant Sci. 2017;8:1–18.
Google Scholar 
Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 2019;20:1160–6.CAS 
PubMed 
Article 

Google Scholar 
Castresana J. Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis. Mol Biol Evol. 2000;17:540–52.CAS 
PubMed 
Article 

Google Scholar 
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013;8:1494–512.CAS 
PubMed 
Article 

Google Scholar 
Farhat S, Florent I, Noel B, Kayal E, Da Silva C, Bigeard E, et al. Comparative time-scale gene expression analysis highlights the infection processes of two amoebophrya strains. Front Microbiol. 2018;9:1–19.Article 

Google Scholar 
Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinforma. 2011;12:323.CAS 
Article 

Google Scholar 
Cachon J. Contribution à l’étude des péridiniens parasites. Cytologie, cycles évolutifs Ann Sci Nat Zool. 1964;6:1–158.
Google Scholar 
Van Dooren GG, Marti M, Tonkin CJ, Stimmler LM, Cowman AF, McFadden GI. Development of the endoplasmic reticulum, mitochondrion and apicoplast during the asexual life cycle of Plasmodium falciparum. Mol Microbiol. 2005;57:405–19.PubMed 
Article 
CAS 

Google Scholar 
Tyler KM, Matthews KR, Gull K. Anisomorphic cell division by African trypanosomes. Protist. 2001;152:367–78.CAS 
PubMed 
Article 

Google Scholar 
Jakob M, Hoffmann A, Amodeo S, Peitsch C, Zuber B, Ochsenreiter T. Mitochondrial growth during the cell cycle of Trypanosoma brucei bloodstream forms. Sci Rep. 2016;6:1–13.Article 
CAS 

Google Scholar 
Hughes L, Borrett S, Towers K, Starborg T, Vaughan S. Patterns of organelle ontogeny through a cell cycle revealed by whole-cell reconstructions using 3D electron microscopy. J Cell Sci. 2017;130:637–47.CAS 
PubMed 

Google Scholar 
Ovciarikova J, Lemgruber L, Stilger KL, Sullivan WJ, Sheiner L. Mitochondrial behaviour throughout the lytic cycle of Toxoplasma gondii. Sci Rep. 2017;7:1–13.Article 
CAS 

Google Scholar 
Nishi M, Hu K, Murray JM, Roos DS. Organellar dynamics during the cell cycle of Toxoplasma gondii. J Cell Sci. 2008;121:1559–68.CAS 
PubMed 
Article 

Google Scholar 
Long M, Marie D, Szymczak J, Toullec J, Bigeard E, Sourisseau M, et al. Dinophyceae can use exudates as weapons against the parasite Amoebophrya sp. (Syndiniales). ISME Commun. 2021;1:34.Article 

Google Scholar 
Harris E, Yoshida K, Cardelli J, Bush J. Rab11-like GTPase associates with and regulates the structure and function of the contractile vacuole system in. Dictyostelium J Cell Sci. 2001;114:3035–45.CAS 
PubMed 
Article 

Google Scholar 
Marshansky V, Rubinstein JL, Grüber G. Eukaryotic V-ATPase: Novel structural findings and functional insights. Biochim Biophys Acta – Bioenerg. 2014;1837:857–79.CAS 
Article 

Google Scholar 
Cox D, Lee DJ, Dale BM, Calafat J, Greenberg S. A Rab11-containing rapidly recycling compartment in macrophages that promotes phagocytosis. Proc Natl Acad Sci USA. 2000;97:680–5.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Vines JH, King JS. The endocytic pathways of Dictyostelium discoideum. Int J Dev Biol. 2019;63:461–71.CAS 
PubMed 
Article 

Google Scholar 
Decelle J, Veronesi G, LeKieffre C, Gallet B, Chevalier F, Stryhanyuk H, et al. Subcellular architecture and metabolic connection in the planktonic photosymbiosis between Collodaria (radiolarians) and their microalgae. Environ Microbiol. 2021;23:6569–86.CAS 
PubMed 
Article 

Google Scholar 
Sigee DC, Kearns LP. Levels of dinoflagellate chromosome-bound metals in conditions of low external ion availability: An X-ray microanalytical study. Tissue Cell. 1981;13:441–51.CAS 
PubMed 
Article 

Google Scholar 
Pinchuk GE, Ammons C, Culley DE, Li SMW, McLean JS, Romine MF, et al. Utilization of DNA as a sole source of phosphorus, carbon, and energy by Shewanella spp.: Ecological and physiological implications for dissimilatory metal reduction. Appl Environ Microbiol. 2008;74:1198–208.CAS 
PubMed 
Article 

Google Scholar 
Caffaro CE, Boothroyd JC. Evidence for Host Cells as the Major Contributor of Lipids in the Intravacuolar Network of Toxoplasma-Infected Cells. Eukaryot Cell. 2011;10:1095–9.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Lopez J, Bittame A, Massera C, Vasseur V, Effantin G, Valat A, et al. Intravacuolar membranes regulate CD8 T cell recognition of membrane-bound Toxoplasma gondii protective antigen. Cell Rep. 2015;13:2273–86.CAS 
PubMed 
Article 

Google Scholar 
Pszenny V, Ehrenman K, Romano JD, Kennard A, Schultz A, Roos DS, et al. A Lipolytic Lecithin:Cholesterol Acyltransferase Secreted by Toxoplasma Facilitates Parasite Replication and Egress. J Biol Chem. 2016;291:3725–46.CAS 
PubMed 
Article 

Google Scholar 
Nolan SJ, Romano JD, Coppens I. Host lipid droplets: An important source of lipids salvaged by the intracellular parasite Toxoplasma gondii. PLoS Pathog. 2017;13:e1006362.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Fox BA, Guevara RB, Rommereim LM, Falla A, Bellini V, Pètre G, et al. Toxoplasma gondii parasitophorous vacuole membrane-associated dense granule proteins orchestrate chronic infection and GRA12 underpins resistance to host gamma interferon. MBio. 2019; 10:e00589-19.Freeman Rosenzweig ES, Xu B, Kuhn Cuellar L, Martinez-Sanchez A, Schaffer M, Strauss M, et al. The eukaryotic CO2-concentrating organelle is liquid-like and exhibits dynamic reorganization. Cell. 2017;171:148–162.e19.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Zeeman SC, Kossmann J, Smith AM. Starch: Its metabolism, evolution, and biotechnological modification in plants. Annu Rev Plant Biol. 2010;61:209–34.CAS 
PubMed 
Article 

Google Scholar 
Qureshi AA, Suades A, Matsuoka R, Brock J, McComas SE, Nji E, et al. The molecular basis for sugar import in malaria parasites. Nature. 2020;578:321–5.CAS 
PubMed 
Article 

Google Scholar 
Blume M, Rodriguez-Contreras D, Landfear S, Fleige T, Soldati-Favre D, Lucius R, et al. Host-derived glucose and its transporter in the obligate intracellular pathogen Toxoplasma gondii are dispensable by glutaminolysis. Proc Natl Acad Sci USA. 2009;106:12998–3003.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Chen LQ, Qu XQ, Hou BH, Sosso D, Osorio S, Fernie AR, et al. Sucrose efflux mediated by SWEET proteins as a key step for phloem transport. Science (80-). 2012;335:207–11.CAS 
Article 

Google Scholar 
Latorraca NR, Fastman NM, Venkatakrishnan AJ, Frommer WB, Dror RO, Feng L. Mechanism of substrate translocation in an alternating access transporter. Cell. 2017;169:96–107.e12.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Amiar S, Katris NJ, Berry L, Dass S, Duley S, Arnold CS, et al. Division and adaptation to host environment of apicomplexan parasites depend on apicoplast lipid metabolic plasticity and host organelle remodeling. Cell Rep. 2020;30:3778–3792.e9.CAS 
PubMed 
Article 

Google Scholar 
Hu X, Binns D, Reese ML. The coccidian parasites Toxoplasma and Neospora dysregulate mammalian lipid droplet biogenesis. J Biol Chem. 2017;292:11009–20.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Gomes AF, Magalhães KG, Rodrigues RM, de Carvalho L, Molinaro R, Bozza PT, et al. Toxoplasma gondii-skeletal muscle cells interaction increases lipid droplet biogenesis and positively modulates the production of IL-12, IFN-g and PGE2. Parasit Vectors. 2014;7:47.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Jacot D, Waller RF, Soldati-Favre D, MacPherson DA, MacRae JI. Apicomplexan energy metabolism: carbon source promiscuity and the quiescence hyperbole. Trends Parasitol. 2016;32:56–70.CAS 
PubMed 
Article 

Google Scholar 
Salcedo-Sora JE, Caamano-Gutierrez E, Ward SA, Biagini GA. The proliferating cell hypothesis: a metabolic framework for Plasmodium growth and development. Trends Parasitol. 2014;30:170–5.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Muñoz-Gómez SA, Wideman JG, Roger AJ, Slamovits CH, Agashe D. The origin of mitochondrial cristae from alphaproteobacteria. Mol Biol Evol. 2017;34:943–56.PubMed 

Google Scholar 
Evers F, Cabrera-Orefice A, Elurbe DM, Kea-te Lindert M, Boltryk SD, Voss TS, et al. Composition and stage dynamics of mitochondrial complexes in Plasmodium falciparum. Nat Commun. 2021;12:1–17.Article 
CAS 

Google Scholar 
Krungkrai J, Prapunwattana P, Krungkrai SR. Ultrastructure and function of mitochondria in gametocytic stage of Plasmodium falciparum. Parasite. 2000;7:19–26.CAS 
PubMed 
Article 

Google Scholar 
Krungkrai J. The multiple roles of the mitochondrion of the malarial parasite. Parasitology 2004;129:511–524. https://doi.org/10.1017/S0031182004005888.Lee JW. Protonic capacitor: elucidating the biological significance of mitochondrial cristae formation. Sci Rep. 2020;10:1–14.Article 
CAS 

Google Scholar 
Stephan T, Brüser C, Deckers M, Steyer AM, Balzarotti F, Barbot M, et al. MICOS assembly controls mitochondrial inner membrane remodeling and crista junction redistribution to mediate cristae formation. EMBO J. 2020;39:1–24.Article 
CAS 

Google Scholar 
Pánek T, Eliáš M, Vancová M, Lukeš J, Hashimi H. Returning to the Fold for Lessons in Mitochondrial Crista Diversity and Evolution. Curr Biol. 2020;30:R575–R588.PubMed 
Article 
CAS 

Google Scholar 
Wideman JG, Muñoz-Gómez SA. The evolution of ERMIONE in mitochondrial biogenesis and lipid homeostasis: An evolutionary view from comparative cell biology. Biochim Biophys Acta – Mol Cell Biol Lipids. 2016. Elsevier B.V., 1861: 900-12.Mühleip A, Kock Flygaard R, Ovciarikova J, Lacombe A, Fernandes P, Sheiner L, et al. ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria. Nat Commun. 2021;12:120.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Flegontov P, Michálek J, Janouškovec J, Lai DH, Jirků M, Hajdušková E, et al. Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites. Mol Biol Evol. 2015;32:1115–31.CAS 
PubMed 
Article 

Google Scholar 
Painter HJ, Morrisey JM, Mather MW, Vaidya AB. Specific role of mitochondrial electron transport in blood-stage Plasmodium falciparum. Nature. 2007;446:88–91.CAS 
PubMed 
Article 

Google Scholar 
Nishida T, Hatama S, Ishikawa Y, Kadota K. Intranuclear coccidiosis in a calf. J Vet Med Sci. 2009;71:1109–13.PubMed 
Article 

Google Scholar 
Pecka Z. Life cycle and ultrastructure of Eimeria stigmosa, the intranuclear coccidian of the goose (Anser anser domesticus). Folia Parasitol (Praha). 1992;39:105–14.CAS 

Google Scholar 
Voleman L, Doležal P. Mitochondrial dynamics in parasitic protists. PLoS Pathog. 2019;15:e1008008.Bílý T, Sheikh S, Mallet A, Bastin P, Pérez‐Morga D, Lukeš J, et al. Ultrastructural changes of the mitochondrion during the life cycle of Trypanosoma brucei. J Eukaryot Microbiol. 2021;68:e12846.Elliott DA, McIntosh MT, Hosgood HD, Chen S, Zhang G, Baevova P, et al. Four distinct pathways of hemoglobin uptake in the malaria parasite Plasmodium falciparum. Proc Natl Acad Sci USA. 2008;105:2463–8.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar  More

Trinchet, J. C. et al. Complications and competing risks of death in compensated viral cirrhosis (ANRS CO12 CirVir prospective cohort). Hepatology 62, 737–750 (2015).Article 

Google Scholar 
Stanaway, J. D. et al. The global burden of viral hepatitis from 1990 to 2013: Findings from the Global Burden of Disease Study 2013. Lancet 388, 1081–1088 (2016).Article 

