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    Plasticity in organic composition maintains biomechanical performance in shells of juvenile scallops exposed to altered temperature and pH conditions

    1.Feely, R. A., Sabine, C. L., Hernandez-Ayon, J. M., Ianson, D. & Hales, B. Evidence for upwelling of corrosive “acidified” water onto the continental shelf. Science 320, 1490–1492 (2008).ADS 
    CAS 
    PubMed 

    Google Scholar 
    2.Hofmann, G. E. et al. High-frequency dynamics of ocean ph: A multi-ecosystem comparison. PLoS ONE 6(12), e28983 (2011).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    3.Kroeker, K. J. et al. Interacting environmental mosaics drive geographic variation in mussel performance and predation vulnerability. Ecol. Lett. 19, 771–779 (2016).PubMed 

    Google Scholar 
    4.Gutiérrez, D. et al. Coastal cooling and increased productivity in the main upwelling zone off Peru since the mid-twentieth century. Geophys. Res. Lett. 38, L07603. https://doi.org/10.1029/2010GL046324 (2011).ADS 
    Article 

    Google Scholar 
    5.Aiken, C. M., Navarrete, S. A. & Pelegrí, J. L. Potential changes in larval dispersal and alongshore connectivity on the central Chilean coast due to an altered wind climate. J. Geophys. Res. 116, G04026. https://doi.org/10.1029/2011JG001731 (2011).ADS 
    Article 

    Google Scholar 
    6.Lagos, N. A., Castilla, J. C. & Broitman, B. Spatial Environmental correlates of intertidal recruitment: A test using barnacles in northern Chile. Ecol. Monogr. 78, 245–261 (2008).
    Google Scholar 
    7.Vargas, C. A. et al. Species-specific responses to ocean acidification should account for local adaptation and adaptive plasticity. Nat. Ecol. Evol. 1, 84. https://doi.org/10.1038/s41559-017-0084 (2017).Article 
    PubMed 

    Google Scholar 
    8.Broitman, B. R. et al. Phenotypic plasticity is not a cline: Thermal physiology of an intertidal barnacle over 20° of latitude. J. Anim. Ecol. 00, 1–12. https://doi.org/10.1111/1365-2656.13514 (2021).Article 

    Google Scholar 
    9.Ramajo, L. et al. Physiological responses of juvenile Chilean scallops (Argopecten purpuratus) to isolated and combined environmental drivers of coastal upwelling. ICES J. Mar. Sci. 76, 1836e1849 (2019).
    Google Scholar 
    10.Saavedra, L. M., Saldías, G., Broitman, B. & Vargas, C. Carbonate chemistry dynamics in shellfish farming areas along the Chilean coast: Natural ranges and biological implications. ICES J. Mar. Sci. 78, 323–339 (2021).
    Google Scholar 
    11.Lardies, M. A. et al. Physiological and histopathological impacts of increased carbon dioxide and temperature on the scallops Argopecten purpuratus cultured under upwelling influences in northern Chile. Aquaculture 479, 455–466 (2017).
    Google Scholar 
    12.Ramajo, L. et al. Upwelling intensity modulates the fitness and physiological performance of coastal species: Implications for the aquaculture of the scallop Argopecten purpuratus in the Humboldt Current System. Sci. Total Environ. 745, 140949 (2020).ADS 
    CAS 
    PubMed 

    Google Scholar 
    13.Bakun, A. Global climate change and intensification of coastal ocean upwelling. Science 247, 198–201 (1990).ADS 
    CAS 
    PubMed 

    Google Scholar 
    14.Wang, D. et al. Intensification and spatial homogenization of coastal upwelling under climate change. Nature 518, 390–394 (2015).ADS 
    CAS 
    PubMed 

    Google Scholar 
    15.Kim, T. W., Barry, J. P. & Micheli, F. The effects of intermittent exposure to low-pH and low-oxygen conditions on survival and growth of juvenile red abalone. Biogeosciences 10, 7255–7262 (2013).ADS 

    Google Scholar 
    16.Ramajo, L. et al. Plasticity and trade-offs in physiological traits of intertidal mussels subjected to freshwater-induced environmental variation. Mar. Ecol. Prog. Ser. 553, 93–109 (2016).ADS 

    Google Scholar 
    17.Leung, J. Y., Connell, S. D., Nagelkerken, I. & Russell, B. D. Impacts of near-future ocean acidification and warming on the shell mechanical and geochemical properties of gastropods from intertidal to subtidal zones. Environ. Sci. Technol. 51, 12097–12103 (2017).ADS 
    CAS 
    PubMed 

    Google Scholar 
    18.Findlay, H. et al. Calcification, a physiological process to be considered in the context of the whole organism. Biogeosciences Discuss. 6, 2267–2284 (2009).ADS 

    Google Scholar 
    19.Waldbusser, G. et al. Saturation-state sensitivity of marine bivalves larvae to ocean acidification. Nat. Clim. Change 5, 273–280 (2015).ADS 
    CAS 

    Google Scholar 
    20.Tunnicliffe, V. et al. Survival of mussels in extremely acidic waters on a submarine volcano. Nat. Geosci. 2, 344–348 (2009).ADS 
    CAS 

    Google Scholar 
    21.Ries, J. B., Cohen, A. L. & McCorkle, D. C. Marine calcifiers exhibit mixed responses to CO2-induced ocean acidification. Geology 37, 1131–1134 (2009).ADS 
    CAS 

    Google Scholar 
    22.Leung, J. Y., Russell, B. D. & Connell, S. D. Mineralogical plasticity acts as a compensatory mechanism to the impacts of ocean acidification. Environ. Sci. Technol. 51, 2652–2659 (2017).ADS 
    CAS 
    PubMed 

    Google Scholar 
    23.Duarte, C. et al. The energetic physiology of juvenile mussels, Mytilus chilensis (Hupe): The prevalent role of salinity under current and predicted pCO2 scenarios. Environ. Pollut. 242, 156–163 (2018).CAS 
    PubMed 

    Google Scholar 
    24.Rodolfo-Metalpa, R. et al. Coral and mollusc resistance to ocean acidification adversely affected by warming. Nat. Clim. Change. 1, 308–312 (2011).ADS 
    CAS 

    Google Scholar 
    25.Waldbusser, G. et al. Slow shell building, a possible trait for resistance to the effects of acute ocean acidification. Limnol. Oceanogr. 61, 1969–1983 (2016).ADS 

    Google Scholar 
    26.Fitzer, S. C. et al. Ocean acidification and temperature increase impact mussel shell shape and thickness: Problematic for protection?. Ecol. Evol. 5, 4875–4884 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    27.Fitzer, S. C., Phoenix, V. R., Cusack, M. & Kamenos, N. A. Ocean acidification impacts mussel control on biomineralization. Sci. Rep. 28, 6218 (2014).
    Google Scholar 
    28.Fitzer, S. C., Cusack, M., Phoenix, V. R. & Kamenos, N. A. Ocean acidification reduces the crystallographic control in juvenile mussel shells. J. Struct. Biol. 188, 39–45 (2014).CAS 
    PubMed 

    Google Scholar 
    29.Fitzer, S. C. et al. Biomineral shell formation under ocean acidification: A shift from order to chaos. Sci. Rep. 6, 21076 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    30.Lagos, N. A. et al. Effects of temperature and ocean acidification on shell characteristics of Argopecten purpuratus: Implications for scallop aquaculture in an upwelling-influenced area. Aquac. Environ. Interact. 8, 357–370 (2016).
    Google Scholar 
    31.Ramajo, L. et al. Biomineralization changes with food supply confer juvenile scallops (Argopecten purpuratus) resistance to ocean acidification. Glob. Chang. Biol. 22, 2025–2203 (2016).ADS 
    PubMed 