Google Scholar 
World Health Organization (WHO). Web Annex B. WHO estimates of the prevalence and incidence of hepatitis C virus infection by WHO region, 2015. In Global Hepatitis Report 2017. https://apps.who.int/iris/bitstream/handle/10665/277005/WHO-CDS-HIV-18.46-eng.pdf?ua=1. Accessed 01 Feb 2021.Smith, D. B. et al. Proposed update to the taxonomy of the genera Hepacivirus and Pegivirus within the Flaviviridae family. J. Gen. Virol. 97(11), 2894–2907 (2016).CAS 
Article 

Google Scholar 
Kapoor, A. et al. Characterization of a canine homolog of hepatitis C virus. Proc Natl Acad Sci USA 108, 11608–11613 (2011).ADS 
CAS 
Article 

Google Scholar 
Quan, P. L. et al. Bats are a major natural reservoir for hepaciviruses and pegiviruses. Proc Natl Acad Sci USA 110, 8194–8199 (2013).ADS 
CAS 
Article 

Google Scholar 
Burbelo, P. D. et al. Serology-enabled discovery of genetically diverse hepaciviruses in a new host. J Virol 86, 6171–6178 (2012).CAS 
Article 

Google Scholar 
Drexler, J. F. et al. Evidence for novel hepaciviruses in rodents. PLoS Pathog 9, e1003438 (2013).CAS 
Article 

Google Scholar 
Shi, Y. New virus, new challenge. Innovation (NY) 1(1), 100005 (2020).
Google Scholar 
Shi, M. et al. The evolutionary history of vertebrate RNA viruses. Nature 556, 197–202 (2018).ADS 
CAS 
Article 

Google Scholar 
Baechlein, C. et al. Identification of a novel hepacivirus in domestic cattle from Germany. J Virol 89, 7007–7015 (2015).CAS 
Article 

Google Scholar 
Corman, V. M. et al. Highly divergent hepaciviruses from African cattle. J Virol. 89, 5876–5882 (2015).CAS 
Article 

Google Scholar 
Simmonds, P. et al. ICTV virus taxonomy profile: Flaviviridae. J Gen Virol 98, 2–3 (2017).CAS 
Article 

Google Scholar 
Elia, G. et al. Genetic heterogeneity of bovine hepacivirus in Italy. Transbound Emerg Dis. 67, 2731–2740 (2020).CAS 
Article 

Google Scholar 
Li, L. L. et al. Detection and characterization of a novel hepacivirus in long-tailed ground squirrels (Spermophilus undulatus) in China. Arch Virol 164(9), 2401–2410 (2019).CAS 
Article 

Google Scholar 
Zhang, X. L. et al. A highly divergent hepacivirus identified in domestic ducks further reveals the genetic diversity of hepaciviruses. Viruses 14(2), 371 (2022).Article 

Google Scholar 
Lu, G., Ou, J., Zhao, J. & Li, S. Presence of a novel subtype of bovine hepacivirus in China and expanded classification of bovine hepacivirus strains worldwide into 7 subtypes. Viruses 11, 843 (2019).CAS 
Article 

Google Scholar 
da Silva, M. S. et al. Comprehensive evolutionary and phylogenetic analysis of Hepacivirus N (HNV). J Gen Virol. 99, 890–896 (2018).Article 

Google Scholar 
Shao, J. W. et al. A novel subtype of bovine hepacivirus identified in ticks reveals the genetic diversity and evolution of bovine hepacivirus. Viruses 13(11), 2206 (2021).CAS 
Article 

Google Scholar 
Baechlein, C. et al. Further characterization of bovine hepacivirus: Antibody response, course of infection, and host tropism. Transbound. Emerg. Dis. 66, 195–206 (2019).CAS 
Article 

Google Scholar 
Varela-Castro, L., Alvarez, V., Sevilla, I. A. & Barral, M. Risk factors associated to a high Mycobacterium tuberculosis complex seroprevalence in wild boar (Sus scrofa) from a low bovine tuberculosis prevalence area. PLoS ONE 15, e0231559 (2020).CAS 
Article 

Google Scholar 
Palombieri, A. et al. Surveillance study of Hepatitis E Virus (HEV) in domestic and wild ruminants in Northwestern Italy. Animals 10(12), 2351 (2020).Article 

Google Scholar 
Bukh, J. Hepatitis C homolog in dogs with respiratory illness. Proc Natl Acad Sci U S A. 108, 12563–12564 (2011).ADS 
CAS 
Article 

Google Scholar 
Elia, G. et al. Identification and genetic characterization of equine hepaciviruses in Italy. Vet. Microbiol. 207, 239–247 (2017).CAS 
Article 

Google Scholar 
Hartlage, A. S., Cullen, J. M. & Kapoor, A. The strange, expanding world of animal hepaciviruses. Annu Rev Virol. 3, 53–75 (2016).CAS 
Article 

Google Scholar 
Canal, C. W. et al. A novel genetic group of bovine hepacivirus in archival serum samples from Brazilian cattle. Biomed Res Int. 2017, 4732520 (2017).Article 

Google Scholar 
Deng, Y., Guan, S. H., Wang, S., Hao, G. & Rasmussen, T. B. The detection and phylogenetic analysis of Bovine Hepacivirus in China. Biomed Res Int. 2018, 6216853 (2018).PubMed 
PubMed Central 

Google Scholar 
Yeşilbağ, K. et al. Presence of bovine hepacivirus in Turkish cattle. Vet. Microbiol. 225, 1–5 (2018).Article 

Google Scholar 
Anggakusuma, et al. Hepacivirus NS3/4A proteases interfere with MAVS signaling in both their cognate animal hosts and humans: Implications for zoonotic transmission. J Virol. 90(23), 10670–10681 (2016).CAS 
Article 

Google Scholar 
El-Attar, L. M. R., Mitchell, J. A., BrooksBrownlie, H., Priestnall, S. L. & Brownlie, J. Detection of non-primate hepaciviruses in UK dogs. Virology 484, 93–102 (2015).CAS 
Article 

Google Scholar 
Thézé, J., Lowes, S., Parker, J. & Pybus, O. G. Evolutionary and phylogenetic analysis of the Hepaciviruses and Pegiviruses. Genome Biol Evol. 7(11), 2996–3008 (2015).Article 

Google Scholar 
Charrel, R. N., de Chesse, R., Decaudin, A., De Micco, P. & de Lamballerie, X. Evaluation of disinfectant efficacy against hepatitis C virus using a RT-PCR-based method. J. Hosp. Infect. 49(2), 129–134 (2001).CAS 
Article 

Google Scholar 
Pavio, N., Doceul, V., Bagdassarian, E. & Johne, R. Recent knowledge on hepatitis E virus in Suidae reservoirs and transmission routes to human. Vet Res. 48(1), 78 (2017).Article 

Google Scholar 
Scherer, C. et al. Moving infections: Individual movement decisions drive disease persistence in spatially structured landscapes. Oikos 129, 651–667 (2020).Article 

Google Scholar 
Tamura, K. & Nei, M. Estimation of the number of nucleotide substitution in the control region of mitochondrial DNA in human and chimpanzees. Mol. Biol. Evol. 10, 512–526 (1993).CAS 
PubMed 

Google Scholar 
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).CAS 
PubMed 
PubMed Central 

Google Scholar  More

Ottenburghs, J. et al. A history of hybrids? Genomic patterns of introgression in the True Geese. BMC Evol. Biol. 17, 14 (2017).Article 

Google Scholar 
Baiz, M. D., Tucker, P. K. & Cortés-Ortiz, L. Multiple forms of selection shape reproductive isolation in a primate hybrid zone. Mol. Ecol. 28, 1056–1069 (2019).CAS 
PubMed 
Article 

Google Scholar 
Slager, D. L. et al. Cryptic and extensive hybridization between ancient lineages of American crows. Mol. Ecol. 29, 956–969 (2020).CAS 
PubMed 
Article 

Google Scholar 
Grant, P. R. & Grant, B. R. Introgressive hybridization and natural selection in Darwin’s finches. Biol. J. Linnean Soc. 117, 812–822 (2016).Article 

Google Scholar 
Pauquet, G., Salzburger, W. & Egger, B. The puzzling phylogeography of the haplochromine cichlid fish Astatotilapia burtoni. Ecol. Evol. 8, 5637–5648 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Schluter, D. Ecological character displacement in adaptive radiation. Am. Nat. 156, S4–S16 (2000).Article 

Google Scholar 
Song, Y. et al. Adaptive introgression of anticoagulant rodent poison resistance by hybridization between old world mice. Curr. Biol. 21, 1296–1301 (2011).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Anderson, R. P., Peterson, A. T. & Gómez-Laverde, M. Using niche-based GIS modeling to test geographic predictions of competitive exclusion and competitive release in South American pocket mice. Oikos 98, 3–16 (2002).Article 

Google Scholar 
Gramlich, S., Wagner, N. D. & Horandl, E. RAD-seq reveals genetic structure of the F-2-generation of natural willow hybrids (Salix L.) and a great potential for interspecific introgression. BMC Plant Biol. 18, 12 (2018).Article 

Google Scholar 
Mavárez, J. et al. Speciation by hybridization in Heliconius butterflies. Nature 441, 868–871 (2006).ADS 
PubMed 
Article 
CAS 

Google Scholar 
Cahill, J. A. et al. Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears. Mol. Ecol. 24, 1205–1217 (2015).PubMed 
PubMed Central 
Article 

Google Scholar 
Djogbénou, L. et al. Evidence of introgression of the ace-1(R) mutation and of the ace-1 duplication in West African Anopheles gambiae s. s. PLoS ONE 3, e2172 (2008).ADS 
PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Enciso-Romero, J. et al. Evolution of novel mimicry rings facilitated by adaptive introgression in tropical butterflies. Mol. Ecol. 26, 5160–5172 (2017).PubMed 
Article 

Google Scholar 
Dasmahapatra, K. K. et al. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature 487, 94–98 (2012).ADS 
CAS 
PubMed Central 
Article 

Google Scholar 
Latch, E. K., Harveson, L. A., King, J. S., Hobson, M. D. & Rhodes, J. R. Assessing hybridization in wildlife populations using molecular markers: a case study in wild turkeys. J. Wildl. Manag. 70, 485–492 (2006).Article 

Google Scholar 
Oliveira, R., Godinho, R., Randi, E. & Alves, P. C. Hybridization versus conservation: are domestic cats threatening the genetic integrity of wildcats (Felis silvestris silvestris) in Iberian Peninsula?. Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci. 363, 2953–2961 (2008).Article 

Google Scholar 
Nichols, P. et al. Secondary contact seeds phenotypic novelty in cichlid fishes. Proc. R. Soc. B Biol. Sci. 282, 8 (2015).
Google Scholar 
Yang, W. Z. et al. Genomic evidence for asymmetric introgression by sexual selection in the common wall lizard. Mol. Ecol. 27, 4213–4224 (2018).CAS 
PubMed 
Article 

Google Scholar 
Boratyński, Z. et al. Introgression of mitochondrial DNA among Myodes voles: consequences for energetics?. BMC Evol. Biol. 11, 355 (2011).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Mondal, M. et al. Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation. Nat. Genet. 48, 1066–1070 (2016).CAS 
PubMed 
Article 

Google Scholar 
Melo-Ferreira, J., Seixas, F. A., Cheng, E., Mills, L. S. & Alves, P. C. The hidden history of the snowshoe hare, Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation. Mol. Ecol. 23, 4617–4630 (2014).CAS 
PubMed 
Article 

Google Scholar 
Mims, M. C., Hulsey, C. D., Fitzpatrick, B. M. & Streelman, J. T. Geography disentangles introgression from ancestral polymorphism in Lake Malawi cichlids. Mol. Ecol. 19, 940–951 (2010).PubMed 
Article 

Google Scholar 
Salazar, C. et al. Genetic evidence for hybrid trait speciation in heliconius butterflies. PLoS Genet. 6, e1000930 (2010).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Naisbit, R. E., Jiggins, C. D. & Mallet, J. Mimicry: developmental genes that contribute to speciation. Evol. Dev. 5, 269–280 (2003).CAS 
PubMed 
Article 

Google Scholar 
Zhang, W., Dasmahapatra, K. K., Mallet, J., Moreira, G. R. P. & Kronforst, M. R. Genome-wide introgression among distantly related Heliconius butterfly species. Genome Biol. 17, 15 (2016).Article 
CAS 

Google Scholar 
Zhang, W., Kunte, K. & Kronforst, M. R. Genome-wide characterization of adaptation and speciation in tiger swallowtail butterflies using De Novo transcriptome assemblies. Genome Biol. Evol. 5, 1233–1245 (2013).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Jones, M. R. et al. Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares. Science (New York, NY). 360, 1355–1358 (2018).ADS 
CAS 
Article 