    Google Scholar 
    32.Osores, S. J. et al. Plasticity and inter-population variability in physiological and life-history traits of the mussel Mytilus chilensis: A reciprocal transplant experiment. J. Exp. Mar. Biol. Ecol. 490, 1–12 (2017).
    Google Scholar 
    33.Telesca, L. et al. Plasticity and environmental heterogeneity predict geographic resilience patterns of foundation species to future change. Glob. Chang. Biol. https://doi.org/10.1111/gcb.14758 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    34.Grenier, C. et al. The combined effects of salinity and pH on shell biomineralization of the edible mussel Mytilus chilensis. Environ. Pollut. 263, 114555 (2020).CAS 
    PubMed 

    Google Scholar 
    35.Kroeker, K. J. et al. Impacts of ocean acidification on marine organisms: Quantifying sensitivities and interaction with warming. Glob. Change Biol. 19, 1884–1896 (2013).ADS 

    Google Scholar 
    36.Mackenzie, C. L. et al. Ocean warming, more than acidification, reduces shell strength in a commercial shellfish species during food limitation. PLoS ONE 9(1), e86764 (2014).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    37.Rykaczewski, R. R. et al. Poleward displacement of coastal upwelling-favorable winds in the ocean’s eastern boundary currents through the 21st century. Geophys. Res. Lett. 42, 6424–6431 (2015).ADS 

    Google Scholar 
    38.Rodríguez-Navarro, A. B. Rapid quantification of avian eggshell microstructure and crystallographic-texture using two-dimensional X-ray diffraction. Br. Poult. Sci. 48, 133–144 (2007).PubMed 

    Google Scholar 
    39.Rodríguez-Navarro, A. B. XRD2DScan: New software for polycrystalline materials characterization using two-dimensional X-ray diffraction. J. Appl. Cryst. 39, 905–909 (2006).
    Google Scholar 
    40.Li, S. et al. Interactive effects of seawater acidification and elevated temperature on biomineralization and amino acid metabolism in the mussel Mytilus edulis. J. Exp. Biol. 218, 3623–3631 (2015).PubMed 

    Google Scholar 
    41.Li, S. et al. Interactive effects of seawater acidification and elevated temperature on the transcriptome and biomineralization in the pearl oyster Pinctada fucata. Environ. Sci. Technol. 50, 1157–1165 (2016).ADS 
    CAS 
    PubMed 

    Google Scholar 
    42.Gestoso, I., Arenas, F. & Olabarria, C. Ecological interactions modulate responses of two intertidal mussel species to changes in temperature and pH. J. Exp. Mar. Biol. 474, 116–125 (2016).
    Google Scholar 
    43.Babarro, J. M., Abad, M. J., Gestoso, I., Silva, E. & Olabarria, C. Susceptibility of two co-existing mytilid species to simulated predation under projected climate change conditions. Hydrobiologia 807, 247–261 (2018).
    Google Scholar 
    44.Barthelat, F., Rim, J. E. & Espinosa, H. D. A review on the structure and mechanical properties of mollusk shells: Perspectives on synthetic biomimetic materials. In Applied Scanning Probe Methods XIII (eds Bhushan, B. & Fuchs, H.) 17–44 (Springer, 2009).
    Google Scholar 
    45.Leung, J. Y. et al. Calcifiers can adjust shell building at the nanoscale to resist ocean acidification. Small 16, 2003186 (2020).CAS 

    Google Scholar 
    46.Chatzinikolaou, E., Grigoriou, P., Keklikoglou, K., Faulwetter, S. & Papageorgiou, N. The combined effects of reduced pH and elevated temperature on the shell density of two gastropod species measured using micro-CT imaging. ICES J. Mar. Sci. 74, 1135–1149 (2017).
    Google Scholar 
    47.Nienhuis, S., Palmer, R. & Harley, C. Elevated CO2 affects shell dissolution rate but not calcification rate in a marine snail. Proc. R. Soc. Lond. B Biol. Sci. 277, 2553–2558 (2010).CAS 

    Google Scholar 
    48.Bourdeau, P. E. Prioritized phenotypic responses to combined predators in a marine snail. Ecology 90, 1659–1669 (2009).PubMed 

    Google Scholar 
    49.Weiner, S. & Addadi, L. Crystallization pathways in biomineralization. Annu. Rev. Mater. Sci. 41, 21–40 (2011).ADS 
    CAS 

    Google Scholar 
    50.Nudelman, F. Nacre biomineralisation: A review on the mechanisms of crystal nucleation (In Seminars in cell & developmental biology), 2–10 (Academic Press, 2015).51.Harper, E. M., Checa, A. G. & Rodríguez-Navarro, A. B. Organization and mode of secretion of the granular prismatic microstructure of Entodesma navicular (Bivalvia: Mollusca). Acta Zool. 90, 132e141 (2009).
    Google Scholar 
    52.Pennington, B. J. & Currey, J. D. A mathematical model for the mechanical properties of scallop shells. J. Zool. 202, 239–263 (1984).
    Google Scholar 
    53.Yevenes, M. A., Lagos, N. A., Farías, L. & Vargas, C. A. Greenhouse gases, nutrients and the carbonate system in the Reloncaví Fjord (Northern Chilean Patagonia): Implications on aquaculture of the mussel, Mytilus chilensis, during an episodic volcanic eruption. Sci. Total Environ. 669, 49–61 (2019).ADS 
    CAS 
    PubMed 

    Google Scholar 
    54.Dickinson, G. H. et al. Interactive effects of salinity and elevated CO2 levels on juvenile eastern oysters, Crassostrea virginica. J. Exp. Biol. 215, 29–43 (2012).CAS 
    PubMed 

    Google Scholar 
    55.Gaylord, B. et al. Functional impacts of ocean acidification in an ecologically critical foundation species. J. Exp. Biol. 214, 2586–2594 (2011).CAS 
    PubMed 

    Google Scholar 
    56.O’Toole-Howes, M. et al. Deconvolution of the elastic properties of bivalve shell nanocomposites from direct measurement and finite element analysis. J. Mater. Res. 34, 2869–2880 (2019).ADS 

    Google Scholar 
    57.Auzoux-Bordenave, S. et al. Ocean acidification impacts growth and shell mineralization in juvenile abalone (Haliotis tuberculata). Mar. Biol. 167, 11 (2020).CAS 

    Google Scholar 
    58.Torres, R. et al. Evaluation of a semiautomatic system for long-term seawater carbonate chemistry manipulation. Rev. Chil. Hist. Nat. 86, 443–451 (2013).
    Google Scholar 
    59.IPCC. Climate Change 2021. The Physical Science Basis. Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (Eds. Masson-Delmotte, V., P. Zhai, A. Pirani, S.L. Connors, C. Péan, S. Berger, N. Caud, Y. Chen, L. Goldfarb, M.I. Gomis, M. Huang, K. Leitzell, E. Lonnoy, J.B.R. Matthews, T.K. Maycock, T. Waterfield, O. Yelekçi, R. Yu, and B. Zhou). Cambridge University Press. In Press. (2021).60.DOE. Handbook of methods for the analysis of the various parameters of the carbon dioxide system in seawater; version 2 (eds. Dickson, A.G. & Goyet, C.), (ORNL/CDIAC, 74, 1994).61.Meinshausen, M. et al. The RPC greenhouse gas concentrations and their extensions from 1765 to 2300. Clim. Change. 109, 213–241 (2011).ADS 
    CAS 

    Google Scholar 
    62.Rahn, D. A., Rosenblüth, B. & Rutllant, J. A. Detecting subtle seasonal transitions of upwelling in North-Central Chile. J. Phys. Oceanogr. 45, 854–867 (2015).ADS 

    Google Scholar 
    63.Meng, Y., Guo, Z., Yao, H., Yeung, K. W. & Thiyagarajan, V. Calcium carbonate unit realignment under acidification: A potential compensatory mechanism in an edible estuarine oyster. Mar. Pollut. Bull. 139, 141–149 (2019).CAS 
    PubMed 

    Google Scholar 
    64.Rasband, W. S. ImageJ U.S. National Institute of Health, Maryland, USA (1997–2020). More

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    An intergenerational androgenic mechanism of female intrasexual competition in the cooperatively breeding meerkat