Google Scholar 
Melville, J. Competition and character displacement in two species of scincid lizards. Ecol. Lett. 5, 386–393 (2002).Article 

Google Scholar 
Pfennig, D. W. & Pfennig, K. S. Character displacement and the origins of diversity. Am. Nat. 176, S26–S44 (2010).PubMed 
PubMed Central 
MATH 
Article 

Google Scholar 
Kooyers, N. J., James, B. & Blackman, B. K. Competition drives trait evolution and character displacement between Mimulus species along an environmental gradient. Evol. Int. J. Org. Evol. 71, 1205–1221 (2017).CAS 
Article 

Google Scholar 
Adams, D. C. & Rohlf, F. J. Ecological character displacement in Plethodon: Biomechanical differences found from a geometric morphometric study. Proc. Natl. Acad. Sci. 97, 4106–4111 (2000).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Grant, P. R. & Grant, B. R. Evolution of character displacement in Darwin’s finches. Science (New York, NY) 313, 224–226 (2006).ADS 
CAS 
Article 

Google Scholar 
Pfennig, D. W. & Murphy, P. J. Character displacement in polyphenic tadpoles. Evol. Int. J. Org. Evol. 54, 1738–1749 (2000).CAS 
Article 

Google Scholar 
Jones, G. Acoustic signals and speciation: the roles of natural and sexual selection in the evolution of cryptic species. Adv. Study Behav. 26, 317–354 (1997).Article 

Google Scholar 
Marsteller, S., Adams, D. C., Collyer, M. L. & Condon, M. Six cryptic species on a single species of host plant: morphometric evidence for possible reproductive character displacement. Ecol. Entomol. 34, 66–73 (2009).Article 

Google Scholar 
Tene Fossog, B. et al. Habitat segregation and ecological character displacement in cryptic African malaria mosquitoes. Evol. Appl. 8, 326–345 (2015).PubMed 
PubMed Central 
Article 

Google Scholar 
Ibáñez, C., García-Mudarra, J. L., Ruedi, M., Stadelmann, B. & Juste, J. The Iberian contribution to cryptic diversity in European bats. Acta Chiropterol. 8, 277–297 (2006).Article 

Google Scholar 
Juste, J. et al. Mitochondrial phylogeography of the long-eared bats (Plecotus) in the Mediterranean Palaearctic and Atlantic Islands. Mol. Phylogenet. Evol. 31, 1114–1126 (2004).CAS 
PubMed 
Article 

Google Scholar 
Schreber J. Die Säugthiere in Abbildungen nach der Natur, mit Beschreibungen. Erlangen – Expedition des Schreber’schen säugthier- und des Esper’schen Schmetterlingswerkes. Ernst Mayr Library of the MCZ, 1774–1855 (Harvard, 1774).Temminck, C. J. Monographies de Mammologie, ou description de quelques genres de Mammifères, dont les espèces ont été observes dans les différens Musées de l’Europe, Vol. 2, No. 302, 26–70 (G. Dufour et Ed. D’Ocagne, 1840).Centeno-Cuadros, A. et al. Comparative phylogeography and asymmetric hybridization between cryptic bat species. J. Zool. Syst. Evol. Res. 57, 1004–1018 (2019).Article 

Google Scholar 
Santos, H. et al. Shaping of bat cryptic distribution in Iberia. Biol. J. Linnean Soc. 112, 150–162 (2014).Article 

Google Scholar 
Novella-Fernandez, R. et al. Broad-scale patterns of geographic avoidance between species emerge in the absence of fine-scale mechanisms of coexistence. Divers. Distrib. 27, 1606–1618 (2021).Article 

Google Scholar 
Neubaum, M. A., Douglas, M. R., Douglas, M. E. & O’Shea, T. J. Molecular ecology of the big brown bat (Eptesicus fuscus): genetic and natural history variation in a hybrid zone. J. Mammal. 88, 1230–1238 (2007).Article 

Google Scholar 
Worthington-Wilmer, J. & Barratt, E. A non-lethal method of tissue sampling for genetic studies of chiropterans. Bat Res. News 37(1), 1–4 (1996).
Google Scholar 
Illumination, I.C.o. A colour appearance model for colour management systems: CIECAM02. Technical Report No CIE 159, 2004 (2004).Maroco, J. Análise estatística com utilização do SPSS. 3ª edição. Edições Silabo (2010).Wickham, H. et al. Welcome to the tidyverse. J. Open Source Softw. 4(43), 1686. https://doi.org/10.21105/joss.01686 (2019).ADS 
Article 

Google Scholar 
Karatzoglou, A., Smola, A., Hornik, K. & Zeileis, A. Kernlab: an S4 package for kernel methods in R. J. Stat. Softw. 11(9), 1–20 (2004).Article 

Google Scholar 
Meyer, D., Dimitriadou, E., Hornik, K., Weingessel, A. & Leisch, F. e1071: Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien. https://cran.r-project.org/web/packages/e1071/index.html (2012).Redgwell, R. D., Szewczak, J. M., Jones, G. & Parsons, S. Classification of echolocation calls from 14 species of bat by support vector machines and ensembles of neural networks. Algorithms 2, 907–924 (2009).Article 

Google Scholar 
Ochoa-López, S. et al. Ontogenetic changes in the targets of natural selection in three plant defenses. New Phytol. 226, 1480–1491 (2020).PubMed 
Article 
CAS 

Google Scholar 
Grant, P. R. & Grant, B. R. Phenotypic and genetics effects of hybridization in Darwin’s finches. Evol. Int. J. Org. Evol. 48, 297–316 (1994).Article 

Google Scholar 
Abzhanov, A., Protas, M., Grant, B. R., Grant, P. R. & Tabin, C. J. Bmp4 and morphological variation of beaks in Darwin’s finches. Science (New York, NY). 305, 1462–1465 (2004).ADS 
CAS 
Article 

Google Scholar 
von Holdt, B. M., Kays, R., Pollinger, J. P. & Wayne, R. K. Admixture mapping identifies introgressed genomic regions in North American canids. Mol. Ecol. 25, 2443–2453 (2016).Article 

Google Scholar 
Santana, S. E., Strait, S. & Dumont, E. R. The better to eat you with: functional correlates of tooth structure in bats. Funct. Ecol. 25, 839–847 (2011).Article 

Google Scholar 
Kalcounis, M. C. & Brigham, R. M. Intraspecific variation in wing loading affects habitat use by little brown bats (Myotis lucifugus). Can. J. Zool. 73, 89–95 (1995).Article 

Google Scholar 
Muijres, F. T., Johansson, L. C., Winter, Y. & Anders, H. Comparative aerodynamic performance of flapping flight in two bat species using time-resolved wake visualization. J. R. Soc. Interface 8, 1418–1428 (2011).PubMed 
PubMed Central 
Article 

Google Scholar 
Bradley, B. J. & Mundy, N. I. The primate palette: the evolution of primate coloration. Evol. Anthropolo. Issues News Rev. 17, 97–111 (2008).Article 

Google Scholar 
Müller, B. & Peichl, L. Retinal cone photoreceptors in microchiropteran bats. Investig. Ophthalmol. Vis. Sci. 46, 2259–2259 (2005).
Google Scholar 
Winter, Y., López, J. & von Helversen, O. Ultraviolet vision in a bat. Nature 425, 612–614 (2003).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Caro, T. The adaptive significance of coloration in mammals. Bioscience 55, 125–136 (2005).Article 

Google Scholar 
Chaverri, G., Ancillotto, L. & Russo, D. Social communication in bats. Biol. Rev. 93, 1938–1954 (2018).PubMed 
Article 

Google Scholar 
Dietz, C., Von Helversen, O. & Nill, D. Bats of Britain, Europe and Northwest Africa 320–333 (A&C Black Publishers Ltd, 2009).
Google Scholar 
Martinoli, A., Mazzamuto, M.V. & Spada, M. Serotine Eptesicus serotinus (Schreber, 1774). In Handbook of the Mammals of Europe, 1–17 (2020).Dinger, G. Winternachweise von Breitflügelfledermaus (Eptesicus serotinus) in Kirchen. Nyctalus (N.F.) 7, 614–616 (1991).
Google Scholar 
Kowalski, K. & Rzebik-Kowalska, B. Mammals of algeria (1991).Novella-Fernandez, R. et al. Trophic resource partitioning drives fine-scale coexistence in cryptic bat species. Ecol. Evol. 10(24), 14122–14136 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
Galván, I., Vargas-Mena, J. C. & Rodríguez-Herrera, B. Tent-roosting may have driven the evolution of yellow skin coloration in Stenodermatinae bats. J. Zool. Syst. Evol. Res. 58, 519–527 (2020).Article 

Google Scholar 
Wang, Z. L., Zhang, D. Y. & Wang, G. Does spatial structure facilitate coexistence of identical competitors. Ecol. Model. 181, 17–23 (2005).Article 

Google Scholar 
Anderson, T. M. et al. Molecular and evolutionary history of melanism in North American gray wolves. Science (New York, NY). 323, 1339–1343 (2009).ADS 
CAS 
PubMed Central 
Article 

Google Scholar 
Mingo-Casas, P. et al. First cases of European bat lyssavirus type 1 in Iberian serotine bats: implications for the molecular epidemiology of bat rabies in Europe. PLoS Negl. Trop. Dis. 12(4), e0006290 (2018).PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Vázquez-Moron, S., Juste, J., Ibáñez, C., Berciano, J. M. & Echevarria, J. E. Phylogeny of European bat Lyssavirus 1 in Eptesicus isabellinus bats, Spain. Emerg. Infect. Dis. 17, 520–523 (2011).PubMed 
PubMed Central 
Article 

Google Scholar 
Burgarella, C. et al. Detection of hybrids in nature: application to oaks (Quercus suber and Q. ilex). Heredity 102, 442–452 (2009).CAS 
PubMed 
Article 

Google Scholar 
Abrams, P. A. Character displacement and niche shift analyzed using consumer-resource models of competition. Theor. Popul. Biol. 29, 107–160 (1986).MathSciNet 
CAS 
PubMed 
MATH 
Article 

Google Scholar  More

Gattuso JP, Frankignoulle M, Wollast R. Carbon and carbonate metabolism in coastal aquatic ecosystems. Annu Rev Ecol Syst. 1998;29:405–34.Article 

Google Scholar 
Arnosti C, Wietz M, Brinkhoff T, Hehemann JH, Probandt D, Zeugner L, et al. The biogeochemistry of marine polysaccharides: sources, inventories, and bacterial drivers of the carbohydrate cycle. Ann Rev Mar Sci. 2021;13:81–108.CAS 
PubMed 
Article 

Google Scholar 
Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, Buchan A, et al. Deciphering ocean carbon in a changing world. Proc Natl Acad Sci USA. 2016;113:3143–51.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Poretsky RS, Sun S, Mou X, Moran MA. Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon. Environ Microbiol. 2010;12:616–27.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Azam F. Microbial control of oceanic carbon flux: The plot thickens. Science.1998;280:694–96.CAS 
Article 

Google Scholar 
Buchan A, LeCleir GR, Gulvik CA, González JM. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nat Rev Microbiol. 2014;12:686–98.CAS 
PubMed 
Article 

Google Scholar 
Bunse C, Bertos-Fortis M, Sassenhagen I, Sildever S, Sjoqvist C, Godhe A, et al. Spatio-temporal interdependence of bacteria and phytoplankton during a baltic sea spring bloom. Front Microbiol. 2016;7:517.PubMed 
PubMed Central 
Article 

Google Scholar 
Cram JA, Chow CE, Sachdeva R, Needham DM, Parada AE, Steele JA, et al. Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years. ISME J. 2015;9:563–80.PubMed 
Article 

Google Scholar 
Seymour JR, Amin SA, Raina JB, Stocker R. Zooming in on the phycosphere: the ecological interface for phytoplankton-bacteria relationships. Nat Microbiol. 2017;2:17065.CAS 
PubMed 
Article 

Google Scholar 
Taylor JD, Cottingham SD, Billinge J, Cunliffe M. Seasonal microbial community dynamics correlate with phytoplankton-derived polysaccharides in surface coastal waters. ISME J. 2014;8:245–8.CAS 
PubMed 
Article 

Google Scholar 
Teeling H, Fuchs BM, Becher D, Klockow C, Gardebrecht A, Bennke CM, et al. Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science.2012;336:608–11.CAS 
PubMed 
Article 