    Study populationWe studied wild meerkats at the Kuruman River Reserve (a ~63 km2 area comprising dry riverbeds, herbaceous flats and grassy dunes) in the Kalahari region of South Africa (26°58′S, 21°49′E)28,48. Our study period (Nov 2011–Apr 2015) included an extended drought, during which female reproductive success tracked rainfall22 (Supplementary Fig. 1). The annual mean population size was 270 animals, in 22 established clans of 4–39 animals15,22. Habituated to close observation ( More

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    The importance of termites and fire to dead wood consumption in the longleaf pine ecosystem

    1.Cornwell, W. K. et al. Plant traits and wood fates across the globe: Rotted, burned, or consumed?. Glob. Change Biol. 15, 2431–2449 (2009).ADS 
    Article 

    Google Scholar 
    2.Ulyshen, M. D. Wood decomposition as influenced by invertebrates. Biol. Rev. 91, 70–85 (2016).Article 

    Google Scholar 
    3.Rayner, A. D. M. & Boddy, L. Fungal Decomposition of Wood: Its Biology and Ecology 587 (Wiley, 1988).
    Google Scholar 
    4.Hyde, J. C., Smith, A. M. S., Ottmar, R. D., Alvarado, E. C. & Morgan, P. The combustion of sound and rotten coarse woody debris: A review. Int. J. Wildland Fire 20, 163–174. https://doi.org/10.1071/WF09113 (2011).Article 

    Google Scholar 
    5.Griffiths, H. M., Ashton, L. A., Evans, T. A., Parr, C. L. & Eggleton, P. Termites can decompose more than half of deadwood in tropical rainforest. Curr. Biol. 29, R118–R119 (2019).Article 
    CAS 

    Google Scholar 
    6.Wu, C. et al. Stronger effects of termites than microbes on wood decomposition in a subtropical forest. For. Ecol. Manage. 493, 119263. https://doi.org/10.1016/j.foreco.2021.119263 (2021).Article 

    Google Scholar 
    7.Jacobsen, R. M., Kauserud, H., Sverdrup-Thygeson, A., Bjorbækmo, M. M. & Birkemoe, T. Wood-inhabiting insects can function as targeted vectors for decomposer fungi. Fungal Ecol. 29, 76–84. https://doi.org/10.1016/j.funeco.2017.06.006 (2017).Article 

    Google Scholar 
    8.Leach, J. G., Orr, L. W. & Christensen, C. Further studies on the interrelationship of insects and fungi in the deterioration of felled Norway pine logs. J. Agric. Res. 55, 129–140 (1937).
    Google Scholar 
    9.Skelton, J. et al. Fungal symbionts of bark and ambrosia beetles can suppress decomposition of pine sapwood by competing with wood-decay fungi. Fungal Ecol. 45, 100926. https://doi.org/10.1016/j.funeco.2020.100926 (2020).Article 

    Google Scholar 
    10.Wikars, L.-O. Dependence on fire in wood-living insects: An experiment with burned and unburned spruce and birch logs. J. Insect Conserv. 6, 1–12. https://doi.org/10.1023/a:1015734630309 (2002).Article 

    Google Scholar 
    11.Holden, S. R., Gutierrez, A. & Treseder, K. K. Changes in soil fungal communities, extracellular enzyme activities, and litter decomposition across a fire chronosequence in Alaskan boreal forests. Ecosystems 16, 34–46. https://doi.org/10.1007/s10021-012-9594-3 (2013).Article 
    CAS 

    Google Scholar 
    12.Ulyshen, M. D., Lucky, A. & Work, T. T. Effects of prescribed fire and social insects on saproxylic beetles in a subtropical forest. Sci. Rep. 10, 9630. https://doi.org/10.1038/s41598-020-66752-w (2020).ADS 
    Article 
    PubMed 
    PubMed Central 
    CAS 

    Google Scholar 
    13.Ulyshen, M. D., Horn, S., Barnes, B. & Gandhi, K. J. K. Impacts of prescribed fire on saproxylic beetles in loblolly pine logs. Insect Conserv. Divers. 3, 247–251 (2010).Article 

    Google Scholar 
    14.Billings, R. F. et al. Bark beetle outbreaks and fire: A devastating combination for Central America’s pine forests. Unasylva 55, 7 (2004).
    Google Scholar 
    15.Ulyshen, M. D., Wagner, T. L. & Mulrooney, J. E. Contrasting effects of insect exclusion on wood loss in a temperate forest. Ecosphere 5, article 47 (2014).16.Van Lear, D. H., Carroll, W. D., Kapeluck, P. R. & Johnson, R. History and restoration of the longleaf pine-grassland ecosystem: Implications for species at risk. For. Ecol. Manag. 211, 150–165 (2005).Article 

    Google Scholar 
    17.Noss, R. F. & Scott, J. M. Endangered Ecosystems of the United States: A Preliminary Assessment of Loss and Degradation. Vol. 28. (US Department of the Interior, National Biological Service, 1995).18.Folkerts, G. W., Deyrup, M. A. & Sisson, D. C. Arthropods associated with xeric longleaf pine habitats in the southeastern United States: A brief overview. Proc. Tall Timbers Fire Ecol. Conf. 18, 159–191 (1993).
    Google Scholar 
    19.Guyette, R. P., Stambaugh, M. C., Dey, D. C. & Muzika, R.-M. Predicting fire frequency with chemistry and climate. Ecosystems 15, 322–335. https://doi.org/10.1007/s10021-011-9512-0 (2012).Article 

    Google Scholar 
    20.Ulyshen, M. D., Horn, S., Pokswinski, S., McHugh, J. V. & Hiers, J. K. A comparison of coarse woody debris volume and variety between old-growth and secondary longleaf pine forests in the southeastern United States. For. Ecol. Manag. 429, 124–132. https://doi.org/10.1016/j.foreco.2018.07.017 (2018).Article 

    Google Scholar 
    21.Hanula, J. L., Ulyshen, M. D. & Wade, D. D. Impacts of prescribed fire frequency on coarse woody debris volume, decomposition and termite activity in the longleaf pine flatwoods of Florida. Forests 3, 317–331 (2012).Article 

    Google Scholar 
    22.Goebel, P. C. et al. Forest Ecosystems of a Lower Gulf Coastal Plain Landscape: Multifactor Classification and Analysis. 47–75. (2001).23.Ulyshen, M. D., Müller, J. & Seibold, S. Bark coverage and insects influence wood decomposition: Direct and indirect effects. Appl. Soil. Ecol. 105, 25–30. https://doi.org/10.1016/j.apsoil.2016.03.017 (2016).Article 

    Google Scholar 
    24.Kirkman, L. K. et al. Productivity and species richness in longleaf pine woodlands: Resource-disturbance influences across an edaphic gradient. Ecology 97, 2259–2271. https://doi.org/10.1002/ecy.1456 (2016).Article 
    PubMed 
    CAS 

    Google Scholar 
    25.Ulyshen, M. D. & Wagner, T. L. Quantifying arthropod contributions to wood decay. Methods Ecol. Evol. 4, 345–352 (2013).Article 

    Google Scholar 
    26.R Core Team. R: A Language and Environment for Statistical Computing (Version 3.6.1). http://www.R-project.org. (R Foundation for Statistical Computing, 2019).27.Bates, D., Mächler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).Article 

    Google Scholar 
    28.Lenth, R., Singmann, H., Love, J., Buerkner, P. & Herve, M. Emmeans: Estimated marginal means, aka least-squares means. R Package Version 1, 3 (2018).
    Google Scholar 
    29.Graves, S., Piepho, H.-P. & Selzer, L. multcompView: Visualizations of paired comparisons. R Package Version 0.1-7. (2015).30.Ulyshen, M. D. Interacting effects of insects and flooding on wood decomposition. PLoS ONE 9, e101867 (2014).31.Stoklosa, A. M. et al. Effects of mesh bag enclosure and termites on fine woody debris decomposition in a subtropical forest. Basic Appl. Ecol. 17, 463–470. https://doi.org/10.1016/j.baae.2016.03.001 (2016).Article 