Google Scholar 
Hernando-Morales V, Varela MM, Needham DM, Cram J, Fuhrman JA, Teira E. Vertical and seasonal patterns control bacterioplankton communities at two horizontally coherent coastal upwelling sites off galicia (NW Spain). Microb Ecol. 2018;76:866–84.Needham DM, Fuhrman JA. Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom. Nat Microbiol. 2016;1:16005.Tada Y, Taniguchi A, Nagao I, Miki T, Uematsu M, Tsuda A, et al. Differing growth responses of major phylogenetic groups of marine bacteria to natural phytoplankton blooms in the western North Pacific Ocean. Appl Environ Microbiol. 2011;77:4055–65.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Williams TJ, Wilkins D, Long E, Evans F, DeMaere MZ, Raftery MJ, et al. The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics. Environ Microbiol. 2013;15:1302–17.CAS 
PubMed 
Article 

Google Scholar 
Ottesen EA, Young CR, Eppley JM, Ryan JP, Chavez FP, Scholin CA, et al. Pattern and synchrony of gene expression among sympatric marine microbial populations. Proc Natl Acad Sci USA. 2013;110:E488–97.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Ottesen EA, Young CR, Gifford SM, Eppley JM, Marin R 3rd, Schuster SC, et al. Ocean microbes. Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages. Science. 2014;345:207–12.CAS 
PubMed 
Article 

Google Scholar 
Beier S, Rivers AR, Moran MA, Obernosterer I. The transcriptional response of prokaryotes to phytoplankton-derived dissolved organic matter in seawater. Environ Microbiol. 2015;17:3466–80.CAS 
PubMed 
Article 

Google Scholar 
Sarmento H, Gasol JM. Use of phytoplankton-derived dissolved organic carbon by different types of bacterioplankton. Environ Microbiol. 2012;14:2348–60.CAS 
PubMed 
Article 

Google Scholar 
Shi Y, McCarren J, DeLong EF. Transcriptional responses of surface water marine microbial assemblages to deep-sea water amendment. Environ Microbiol. 2012;14:191–206.CAS 
PubMed 
Article 

Google Scholar 
Vorobev A, Sharma S, Yu M, Lee J, Washington BJ, Whitman WB, et al. Identifying labile DOM components in a coastal ocean through depleted bacterial transcripts and chemical signals. Environ Microbiol. 2018;20:3012–30.CAS 
PubMed 
Article 

Google Scholar 
Moran MA, Belas R, Schell MA, González JM, Sun F, Sun S, et al. Ecological genomics of marine Roseobacters. Appl Environ Microbiol. 2007;73:4559–69.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Nowinski B, Moran MA. Niche dimensions of a marine bacterium are identified using invasion studies in coastal seawater. Nat Microbiol. 2021;6:524–32.CAS 
PubMed 
Article 

Google Scholar 
Rinta-Kanto JM, Sun S, Sharma S, Kiene RP, Moran MA. Bacterial community transcription patterns during a marine phytoplankton bloom. Environ Microbiol. 2012;14:228–39.CAS 
PubMed 
Article 

Google Scholar 
Sharma AK, Becker JW, Ottesen EA, Bryant JA, Duhamel S, Karl DM, et al. Distinct dissolved organic matter sources induce rapid transcriptional responses in coexisting populations of Prochlorococcus, Pelagibacter and the OM60 clade. Environ Microbiol. 2013;16:2815–30.PubMed 
Article 
CAS 

Google Scholar 
Kieft B, Li Z, Bryson S, Hettich RL, Pan C, Mayali X, et al. Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits. Proc Natl Acad Sci USA. 2021;118:e2101178118.McCarren J, Becker JW, Repeta DJ, Shi Y, Young CR, Malmstrom RR, et al. Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proc Natl Acad Sci USA. 2010;107:16420–7.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Sosa OA, Gifford SM, Repeta DJ, DeLong EF. High molecular weight dissolved organic matter enrichment selects for methylotrophs in dilution to extinction cultures. ISME J. 2015;9:2725–39.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Pontiller B, Martínez-García S, Lundin D, Pinhassi J. Labile dissolved organic matter compound characteristics select for divergence in marine bacterial activity and transcription. Front Microbiol. 2020;11:588778.PubMed 
PubMed Central 
Article 

Google Scholar 
Bryson S, Li Z, Chavez F, Weber PK, Pett-Ridge J, Hettich RL, et al. Phylogenetically conserved resource partitioning in the coastal microbial loop. ISME J. 2017;11:2781–92.PubMed 
PubMed Central 
Article 

Google Scholar 
Joglar V, Prieto A, Barber-Lluch E, Hernández-Ruiz M, Fernández E, Teira E. Spatial and temporal variability in the response of phytoplankton and prokaryotes to B-vitamin amendments in an upwelling system. Biogeosciences.2020;17:2807–23.Article 

Google Scholar 
Martínez-García S, Fernández E, Álvarez-Salgado XA, González J, Lønborg C, Marañón E, et al. Differential responses of phytoplankton and heterotrophic bacteria to organic and inorganic nutrient additions in coastal waters off the NW Iberian Peninsula. Mar Ecol Prog Ser. 2010;416:17–33.Article 
CAS 

Google Scholar 
Welschmeyer NA. Fluorometric analysis of chlorophyll a in the presence of chlorophyll b and pheopigments. Limnol Oceanogr. 1994;39:1985–92.CAS 
Article 

Google Scholar 
Parsons TR, Maita Y, Lalli CM. Fluorometric determination of chlorophylls. A manual of chemical & biological methods for seawater analysis: Oxford, UK: Pergamon Press; 1984. p. 107–09.Hansen H, Grasshoff K. Automated chemical analysis. Methods of seawater analysis. 2nd ed: Verlag Chemie, Weinheim; 1983. p. 347–95.Álvarez-Salgado XA, Miller AEJ. Simultaneous determination of dissolved organic carbon and total dissolved nitrogen in seawater by high temperature catalytic oxidation: conditions for precise shipboard measurements. Mar Chem. 1998;62:325–33.Article 

Google Scholar 
Calvo-Díaz A, Morán XAG. Seasonal dynamics of picoplankton in shelf waters of the southern Bay of Biscay. Aquat Micro Ecol. 2006;42:159–74.Article 

Google Scholar 
Smith DC, Farooq A. A simple, economical method for measuring bacterial protein synthesis rates in seawater using 3H-leucine. Mar Micro Food Webs. 1992;6:107–14.
Google Scholar 
Parada AE, Needham DM, Fuhrman JA. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol. 2016;18:1403–14.CAS 
PubMed 
Article 

Google Scholar 
Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, Ferrera I, Sarmento H, et al. Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. Environ Microbiol. 2014;16:2659–71.CAS 
PubMed 
Article 

Google Scholar 
Straub D, Blackwell N, Langarica-Fuentes A, Peltzer A, Nahnsen S, Kleindienst S. Interpretations of environmental microbial community studies are biased by the selected 16S rRNA (Gene) amplicon sequencing pipeline. Front Microbiol. 2020;11:1–18.Article 

Google Scholar 
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.CAS 
PubMed 
Article 

Google Scholar 
Poretsky RS, Gifford S, Rinta-Kanto J, Vila-Costa M, Moran MA. Analyzing gene expression from marine microbial communities using environmental transcriptomics. J Vis Exp. 2009;24:1–6.
Google Scholar 
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. 2011;17:10–12.Article 

Google Scholar 
Joshi NA, Fass JN. Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files. 2011. https://github.com/najoshi/sickle.Del Fabbro C, Scalabrin S, Morgante M, Giorgi FM. An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLoS One. 2013;8:1–13.
Google Scholar 
Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics.2015;31:1674–6.CAS 
PubMed 
Article 

Google Scholar 
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 2010;11:119.Article 
CAS 

Google Scholar 
Rognes T, Flouri T, Nichols B, Quince C, Mahe F. VSEARCH: a versatile open source tool for metagenomics. PeerJ.2016;4:e2584.PubMed 
PubMed Central 
Article 

Google Scholar 
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60.CAS 
PubMed 
Article 

Google Scholar 
Huson DH, Beier S, Flade I, Górska A, El-Hadidi M, Mitra S, et al. MEGAN community edition – interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput Biol. 2016;12:1–12.Article 
CAS 

Google Scholar 
Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, et al. dbCAN2: A meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2018;46:W95–101.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Gloor GB, Wu JR, Pawlowsky-Glahn V, Egozcue JJ. It’s all relative: analyzing microbiome data as compositions. Ann Epidemiol. 2016;26:322–9.PubMed 
Article 

Google Scholar 
R Core Team. R: A language and environment for statistical computing. 4.1.0 ed. Vienna, Austria: R Foundation for Statistical Computing; 2021.Cottrell MT, Kirchman DL. Transcriptional control in marine copiotrophic and oligotrophic bacteria with streamlined genomes. Appl Environ Microbiol. 2016;82:6010–18.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Giovannoni SJ. SAR11 bacteria: The most abundant plankton in the oceans. Ann Rev Mar Sci. 2017;9:231–55.PubMed 
Article 

Google Scholar 
Newton RJ, Griffin LE, Bowles KM, Meile C, Gifford S, Givens CE, et al. Genome characteristics of a generalist marine bacterial lineage. ISME J. 2010;4:784–98.CAS 
PubMed 
Article 

Google Scholar 
Allers E, Gomez-Consarnau L, Pinhassi J, Gasol JM, Simek K, Pernthaler J. Response of Alteromonadaceae and Rhodobacteriaceae to glucose and phosphorus manipulation in marine mesocosms. Environ Microbiol. 2007;9:2417–29.CAS 
PubMed 
Article 

Google Scholar 
Alonso C, Pernthaler J. Roseobacter and SAR11 dominate microbial glucose uptake in coastal North Sea waters. Environ Microbiol. 2006;8:2022–30.CAS 
PubMed 
Article 

Google Scholar 
Noell SE, Giovannoni SJ. SAR11 bacteria have a high affinity and multifunctional glycine betaine transporter. Environ Microbiol. 2019;21:2559–75.CAS 
PubMed 
Article 

Google Scholar 
Sowell SM, Wilhelm LJ, Norbeck AD, Lipton MS, Nicora CD, Barofsky DF, et al. Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J. 2009;3:93–105.CAS 
PubMed 
Article 

Google Scholar 
Chenard C, Wijaya W, Vaulot D, Lopes Dos Santos A, Martin P, Kaur A, et al. Temporal and spatial dynamics of bacteria, archaea and protists in equatorial coastal waters. Sci Rep. 2019;9:16390.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Pajares S, Varona-Cordero F, Hernández-Becerril DU. Spatial distribution patterns of bacterioplankton in the oxygen minimum zone of the tropical mexican pacific. Micro Ecol. 2020;80:519–36.CAS 
Article 

Google Scholar 
Signori CN, Pellizari VH, Enrich-Prast A, Sievert SM. Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula. Deep-Sea Res Pt Ii. 2018;149:150–60.Article 

Google Scholar 
Ling SK, Xia J, Liu Y, Chen GJ, Du ZJ. Agarilytica rhodophyticola gen. nov., sp. nov., isolated from Gracilaria blodgettii. Int J Syst Evol Microbiol. 2017;67:3778–83.CAS 
PubMed 
Article 

Google Scholar 
Cheng H, Zhang S, Huo YY, Jiang XW, Zhang XQ, Pan J, et al. Gilvimarinus polysaccharolyticus sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Gilvimarinus. Int J Syst Evol Microbiol. 2015;65:562–69.CAS 
PubMed 
Article 

Google Scholar 
Malmstrom RR, Kiene RP, Cottrell MT, Kirchman DL. Contribution of SAR11 bacteria to dissolved dimethylsulfoniopropionate and amino acid uptake in the North Atlantic ocean. Appl Environ Microbiol. 2004;70:4129–35.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Kirchman DL. Growth rates of microbes in the oceans. Ann Rev Mar Sci. 2016;8:285–309.PubMed 
Article 

Google Scholar 
Durham BP, Dearth SP, Sharma S, Amin SA, Smith CB, Campagna SR, et al. Recognition cascade and metabolite transfer in a marine bacteria-phytoplankton model system. Environ Microbiol. 2017;19:3500–13.CAS 
PubMed 
Article 

Google Scholar 
Ferrer-González FX, Widner B, Holderman NR, Glushka J, Edison AS, Kujawinski EB, et al. Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy. ISME J. 2021;15:762–73.PubMed 
Article 
CAS 

Google Scholar 
Landa M, Burns AS, Roth SJ, Moran MA. Bacterial transcriptome remodeling during sequential co-culture with a marine dinoflagellate and diatom. ISME J. 2017;11:2677–90.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Pedler BE, Aluwihare LI, Azam F. Single bacterial strain capable of significant contribution to carbon cycling in the surface ocean. Proc Natl Acad Sci USA. 2014;111:7202–7.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Koch H, Dürwald A, Schweder T, Noriega-Ortega B, Vidal-Melgosa S, Hehemann JH, et al. Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides. ISME J. 2019;13:92–103.CAS 
PubMed 
Article 

Google Scholar 
López-Pérez M, Gonzaga A, Martin-Cuadrado AB, Onyshchenko O, Ghavidel A, Ghai R, et al. Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph. Sci Rep. 2012;2:696.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Bergauer K, Fernandez-Guerra A, Garcia JAL, Sprenger RR, Stepanauskas R, Pachiadaki MG, et al. Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics. Proc Natl Acad Sci USA. 2018;115:E400–8.CAS 
PubMed 
Article 

Google Scholar 
Hou S, López-Pérez M, Pfreundt U, Belkin N, Stüber K, Huettel B, et al. Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise. ISME J. 2018;12:981–96.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Pinhassi J, Sala MM, Havskum H, Peters F, Guadayol O, Malits A, et al. Changes in bacterioplankton composition under different phytoplankton regimens. Appl Environ Microbiol. 2004;70:6753–66.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Riemann L, Steward GF, Azam F. Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl Environ Microbiol. 2000;66:578–87.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Cottrell MT, Kirchman DL. Natural assemblages of marine Proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl Environ Microbiol. 2000;66:1692–7.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Krüger K, Chafee M, Ben Francis T, Glavina Del Rio T, Becher D, Schweder T, et al. In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes. ISME J. 2019;13:2800–16.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Ben Hania W, Joseph M, Bunk B, Spröer C, Klenk HP, Fardeau ML, et al. Characterization of the first cultured representative of a Bacteroidetes clade specialized on the scavenging of cyanobacteria. Environ Microbiol. 2017;19:1134–48.PubMed 
Article 
CAS 

Google Scholar 
Fernández-Gómez B, Richter M, Schüler M, Pinhassi J, Acinas SG, González JM, et al. Ecology of marine Bacteroidetes: a comparative genomics approach. ISME J. 2013;7:1026–37.PubMed 
PubMed Central 
Article 
CAS 

Google Scholar 
Orsi WD, Smith JM, Liu S, Liu Z, Sakamoto CM, Wilken S, et al. Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean. ISME J. 2016;10:2158–73.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Xing P, Hahnke RL, Unfried F, Markert S, Huang S, Barbeyron T, et al. Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom. ISME J. 2015;9:1410–22.CAS 
PubMed 
Article 

Google Scholar 
Sichert A, Corzett CH, Schechter MS, Unfried F, Markert S, Becher D, et al. Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan. Nat Microbiol. 2020;5:1026–39.Ivanova AA, Naumoff DG, Miroshnikov KK, Liesack W, Dedysh SN. Comparative genomics of four Isosphaeraceae Planctomycetes: a common pool of plasmids and glycoside hydrolase genes shared by Paludisphaera borealis PX4(T), Isosphaera pallida IS1B(T), Singulisphaera acidiphila DSM 18658(T), and Strain SH-PL62. Front Microbiol. 2017;8:412.PubMed 
PubMed Central 
Article 

Google Scholar 
Vidal-Melgosa S, Sichert A, Francis TB, Bartosik D, Niggemann J, Wichels A, et al. Diatom fucan polysaccharide precipitates carbon during algal blooms. Nat Commun. 2021;12:1150.CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Le Costaouëc T, Unamunzaga C, Mantecon L, Helbert W. New structural insights into the cell-wall polysaccharide of the diatom Phaeodactylum tricornutum. Algal Res. 2017;26:172–9.Article 

Google Scholar 
Francis TB, Bartosik D, Sura T, Sichert A, Hehemann JH, Markert S, et al. Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom. ISME J. 2021;15:2336–50.Bode A, Estévez MG, Varela M, Vilar JA. Annual trend patterns of phytoplankton species abundance belie homogeneous taxonomical group responses to climate in the NE Atlantic upwelling. Mar Environ Res. 2015;110:81–91.CAS 
PubMed 
Article 

Google Scholar 
Cermeño P, Marañón E, Pérez V, Serret P, Fernández E, Castro CG. Phytoplankton size structure and primary production in a highly dynamic coastal ecosystem (Ría de Vigo, NW-Spain): Seasonal and short-time scale variability. Estuar Coast Shelf Sci. 2006;67:251–66.Article 

Google Scholar 
Nogueira E, Pérez FF, Rı́os AF. Modelling thermohaline properties in an estuarine upwelling ecosystem (Rı́a de Vigo: NW Spain) using box-jenkins transfer function models. Estuar Coast Shelf Sci. 1997;44:685–702.Article 

Google Scholar 
Broullón E, López-Mozos M, Reguera B, Chouciño P, Doval MD, Fernández-Castro B, et al. Thin layers of phytoplankton and harmful algae events in a coastal upwelling system. Prog Oceanogr. 2020;189:102449.Fraga F. Upwelling off the Galician Coast, Northwest Spain. In: Richards FA, editor. Coastal Upwelling. Washington: American Geophysical Union; 1981. p. 176–82.Nogueira E, Figueiras FG. The microplankton succession in the Ría de Vigo revisited: species assemblages and the role of weather-induced, hydrodynamic variability. J Mar Syst. 2005;54:139–55.Article 

Google Scholar 
Pitcher GC, Walker DR, Mitchellinnes BA, Moloney CL. Short-term variability during an anchor station study in the southern Benguela Upwelling System – phytoplankton dynamics. Prog Oceanogr. 1991;28:39–64.Article 

Google Scholar 
Smayda TJ, Trainer VL. Dinoflagellate blooms in upwelling systems: Seeding, variability, and contrasts with diatom bloom behaviour. Prog Oceanogr. 2010;85:92–107.Article 

Google Scholar 
Wilkerson FP, Lassiter AM, Dugdale RC, Marchi A, Hogue VE. The phytoplankton bloom response to wind events and upwelled nutrients during the CoOP WEST study. Deep-Sea Res Pt Ii. 2006;53:3023–48.Article 

Google Scholar 
Reintjes G, Arnosti C, Fuchs B, Amann R. Selfish, sharing and scavenging bacteria in the Atlantic Ocean: a biogeographical study of bacterial substrate utilisation. ISME J. 2019;13:1119–32.CAS 
PubMed 
Article 

Google Scholar 
Mayali X, Weber PK, Pett-Ridge J. Taxon-specific C/N relative use efficiency for amino acids in an estuarine community. FEMS Microbiol Ecol. 2013;83:402–12.CAS 
PubMed 
Article 

Google Scholar  More

Parmesan, C. & Yohe, G. A globally coherent fingerprint of climate change impacts across natural systems. Nature 421, 37–42 (2003).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Ellis, E. C. et al. Used planet: a global history. Proc. Natl Acad. Sci. USA 110, 7978–7985 (2013).ADS 
CAS 
PubMed Central 
Article 
PubMed 

Google Scholar 
Marlon, J. R. et al. Global biomass burning: a synthesis and review of Holocene paleofire records and their controls. Quat. Sci. Rev. 65, 5–25 (2013).ADS 
Article 

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

Google Scholar 
Barnosky, A. D. et al. Approaching a state shift in Earth’s biosphere. Nature 52, 52–58 (2012).ADS 
Article 
CAS 

Google Scholar 
Boivin, N. L. et al. Ecological consequences of human niche construction: examining long-term anthropogenic shaping of global species distributions. Proc. Natl Acad. Sci. USA 113, 6388–6396 (2016).CAS 
PubMed Central 
Article 
PubMed 

Google Scholar 
Petrozzi, F. et al. Surveys of mammal communities in a system of five forest reserves suggest an ongoing biotic homogenization process for the Niger Delta (Nigeria). Trop. Zool. 28, 95–113 (2015).Article 

Google Scholar 
Chen, I.-C., Hill, J. K., Ohlemüller, R., Roy, D. B. & Thomas, C. D. Rapid range shifts of species associated with high levels of climate warming. Science 333, 1024–1026 (2011).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Estes, J. A. et al. Trophic downgrading of planet Earth. Science 333, 301–306 (2011).ADS 
CAS 
Article 
PubMed 

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

Google Scholar 
Sax, D. F. & Gaines, S. D. Species diversity: from global decreases to local increases. Trends Ecol. Evol. 18, 561–566 (2003).Article 

Google Scholar 
Vellend, M. et al. Global meta-analysis reveals no net change in local-scale plant biodiversity over time. Proc. Natl Acad. Sci. USA 110, 19456–19459 (2013).ADS 
CAS 
PubMed Central 
Article 
PubMed 

Google Scholar 
Finderup Nielsen, T., Sand‐Jensen, K., Dornelas, M. & Bruun, H. H. More is less: net gain in species richness, but biotic homogenization over 140 years. Ecol. Lett. 22, 1650–1657 (2019).Article 
PubMed 

Google Scholar 
Baiser, B., Olden, J. D., Record, S., Lockwood, J. L. & McKinney, M. L. Pattern and process of biotic homogenization in the New Pangaea. Proc. R. Soc. Lond. B: Biol. Sci. 279, 4772–4777 (2012).
Google Scholar 
Longman, E. K., Rosenblad, K. & Sax, D. F. Extreme homogenization: the past, present and future of mammal assemblages on islands. Glob. Ecol. Biogeogr. 27, 77–95 (2018).Article 

Google Scholar 
Spear, D. & Chown, S. L. Taxonomic homogenization in ungulates: patterns and mechanisms at local and global scales. J. Biogeogr. 35, 1962–1975 (2008).Article 

Google Scholar 
Tóth, A. B., Lyons, S. K. & Behrensmeyer, A. K. A century of change in Kenya’s mammal communities: increased richness and decreased uniqueness in six protected areas. PLoS ONE 9, e93092 (2014).ADS 
PubMed Central 
Article 
CAS 
PubMed 

Google Scholar 
Qian, H. & Ricklefs, R. E. The role of exotic species in homogenizing the North American flora. Ecol. Lett. 9, 1293–1298 (2006).Article 
PubMed 

Google Scholar 
Muthukrishnan, R. & Larkin, D. J. Invasive species and biotic homogenization in temperate aquatic plant communities. Glob. Ecol. Biogeogr. 29, 656–667 (2020).Article 

Google Scholar 
Early, R. et al. Global threats from invasive alien species in the twenty-first century and national response capacities. Nat. Commun. 7 1–9 (2016).Olden, J. D. & Poff, N. L. Toward a mechanistic understanding and prediction of biotic homogenization. Am. Naturalist 162, 442–460 (2003).Article 

Google Scholar 
McKinney, M. L. & Lockwood, J. L. Biotic homogenization: a few winners replacing many losers in the next mass extinction. Trends Ecol. Evol. 14, 450–453 (1999).CAS 
Article 
PubMed 

Google Scholar 
Vellend, M. et al. Homogenization of forest plant communities and weakening of species–environment relationships via agricultural land use. J. Ecol. 95, 565–573 (2007).Article 

Google Scholar 
Byers, J. E., Wright, J. T. & Gribben, P. E. Variable direct and indirect effects of a habitat‐modifying invasive species on mortality of native fauna. Ecology 91, 1787–1798 (2010).Article 
PubMed 

Google Scholar 
Didham, R. K., Tylianakis, J. M., Gemmell, N. J., Rand, T. A. & Ewers, R. M. Interactive effects of habitat modification and species invasion on native species decline. Trends Ecol. Evol. 22, 489–496 (2007).Article 
PubMed 

Google Scholar 
Tilman, D. et al. The influence of functional diversity and composition on ecosystem processes. Science 277, 1300–1302 (1997).CAS 
Article 

Google Scholar 
Lavery, T. H., Posala, C. K., Tasker, E. M. & Fisher, D. O. Ecological generalism and resilience of tropical island mammals to logging: a 23 year test. Glob. Change Biol. 26, 3285–3293 (2020).ADS 
Article 

Google Scholar 
Smith, F. A., Smith, R. E. E., Lyons, S. K. & Payne, J. L. Body size downgrading of mammals over the late Quaternary. Science 360, 310–313 (2018).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Sinclair, A. Mammal population regulation, keystone processes and ecosystem dynamics. Philos. Trans. R. Soc. B: Biol. Sci. 358, 1729–1740 (2003).CAS 
Article 

Google Scholar 
Ellison, A. M. et al. Loss of foundation species: consequences for the structure and dynamics of forested ecosystems. Front. Ecol. Environ. 3, 479–486 (2005).Article 

Google Scholar 
O’Connor, N. E. & Crowe, T. P. Biodiversity loss and ecosystem functioning: distinguishing between number and identity of species. Ecology 86, 1783–1796 (2005).Article 

Google Scholar 
Yachi, S. & Loreau, M. Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis. Proc. Natl Acad. Sci. USA 96, 1463–1468 (1999).ADS 
CAS 
PubMed Central 
Article 
PubMed 

Google Scholar 
Barnosky, A. D. et al. Merging paleobiology with conservation biology to guide the future of terrestrial ecosystems. Science 355, eaah4787 (2017).Article 
CAS 
PubMed 