    Google Scholar 
    32.Kampichler, C. & Bruckner, A. The role of microarthropods in terrestrial decomposition: A meta-analysis of 40 years of litterbag studies. Biol. Rev. 84, 375–389 (2009).Article 

    Google Scholar 
    33.Mackensen, J., Bauhus, J. & Webber, E. Decomposition rates of coarse woody debris—A review with particular emphasis on Australian tree species. Aust. J. Bot. 51, 27–37 (2003).Article 

    Google Scholar  More

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    Mathematical model for predicting oxygen concentration in tilapia fish farms

    Dissolved oxygen modelThe dissolved oxygen in this model had a number of interactions to consider. Oxygen consumption through the processes of both respiration and nitrification. On the other hand, the water receives oxygen through water agitation as it is pumped through the system and from the oxygen generator. Oxygen is added to the water by oxygen generator and flow aeration (Fig. 1).Figure 1Dissolved oxygen model.Full size imageThe required oxygen supplementation is a sum of the pervious components as follows:$$ DO_{FR} + DO_{B} + DO_{N} = DO_{sup } + DO_{PF} $$
    (1)
    where DOFR is the dissolved oxygen consumption through fish respiration, g O2 m−3 h−1. DOB is the dissolved oxygen consumption through the biofilter, g O2 m−3 h−1. DON is the dissolved oxygen consumption through nitrification, g O2 m−3 h−1. DOPF is the dissolved oxygen addition through pipe flow, g O2 m−3 h−1. DOsup is the required oxygen supplementation (oxygen generator), g O2 m−3 h−1.The rate of change in DO concentration in fish tank:$$ frac{dDO}{{dt}} = DO_{FR} + DO_{B} + DO_{N} – DO_{PF} $$
    (2)
    where (frac{dDO}{{dt}}) is the rate of change in DO concentration during the time interval, g O2 m−3 h−1. dt is the rate of change in the time interval, hAfter calculating oxygen concentration for each element at each time step, the net oxygen change is then added to or subtracted from the previous time step`s oxygen concentration. DO concentrations can be calculated at any time (t) as:$$ DO_{t} = DO_{t – 1} + left( {frac{dDO}{{dt}} cdot dt} right) $$
    (3)
    where DOt is the DO concentration (g m−3) at time t. DOt−1 is the DO concentration (g m−3) at time t−1.The rate of oxygen consumption through fish respiration can be calculated on water temperature and average fish weight. This calculation is shown in the following equation10:$$ FR = 2014.45 + 2.75W – 165.2T + 0.007W^{2} + 3.93T^{2} – 0.21WT $$
    (4)
    $$ DO_{FR} = frac{FR times SD}{{1000}} $$
    (5)
    where FR is rate of oxygen consumption through fish respiration, mg O2 kg−1 fish. h−1. W is average of individual fish mass, g. T is water temperature, °C. SD is the stocking density of fish, kg m−3.The correlation coefficient for the equation was 0.99. Data used in preparing the equation ranged from 20 to 200 g for fish weight and from 24 to 32 °C.The rate of oxygen consumption through nitrification is calculated in terms of Total Ammonia Nitrogen (TAN) that is converted from ammonia to nitrate. The rate found in the literature is 4.57 g O2 g−1 TAN6.The oxygen consumption in nitrification process can be calculated as11:$$ DO_{N} = 4.57 times K_{NR} times {{{text{Nr}}} mathord{left/ {vphantom {{{text{Nr}}} {text{V}}}} right. kern-nulldelimiterspace} {text{V}}} $$
    (6)
    $$ K_{NR} = 0.1left( {1.08} right)^{{left( {T – 20} right)}} $$
    (7)
    $$ Nr = frac{{0.03 times F_{r} times W times N_{F} }}{24 times 1000} $$
    (8)
    where KNR is the coefficient of nitrification. Nr is the nitrification rate, g TAN h−1. Fr is the feeding ratio, % of body fish day−1. NF is the number of fish. V is the water volume, m3.The feeding ratio can be calculated as the following equation:$$ F_{r} = 17.02 times e^{{left[ {{raise0.7exhbox{${left( {ln W + 1.14} right)^{2} }$} !mathord{left/ {vphantom {{left( {ln W + 1.14} right)^{2} } { – 19.52}}}right.kern-nulldelimiterspace} !lower0.7exhbox{${ – 19.52}$}}} right]}} $$
    (9)
    The bacteria in the biofilter are a second source of oxygen consumption. Lawson explains that the biofilter oxygen demand is approximated 2.3 times the BOD5 production rate of fish6. The oxygen consumption of the biofilter is calculated using following equation:$$ DO_{B} = frac{{(2.3)left( {BOD_{5} } right)left( {W_{n} } right)}}{{left( V right)left( {24} right)left( {1000} right)}} $$
    (10)
    where BOD5 is average unfiltered BOD5 excretion rate, 2160 mg O2 kg−1 fish day−1. Wn is biomass, kg fish.The water pumping cycle was a source of oxygen addition to the system. The amount of oxygen addition through the water pumping cycle was calculated on an hourly basis. The method of calculating aeration from a pipe is detailed by12:$$ DO_{PF} = frac{PC times f times E times OTR}{V} $$
    (11)
    where PC is pump cycle length, h. f is pumping frequency, h−1. E is efficiency, %. OTR is oxygen transfer rate, g O2 h−1.This model sums the DOFR, DOB, DON, and DOPF to determine the supplemental DO demand in kg h−1. This number can be used to estimate the oxygen consumption if pure oxygen transfers system is used.Fish growth modelFish growth is affected by environmental and physical factors, such as water temperature, dissolved oxygen, unionized ammonia, photoperiod, fish stocking density, food availability, and food quality.In order to calculate the fish growth rate (g day−1) for individual fish, the following model was used13 as it includes the main environmental factors influencing fish growth. These factors are temperature, dissolved oxygen and unionized ammonia.$$ FGR = left( {0.2919 , tau , kappa , delta , varphi , h , f , W^{m} } right) – K.W^{n} $$
    (12)
    Where FGR is the fish growth rate, g day−1. τ is the temperature factor (0  > τ  к  δ  φ  ƒ  More