Google Scholar 
Mihoub, J.-B. et al. Setting temporal baselines for biodiversity: the limits of available monitoring data for capturing the full impact of anthropogenic pressures. Sci. Rep. 7, 1–13 (2017).CAS 
Article 

Google Scholar 
Beller, E. et al. Toward principles of historical ecology. Am. J. Bot. 104, 645–648 (2017).Article 
PubMed 

Google Scholar 
Dietl, G. P. et al. Conservation paleobiology: leveraging knowledge of the past to inform conservation and restoration. Annu. Rev. Earth Planet. Sci. 43, 79–103 (2015).ADS 
CAS 
Article 

Google Scholar 
Stephens, L. et al. Archaeological assessment reveals Earth’s early transformation through land use. Science 365, 897–902 (2019).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Ellis, E. C. et al. People have shaped most of terrestrial nature for at least 12,000 years. Proc. Natl Acad. Sci. USA 118 e2023483118 (2021).Waters, M. R. Late Pleistocene exploration and settlement of the Americas by modern humans. Science 365 https://doi.org/10.1126/science.aat5447 (2019).Bennett, M. R. et al. Evidence of humans in North America during the last glacial maximum. Science 373, 1528–1531 (2021).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Lisiecki, L. E. & Raymo, M. E. Plio–Pleistocene climate evolution: trends and transitions in glacial cycle dynamics. Quat. Sci. Rev. 26, 56–69 (2007).ADS 
Article 

Google Scholar 
Lyons, S. K., Smith, F. A. & Brown, J. H. Of mice, mastodons and men: human-mediated extinctions on four continents. Evol. Ecol. Res. 6, 339–358 (2004).
Google Scholar 
Barnosky, A. D. Megafauna biomass tradeoff as a driver of Quaternary and future extinctions. Proc. Natl Acad. Sci. USA 105, 11543–11548 (2008).ADS 
CAS 
PubMed Central 
Article 
PubMed 

Google Scholar 
Koch, P. L. & Barnosky, A. D. Late Quaternary extinctions: state of the debate. Ann. Rev. Ecol. Evol. Syst. 37 215–250 (2006).Faith, J. T. & Surovell, T. A. Synchronous extinction of North America’s Pleistocene mammals. Proc. Natl Acad. Sci. USA 106, 20641–20645 (2009).ADS 
CAS 
PubMed Central 
Article 
PubMed 

Google Scholar 
Pineda-Munoz, S., Wang, Y., Lyons, S. K., Tóth, A. B. & McGuire, J. L. Mammal species occupy different climates following the expansion of human impacts. Proc. Natl Acad. Sci. USA 118, e1922859118 (2021).Graham, R. W. et al. Spatial response of mammals to late quaternary environmental fluctuations. Science 272, 1601–1606 (1996).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Blois, J. L., McGuire, J. L. & Hadly, E. A. Small mammal diversity loss in response to late-Pleistocene climatic change. Nature 465, 771–775 (2010).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Stewart, J. R., Lister, A. M., Barnes, I. & Dalén, L. Refugia revisited: individualistic responses of species in space and time. Proc. R. Soc. B: Biol. Sci. 277, 661 (2010).Article 

Google Scholar 
Lyons, S. K., Wagner, P. J. & Dzikiewicz, K. Ecological correlates of range shifts of Late Pleistocene mammals. Philos. Trans. R. Soc. B: Biol. Sci. 365, 3681–3693 (2010).Article 

Google Scholar 
Lyons, S. K. et al. The changing role of mammal life histories in Late Quaternary extinction vulnerability on continents and islands. Biol. Lett. 12, https://doi.org/10.1098/rsbl.2016.0342 (2016).Pineda‐Munoz, S. et al. Body mass‐related changes in mammal community assembly patterns during the late Quaternary of North America. Ecography 44, 56–66 (2021).Article 

Google Scholar 
Lyons, S. K. A quantitative model for assessing community dynamics of Pleistocene mammals. Am. Naturalist 165, E168–E185 (2005).Article 

Google Scholar 
Lyons, S. K. et al. Holocene shifts in the assembly of plant and animal communities implicate human impacts. Nature 529, 80–83 (2016).ADS 
Article 
CAS 
PubMed 

Google Scholar 
Pires, M. M. et al. Pleistocene megafaunal interaction networks became more vulnerable after human arrival. Proc. R. Soc. B: Biol. Sci. 282, 20151367 (2015).Article 

Google Scholar 
Pires, M. M., Guimarães, P. R., Galetti, M. & Jordano, P. Pleistocene megafaunal extinctions and the functional loss of long‐distance seed‐dispersal services. Ecography 41, 153–163 (2018).Article 

Google Scholar 
Galetti, M. et al. Ecological and evolutionary legacy of megafauna extinctions. Biol. Rev. 93, 845–862 (2018).Article 
PubMed 

Google Scholar 
Olden, J. D., Lockwood, J. L. & Parr, C. L. In Conservation biogeography (eds. Ladle, R. & Whittaker, R. J.) Ch. 9, 224–243 (John Wiley & Songs, 2011).Koleff, P., Gaston, K. J. & Lennon, J. J. Measuring beta diversity for presence-absence data. J. Anim. Ecol. 72, 367–382 (2003).Article 

Google Scholar 
Alroy, J. A new twist on a very old binary similarity coefficient. Ecology 96, 575–586 (2015).Article 
PubMed 

Google Scholar 
Ulrich, W. & Gotelli, N. J. Null model analysis of species nestedness patterns. Ecology 88, 1824–1831 (2007).Article 
PubMed 

Google Scholar 
Behrensmeyer, A. K., Western, D. & Boaz, D. E. D. New perspectives in vertebrate paleoecology from a recent bone assemblage. Paleobiology 5, 12–21 (1979).Article 

Google Scholar 
Behrensmeyer, A. K. & Dechant Boaz, D. E. In Fossils in the Making (ed. Behrensmeyer, A.K.) 72–92 (University of Chicago Press, 1980).Andrews, P. Owls, caves and fossils: predation, preservation and accumulation of small mammal bones in caves, with an analysis of the Pleistocene cave faunas from Westbury-sub-Mendip, Somerset, UK (University of Chicago Press, 1990).Badgley, C. Tectonics, topography, and mammalian diversity. Ecography 33, 220–231 (2010).
Google Scholar 
Buckley, L. B. & Jetz, W. Linking global turnover of species and environments. Proc. Natl Acad. Sci. USA 105, 17836–17841 (2008).ADS 
CAS 
PubMed Central 
Article 
PubMed 

Google Scholar 
Qian, H., Badgley, C. & Fox, D. L. The latitudinal gradient of beta diversity in relation to climate and topography for mammals in North America. Glob. Ecol. Biogeogr. 18, 111–122 (2009).Article 

Google Scholar 
Lorenz, D. J., Nieto-Lugilde, D., Blois, J. L., Fitzpatrick, M. C. & Williams, J. W. J. S. d. Downscaled and debiased climate simulations for North America from 21,000 years ago to 2100AD. 3, 160048 (2016).Rosenblad, K. C. & Sax, D. F. A new framework for investigating biotic homogenization and exploring future trajectories: Oceanic island plant and bird assemblages as a case study. Ecography 40, 1040–1049 (2017).Article 

Google Scholar 
Kortz, A. R. & Magurran, A. E. Increases in local richness (α-diversity) following invasion are offset by biotic homogenization in a biodiversity hotspot. Biol. Lett. 15, 20190133 (2019).PubMed Central 
Article 
PubMed 

Google Scholar 
Castro, S. A. et al. Partitioning β-diversity reveals that invasions and extinctions promote the biotic homogenization of Chilean freshwater fish fauna. PLoS ONE 15, e0238767 (2020).CAS 
PubMed Central 
Article 
PubMed 

Google Scholar 
Peoples, B. K., Davis, A. J., Midway, S. R., Olden, J. D. & Stoczynski, L. Landscape-scale drivers of fish faunal homogenization and differentiation in the eastern United States. Hydrobiologia 847, 3727–3741 (2020).Article 

Google Scholar 
Blois, J. L., Williams, J. W., Fitzpatrick, M. C., Jackson, S. T. & Ferrier, S. Space can substitute for time in predicting climate-change effects on biodiversity. Proc. Natl Acad. Sci. USA 110, 9374–9379 (2013).ADS 
CAS 
PubMed Central 
Article 
PubMed 

Google Scholar 
Qian, H. & Xiao, M. Global patterns of the beta diversity energy relationship in terrestrial vertebrates. Acta Oecol 39, 67–71 (2012).ADS 
Article 

Google Scholar 
Fritz, S. A. et al. Twenty-million-year relationship between mammalian diversity and primary productivity. Proc. Natl Acad. Sci. USA 113, 10908–10913 (2016).ADS 
CAS 
PubMed Central 
Article 
PubMed 

Google Scholar 
Figueirido, B., Janis, C. M., Pérez-Claros, J. A., Renzi, M. D. & Palmqvist, P. Cenozoic climate change influences mammalian evolutionary dynamics. Proc. Natl Acad. Sci. USA 109, 722–727 (2012).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Barnosky, A. D., Hadly, E. A. & Bell, C. J. Mammalian response to global warming on varied temporal scales. J. Mammal. 84, 354–368 (2003).Article 

Google Scholar 
Fraser, D., Hassall, C., Gorelick, R. & Rybczynski, N. Mean annual precipitation explains spatiotemporal patterns of Cenozoic mammal beta diversity and latitudinal diversity gradients in North America. PloS ONE 9, e106499 (2014).ADS 
PubMed Central 
Article 
CAS 
PubMed 

Google Scholar 
Darroch, S. A. F., Webb, A. E., Longrich, N. & Belmaker, J. Palaeocene–Eocene evolution of beta diversity among ungulate mammals in North America. Glob. Ecol. Biogeogr. 23, 757–768 (2014).Article 

Google Scholar 
Clark, P. U. et al. Global climate evolution during the last deglaciation. Proc. Natl Acad. Sci. USA 109, E1134–E1142 (2012).CAS 
PubMed Central 
PubMed 

Google Scholar 
Andersen, K. K. et al. High-resolution record of Northern Hemisphere climate extending into the last interglacial period. Nature 431, 147 (2004).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Hodell, D. A. et al. Anatomy of Heinrich Layer 1 and its role in the last deglaciation. Paleoceanography 32, 284–303 (2017).ADS 
Article 

Google Scholar 
McManus, J. F., Francois, R., Gherardi, J.-M., Keigwin, L. D. & Brown-Leger, S. Collapse and rapid resumption of Atlantic meridional circulation linked to deglacial climate changes. Nature 428, 834–837 (2004).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Thiagarajan, N., Subhas, A. V., Southon, J. R., Eiler, J. M. & Adkins, J. F. Abrupt pre-Bølling–Allerød warming and circulation changes in the deep ocean. Nature 511, 75–78 (2014).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Alley, R. B. The Younger Dryas cold interval as viewed from central Greenland. Quat. Sci. Rev. 19, 213–226 (2000).ADS 
Article 

Google Scholar 
Lyons, S. K. A quantitative assessment of the range shifts of Pleistocene mammals. J. Mammal. 84, 385–402 (2003).Article 

Google Scholar 
Davis, M. What North America’s skeleton crew of megafauna tells us about community disassembly. Proc. R. Soc. B. 284, 20162116 (2017).PubMed Central 
Article 
PubMed 

Google Scholar 
Tóth, A. B. et al. Reorganization of surviving mammal communities after the end-Pleistocene megafaunal extinction. Science 365, 1305–1308 (2019).ADS 
Article 
CAS 
PubMed 

Google Scholar 
Ripple, W. J. et al. Status and ecological effects of the world’s largest carnivores. Science 343, 1241484 (2014).Article 
CAS 
PubMed 

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

Google Scholar 
Owen-Smith, R. N. Megaherbivores: the influence of very large body size on ecology (Cambridge university press, 1992).Doughty, C. E. et al. Global nutrient transport in a world of giants. Proceedings of the National Academy of Sciences USA (2015).Araujo, B. B., Oliveira-Santos, L. G. R., Lima-Ribeiro, M. S., Diniz-Filho, J. A. F. & Fernandez, F. A. Bigger kill than chill: the uneven roles of humans and climate on late Quaternary megafaunal extinctions. Quat. Int. 431, 216–222 (2017).Article 

Google Scholar 
Stewart, M., Carleton, W. C. & Groucutt, H. S. Climate change, not human population growth, correlates with Late Quaternary megafauna declines in North America. Nat. Commun. 12, 1–15 (2021).Article 
CAS 

Google Scholar 
Gill, J. L., Williams, J. W., Jackson, S. T., Lininger, K. B. & Robinson, G. S. Pleistocene megafaunal collapse, novel plant communities, and enhanced fire regimes in North America. Science 326, 1100–1103 (2009).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Johnson, C. N. Ecological consequences of Late Quaternary extinctions of megafauna. Proc. R. Soc. Lond. B: Biol. Sci., rspb 2008, 1921 (2009).
Google Scholar 
Barnosky, A. D. et al. Variable impact of late-Quaternary megafaunal extinction in causing ecological state shifts in North and South America. Proc. Natl Acad. Sci. USA 113, 856–861 (2016).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Kelt, D. A. & Van Vuren, D. Energetic constraints and the relationship between body size and home range area in mammals. Ecology 80, 337–340 (1999).Article 

Google Scholar 
McKinney, M. L. Urbanization as a major cause of biotic homogenization. Biol. Conserv. 127, 247–260 (2006).Article 

Google Scholar 
Arnan, X., Cerdá, X. & Rodrigo, A. Do Forest Fires Make Biotic Communities Homogeneous or Heterogeneous? Patterns of taxonomic, functional, and phylogenetic ant beta diversity at local and regional landscape scales. Front. Forests Glob. Change 3, https://doi.org/10.3389/ffgc.2020.00067 (2020).Gámez-Virués, S. et al. Landscape simplification filters species traits and drives biotic homogenization. Nat. Commun. 6, 1–8 (2015).Article 
CAS 

Google Scholar 
Luque-Larena, J. J. et al. Recent large-scale range expansion and outbreaks of the common vole (Microtus arvalis) in NW Spain. Basic Appl. Ecol. 14, 432–441 (2013).Article 

Google Scholar 
Clavel, J., Julliard, R. & Devictor, V. Worldwide decline of specialist species: toward a global functional homogenization? Front. Ecol. Environ. 9, 222–228 (2011).Article 

Google Scholar 
Rader, R., Bartomeus, I., Tylianakis, J. M. & Laliberté, E. The winners and losers of land use intensification: Pollinator community disassembly is non‐random and alters functional diversity. Divers. Distrib. 20, 908–917 (2014).Article 

Google Scholar 
Tilman, D. et al. Forecasting agriculturally driven global environmental change. science 292, 281–284 (2001).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Price, T. D. Ancient farming in eastern North America. Proc. Natl Acad. Sci. USA 106, 6427–6428 (2009).ADS 
CAS 
PubMed Central 
Article 
PubMed 

Google Scholar 
Smith, B. D. The origins of agriculture in the Americas. Evolut. Anthropol.: Issues, N., Rev. 3, 174–184 (1994).Article 

Google Scholar 
Olden, J. D., Poff, N. L. & McKinney, M. L. Forecasting faunal and floral homogenization associated with human population geography in North America. Biol. Conserv. 127, 261–271 (2006).Article 

Google Scholar 
Olden, J. D., LeRoy Poff, N., Douglas, M. R., Douglas, M. E. & Fausch, K. D. Ecological and evolutionary consequences of biotic homogenization. Trends Ecol. Evol. 19, 18–24 (2004).Article 
PubMed 

Google Scholar 
Mori, A. S., Furukawa, T. & Sasaki, T. Response diversity determines the resilience of ecosystems to environmental change. Biol. Rev. 88, 349–364 (2013).Article 
PubMed 

Google Scholar 
Ellis, E. C. & Ramankutty, N. Putting people in the map: anthropogenic biomes of the world. Front. Ecol. Environ. 6, 439–447 (2008).Article 

Google Scholar 
Toivanen, T. et al. The many Anthropocenes: a transdisciplinary challenge for the Anthropocene research. Anthropocene Rev. 4, 183–198 (2017).Article 

Google Scholar 
Biotic homogenization (Github, 2022).Brown, J. H. & Nicoletto, P. F. Spatial scaling of species composition: body masses of North American Land Mammals. Am. Naturalist 138, 1478–1512 (1991).Article 

Google Scholar 
Lyons, S. K. & Smith, F. A. In Animal body size: linking pattern and process across space, time, and taxonomic group (eds. Smith & S. Kathleen Lyons) (University of Chicago Press, 2013).Graham, R. W. & E. L. Lundelius, J. FAUNMAP II: New data for North America with a temporal extension for the Blancan, Irvingtonian and early Rancholabrean. FAUNMAP II Database, version 1.0., 2010).Haslett, J. & Parnell, A. A simple monotone process with application to radiocarbon-dated depth chronologies. J. Roy. Stat. Soc. Ser. C. (Appl. Stat.) 57, 399–418 (2008).MathSciNet 
MATH 
Article 

Google Scholar 
Pebesma, E. J. & Bivand, R. S. Classes and methods for spatial data in R. R News 5 (2005).raster: Geographic data analysis and modeling version 3.4-10 (2021).mapdata: Extra Map Database. R package version 2.3.0. (2018).maps: Draw Geographical Maps version 3.4.0 (2021).Wickham, H. ggplot2: elegant graphics for data analysis (Springer-Verlag, 2016).Grimm, E. C., Maher, L. J. Jr & Nelson, D. M. The magnitude of error in conventional bulk-sediment radiocarbon dates from central North America. Quatern. Res 72, 301–308 (2009).ADS 
CAS 
Article 

Google Scholar 
Whittaker, R. H. Vegetation of the Siskiyou mountains, Oregon and California. Ecol. Monogr. 30, 279–338 (1960).Article 

Google Scholar 
R: A language and environment for statistical computing (R Foundation for Statistical Computing, Vienna, Austria, 2020).Baselga, A. & Orme, D. Package ‘betapart’. (2012).Package vegan version 2.5-7 (2012).Vavrek, M. J. fossil: palaeoecological and palaeogeographical analysis tools. Palaeontologia Electron. 14, 1T (2011).
Google Scholar 
Marschner, I. C. glm2: Fitting generalized linear models with convergence problems. R. J. 3, 12–15 (2011).Article 

Google Scholar 
Baselga, A. Partitioning the turnover and nestedness components of beta diversity. Glob. Ecol. Biogeogr. 19, 134–143 (2010).Article 

Google Scholar 
Anderson, M. J., Ellingsen, K. E. & McArdle, B. H. Multivariate dispersion as a measure of beta diversity. Ecol. Lett. 9, 683–693 (2006).Article 
PubMed 

Google Scholar 
Nekola, J. C. & McGill, B. J. Scale dependency in the functional form of the distance decay relationship. Ecography 37, 309–320 (2014).Article 

Google Scholar 
Legendre, P. & De Cáceres, M. Beta diversity as the variance of community data: dissimilarity coefficients and partitioning. Ecol. Lett. 16, 951–963 (2013).Article 
PubMed 

Google Scholar 
Marion, Z. H., Fordyce, J. A. & Fitzpatrick, B. M. Pairwise beta diversity resolves an underappreciated source of confusion in calculating species turnover. Ecology 98, 933–939 (2017).Article 
PubMed 

Google Scholar 
Calenge, C. A collection of tools for the estimation of animals home range. (2017).Ulrich, W. et al. Species richness correlates of raw and standardized co‐occurrence metrics. Glob. Ecol. Biogeogr. 27, 395–399 (2018).Article 

Google Scholar 
Gotelli, N. J. Null model analysis of species co-occurrence patterns. Ecology 81, 2606–2621 (2000).Article 

Google Scholar 
Newell, N. D. Adequacy of the fossil record. J. Paleontol. 33, 488–499 (1959).
Google Scholar 
Raup, D. M. Biases in the fossil record of species and genera. Bull. Carnegie Mus. Nat. Hist. 13, 85–91 (1979).
Google Scholar 
Kidwell, S. M. & Holland, S. M. The quality of the fossil record: implications for evolutionary analyses. Annu. Rev. Ecol. Syst. 33, 561–588 (2002).Article 

Google Scholar 
Benton, M. J., Dunhill, A. M., Lolyd, G. T. & Marx, F. G. In Comparing the geological and fossil records: implications for biodiversity studies Vol. 358 (eds. McGowan, A. J. & A. B. Smith, A. B.) 63–94 (Geological Society of London, 2011).Graham, C. H. & Fine, P. V. A. Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time. Ecol. Lett. 1265–1277 (2008).Patterson, B. D. et al. Digital Distribution Maps of the Mammals of the Western Hemisphere, version 3.0. NatureServe, (Arlington, Virginia, USA, 2007).Wilson, D. E. & Reeder, D. M. Mammal species of the world:ataxonomic and geographic reference. 3rd edition. (Johns Hopkins University Press,Baltimore, Maryland, 2,142 pp 2005).Fraser, D. & Lyons, S. K. Biotic interchange has structured Western Hemisphere mammal communities. Glob. Ecol. Biogeogr. 26, 1408–1422 (2017).Article 

Google Scholar 
Bivand, R. & Lewin-Koh, N. J. Maptools: Tools for Reading and Handling Spatial Objects R package (2021).Hurlbert, A. H. & Jetz, W. Species richness, hotspots, and the scale dependence of range maps in ecology and conservation. Proc. Natl Acad. Sci. USA 104, 13384–13389 (2007).ADS 
CAS 
PubMed Central 
Article 
PubMed 

Google Scholar 
Bivand, R. S., Pebesma, E. J. & Gomez-Rubio, V. Applied spatial data analysis with R. (Springer, 2008).Currie, D. J. et al. Predictions and tests of climate-based hypotheses of broad-scale variation in taxonomic richness. Ecol. Lett. 7, 1121–1134 (2004).Article 

Google Scholar  More

Biere, J. M. & Uetz, G. W. Web orientation in the spider Micrathena gracilis (Araneae: Araneidae). Ecology 62(2), 336–344 (1981).Article 

Google Scholar 
Korb, J. & Linsenmair, K. E. The architecture of termite mounds: a result of a trade-off between thermoregulation and gas exchange? Behav. Ecol. 10(3), 312–316 (1999).Article 

Google Scholar 
Hansell, M. H. Bird nests and construction behaviour (Cambridge University Press, 2000).Book 

Google Scholar 
Kawase, H., Okata, Y. & Ito, K. Role of huge geometric circular structures in the reproduction of a Marine Pufferfish. Sci. Rep. 3, 1–5 (2013).Article 

Google Scholar 
Dawkins, R. The extended phenotype 295 (Oxford University Press, 1982).
Google Scholar 
Odling-Smee, F. J., Laland, K. N. & Feldman, M. W. Niche construction. Am. Nat. 147(4), 641–648 (1996).Article 

Google Scholar 
Odling-Smee, F. J., Laland, K. N. & Feldman, M. W. Niche construction: the Neglected process in evolution (Princeton University Press, 2003).
Google Scholar 
Short, L. L. Burdens of the picid hole-excavating habit. Wilson Bull. 91(1), 16–28 (1979).
Google Scholar 
Wiebe, K. L., Koenig, W. D. & Martin, K. Costs and benefits of nest reuse versus excavation in cavity-nesting birds. Ann. Zool. Fenn. 44(3), 209–217 (2007).
Google Scholar 
Landler, L. et al. Global trends in woodpecker cavity orientation: latitudinal and continental effects suggest regional climate influence. Acta Ornithol. 49(2), 257–266 (2014).Article 

Google Scholar 
Ojeda, V. et al. Latitude does not influence cavity entrance orientation of South American avian excavators. Auk 138(1), ukaa064 (2021).Article 

Google Scholar 
Wiebe, K. L. Microclimate of tree cavity nests: is it important for reproductive success in Northern Flickers? Auk 118(2), 412–421 (2001).Article 

Google Scholar 
Schaaf, A. A. Effects of sun exposure and vegetation cover on Woodpecker nest orientation in subtropical forests of South America. J. Ethol. 38, 117–120 (2019).Article 

Google Scholar 
Hooge, P. N., Stanback, M. T. & Koenig, W. D. Nest-site selection in the acorn woodpecker. Auk 116(1), 45–54 (1999).Article 

Google Scholar 
Schaaf, A. A. & de la Pena, M. R. Bird nest orientation and local temperature: an analysis over three decades. Ecology 20, e03042 (2020).
Google Scholar 
Charter, M. et al. Does nest box location and orientation affect occupation rate and breeding success of barn owls Tyto alba in a semi-arid environment? Acta Ornithol. 45(1), 115–119 (2010).Article 

Google Scholar 
Butler, M. W., Whitman, B. A. & Dufty, A. M. Nest box temperature and hatching success of American kestrels varies with nest box orientation. Wilson J. Ornithol. 121(4), 778–782 (2009).Article 

Google Scholar 
Goodenough, A. E. et al. Nestbox orientation: a species-specific influence on occupation and breeding success in woodland passerines. Bird Study 55(2), 222–232 (2008).Article 

Google Scholar 
Viñuela, J. & Sunyer, C. Nest orientation and hatching success of black kites milvus migrans in Spain. Ibis 134(4), 340–345 (1992).Article 

Google Scholar 
Larson, E. R. et al. How does nest box temperature affect nestling growth rate and breeding success in a parrot?. Emu 115(3), 247–255 (2015).Article 

Google Scholar 
Austin, G. T. Nesting success of the cactus wren in relation to nest orientation. Condor 76(2), 216–217 (1974).Article 

Google Scholar 
Verbeek, N. A. Nesting success and orientation of water pipit Anthus spinoletta nests. Ornis Scand. 25, 37–39 (1981).Article 

Google Scholar 
Conner, R. N. & Rudolph, D. C. Excavation dynamics and use patterns of red-cockaded woodpecker cavities: relationships with cooperative breeding. Red cockaded Woodpecker: recovery, ecology, and management. Center for Applied Studies in Forestry, College of Forestry, Stephen F. Austin State University, Nacogdoches, TX, 1995: 343–352.Harding, S. R. & Walters, J. R. Dynamics of cavity excavation by red-cockaded woodpeckers. In Red-Cockaded Woodpecker: Road to Recovery (eds Costa, R. & Daniels, S.) 412–422 (Hancock House, 2004).
Google Scholar 
Harding, S. R. & Walters, J. R. Processes regulating the population dynamics of red-cockaded woodpecker cavities. J. Wildl. Manage. 66(4), 1083–1095 (2002).Article 

Google Scholar 
Dennis, J. V. The yellow-shafted flicker (Colaptes Auratus) on Nantucket Island, Massachusetts. Bird Banding 40(4), 290–308 (1969).Article 

Google Scholar 
Baker, W. W. Progress report on life history studies of the red-cockaded woodpecker at Tall Timbers Research Station. Ecology and Management of the Redcockaded Woodpecker 44–59 (US Bureau of Sport Fisheries and Wildlife and Tall Timbers Research Station, 1971).
Google Scholar 
Dennis, J. V. Species using red-cockaded woodpecker holes in Northeastern South Carolina. Bird-Banding 42(2), 79–87 (1971).Article 

Google Scholar 
Conner, R. N. et al. Red-cockaded woodpecker nest-cavity selection: relationships with cavity age and resin production. Auk 115(2), 447–454 (1998).Article 

Google Scholar 
Conner, R. N. Orientation of entrances to woodpecker nest cavities. Auk 92(2), 371–374 (1975).Article 

Google Scholar 
Copeyon, C. K., Walters, J. R. & Carter, J. III. Induction of red-cockaded woodpecker group formation by artificial cavity construction. J. Wildl. Manage. 55(4), 549–556 (1991).Article 

Google Scholar 
Locke, B. A. & Conner, R. N. A statistical analysis of the orientation of entrances to redcockaded woodpecker cavities. In Red-Cockaded Woodpecker Symposium II (Florida Game and Fresh Water Fish Commission, 1983).
Google Scholar 
Lay, D. W., Red-cockaded woodpecker study. Texas Parks and Wildlife Department. Project W-80-R-16. 1973. p. 33.Jones, H. K. & Ott, F. T. Some characteristics of red-cockaded woodpecker cavity trees in Georgia. Oriole 38, 33–39 (1973).
Google Scholar 
Hopkins, M. L. & Lynn, T. E. Jr. Some characteristics of red-cockaded woodpecker cavity trees and management implications in South Carolina. Ecology and Management of The Red-Cockaded Woodpecker 140–169 (US Bureau of Sport Fishing and Wildlife and Tall Timbers Research Station, 1971).
Google Scholar 
Wood, D. A. Foraging and colony habitat characteristics of the red-cockaded woodpecker in Oklahoma. In Red-Cockaded Woodpecker Symposium II 51–58 (Florida Game and Fresh Water Fish Commission, 1983).
Google Scholar 
Kalisz, P. J. & Boettcher, S. E. Active and abandoned red-cockaded woodpecker habitat in Kentucky. J. Wildl. Manage. 25, 146–154 (1991).Article 

Google Scholar 
Walters, J. R., Doerr, P. D. & J. H. Carter, III. The cooperative breeding system of the red cockaded woodpecker. Ethology 78, 275–305 (1988).Article 

Google Scholar 
Batschelet, E. Circular statistics in biology (Academic Press, 1981).MATH 

Google Scholar 
Agostinelli, C. & U. Lund, R package “circular”: circular statistics. R package version 0.4-7. https://r-forge.r-project.org/projects/circular (2013).Hijmans, R. J. & Etten, J. V. Raster: Geographic analysis and modeling with raster data. R package version 2.0-12 (2012).R Development Core Team R. A language and environment for statistical computing (R Foundation for Statistical Computing, 2012).
Google Scholar 
Goslee, S. C. & Urban, D. L. The ecodist package for dissimilarity-based analysis of ecological data. J. Stat. Softw. 22(7), 1–19 (2007).Article 

Google Scholar 
Cox, N. J. Speaking Stata: In praise of trigonometric predictors. Stand. Genomic Sci. 6(4), 561–579 (2006).
Google Scholar 
Smith, J. A. et al. How effective is the Safe Harbor program for the conservation of Red-cockaded Woodpeckers? Condor Ornithol. Appl. 120(1), 223–233 (2018).
Google Scholar 
Zuur, A. et al. Mixed effects models and extensions in ecology with R (Springer, 2009).MATH 
Book 

Google Scholar 
Bates, D., et al., lme4: Linear mixed-effects models using Eigen and S4. 2014: http://CRAN.R-project.org/package=lme4.Conner, R. N., Rudolph, D. C. & Walters, J. R. The red-cockaded woodpecker: surviving in a fire-maintained ecosystem (University of Texas Press, 2001).Book 

Google Scholar 
Rudolph, D. C., Kyle, H. & Conner, R. N. Red-cockaded woodpeckers vs rat snakes: the effectiveness of the resin barrier. Wilson Bull. 102(1), 14–22 (1990).
Google Scholar 
Conner, R. N. The effect of tree hardness on woodpecker nest entrance orientation. Auk 94(2), 369–370 (1977).Article 

Google Scholar 
Jackson, J. A. & Jackson, B. J. Ecological relationships between fungi and woodpecker cavity sites. Condor 106(1), 37–49 (2004).Article 

Google Scholar 
Jusino, M. A. et al. Experimental evidence of a symbiosis between red-cockaded woodpeckers and fungi. Proc. R. Soc. B Biol. Sci. 2016(283), 20160106 (1827).
Google Scholar 
Losin, N. et al. Relationship between aspen heartwood rot and the location of cavity excavation by a primary cavity-nester, the Red-naped Sapsucker. Condor 108(3), 706–710 (2006).Article 

Google Scholar 
Williamson, L., Garcia, V. & Walters, J. R. Life history trait differences in isolated populations of the endangered Red-cockaded Woodpecker. Ornis Hungar. 24(1), 55–68 (2016).Article 

Google Scholar 
DeMay, S. M. & Walters, J. R. Variable effects of a changing climate on lay dates and productivity across the range of the Red-cockaded Woodpecker. Condor 20, 20 (2019).
Google Scholar 
Garcia, V. Lifetime fitness and changing life history traits in red-cockaded woodpeckers (Virginia Tech, 2014).
Google Scholar 
Delmore, K. E. & Irwin, D. E. Hybrid songbirds employ intermediate routes in a migratory divide. Ecol. Lett. 17(10), 1211–1218 (2014).PubMed 
Article 

Google Scholar 
Helbig, A. J. Inheritance of migratory direction in a bird species: a cross-breeding experiment with SE-and SW-migrating blackcaps (Sylvia atricapilla). Behav. Ecol. Sociobiol. 28(1), 9–12 (1991).Article 

Google Scholar  More

Phycosphere pH of single phytoplankton cellsThe pH in the phycosphere of a single cell Chlamydomonas concordia (~5 µm diameter) exposed to 140 μmol photons m−2 s−1 was 8.27 ± 0.01 (179 measurements), while the pH of bulk seawater was 8.01 ± 0.01 (160 measurements) (Fig. 1c). The observed pH variation near the cell surface was 150 µmol m−2 s−1 [33]. At light intensities More

Coupled model experiments for detecting vegetation-climate feedbackWe quantified changes of near-surface (2-m) air temperature (Ta) in response to the observed NH greening for all active growing seasons during 1982–2014 using IPSL-CM. We defined the three growing seasons (spring, summer, and autumn) across the entire NH domain as periods of March-April-May (MAM), June-July-August (JJA), and September-October-November (SON), respectively. For each season, a pair of transient numerical experiments was performed by modifying LAI: a dynamic vegetation experiment (SCE) forced by annually and seasonally varying LAI from satellite observations36, and three seasonal control experiments (({{{{{{rm{LAI}}}}}}}_{{{{{{rm{CTL}}}}}}}^{{{{{{rm{MAM}}}}}}}), ({{{{{{rm{LAI}}}}}}}_{{{{{{rm{CTL}}}}}}}^{{{{{{rm{JJA}}}}}}}), and ({{{{{{rm{LAI}}}}}}}_{{{{{{rm{CTL}}}}}}}^{{{{{{rm{SON}}}}}}}) for MAM, JJA, and SON, respectively) forced by annually varying LAI for all seasons, except in the season of interest when the LAI was fixed to the climatological conditions observed during 1982–2014 (Fig. S1). For all experiments, other boundary conditions, including sea surface temperature (SST), sea ice fraction (SIC), and atmospheric CO2 concentrations, were kept consistent (Methods). Therefore, differences between SCE and the control experiments characterized the effects of the observed LAI changes on Ta (hereafter denoted as ΔTa), both intra- and inter-seasonally. Multimember paired ensembles were generated for each coupled model experiment by performing 30 repeated runs but with different initial conditions (see Methods).The capacity of the IPSL-CM GCM for simulating the seasonal variations and spatial patterns of Ta was assessed by comparing the SCE simulation results with the observation-based Ta data (Methods). Throughout most of the growing season (May to October), the SCE simulation well reproduced the increasing trend and interannual variability of the NH land mean Ta observed during 1982–2014 (Fig. S2). Observational data showed that the strongest NH warming occurred in early spring (March and April) and late autumn (November). However, the SCE simulation failed to capture the exceptionally strong warming during the transitional seasons, leading to the underestimation of the annual mean warming trend (SCE: 0.237 ± 0.024 °C decade−1; observed: 0.362 ± 0.048 °C decade−1). This underestimation stemmed from a negative bias in the increase of downwelling shortwave radiation, possibly due to an absence of short-lived forcing and bias in the cloud systems37. Overall, the SCE reproduced the geographical patterns of seasonal warming reasonably well (Fig. S3), which strengthened our confidence in the model projections. Notably, it successfully captured the observed amplified warming over pan-arctic and semi-arid regions, as well as the few cases of regional cooling, such as that over northwestern North America during MAM (Fig. S3).Intra-seasonal temperature responses to NH LAI changesFor the period from 1982 to 2014, satellite-retrieved LAI showed statistically significant increasing trends (p  0.1), strong and significant JJA cooling (−0.044 ± 0.008 °C decade−1, p  0.1) (intra-seasonal feedbacks shown in Fig. 1b). The LAI-induced JJA Ta trend was equivalent to cooling of −0.15 ± 0.03 °C in JJA over the study period, offsetting the overall SCE-simulated near-surface air warming over this period by ~12.5%. This strong JJA cooling was further supported by a significant negative correlation (r = −0.64, p  0.1) or SON (r = 0.07, p  > 0.1) (Fig. S4a, c), during which the LAI-induced changes accounted for only 1.3% (MAM) and −3.2% (SON) of the concurrent greenhouse warming. We also verified the robustness of our results by performing equilibrium experiments with an independent model, the NCAR Community Atmosphere Model coupled with Community Land Model (CAM-CLM, Methods). Indeed, this model generated a similarly strong LAI-induced cooling in JJA (−0.18 °C, p  0.1) and SON (−0.05 °C, p  > 0.1) (Fig. S5).Fig. 1: Intra- and inter-seasonal temperature responses to leaf area index (LAI) changes.a Monthly trends (shadings) of Northern Hemisphere (NH) mean LAI during 1982–2014 used as input to the seasonal simulations. The dashed curve and transparent bars indicate trends of monthly LAI and seasonally aggregated LAI values, respectively. b Linear trends of Ta driven by LAI changes within the same season (intra-seasonal) and other growing seasons (inter-seasonal). Error bars in a, b indicate uncertainty ranges [1 – standard deviation (SD)]. c Monthly trends of LAI-induced air temperature changes (ΔTa), with red and blue shadings representing positive and negative trends, respectively. The bottom panel shows the overall ΔTa trends induced by LAI changes in all growing seasons, calculated as the sum of ΔTa trends from the three seasonal runs shown separately in the above panels. ***p  More