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    Global controls on phosphatization of fossils during the toarcian oceanic anoxic event

    1.Seilacher, A. Begriff und Bedeutung der Fossil-Lagerstätten. Neues Jahrbuch für Geologie und Paläontologie Monatshefte 34–39 (1970).2.Bottjer, D. J., Etter, W., Hagadorn, J. W. & Tang, C. M. Exceptional Fossil Preservation. A Unique View on the Evolution of Marine Life. (2002).3.Schiffbauer, J. D. & Laflamme, M. Lagerstätten through time: A collection of exceptional preservational pathways from the terminal Neoproterozoic through today. Palaios 27, 275–278 (2012).ADS 

    Google Scholar 
    4.Briggs, D. E. G. The role of decay and mineralization in the preservation of soft-bodied fossils. Ann. Rev. Earth Planet. Sci. 31, 275–301 (2003).ADS 
    CAS 

    Google Scholar 
    5.Allison, P. A. & Briggs, D. E. G. Exceptional fossil record: distribution of soft-tissue preservation through the Phanerozoic. Geology 21, 527–530 (1993).ADS 

    Google Scholar 
    6.Muscente, A. D. et al. Exceptionally preserved fossil assemblages through geologic time and space. Gondwana Res. 48, 164–188 (2017).ADS 
    CAS 

    Google Scholar 
    7.Ansorge, J. Insects from the Lower Toarcian of Middle Europe and England. Acta Zool. Crac. 46, 291–310 (2003).
    Google Scholar 
    8.Klug, C., Riegraf, W. & Lehmann, J. Soft-part preservation in heteromorph ammonites from the Cenomanian-Turonian Boundary Event (OAE 2) in north-west Germany. Palaeontology 55, 1307–1331 (2012).
    Google Scholar 
    9.Martindale, R. C., Them, T. R., Gill, B. C., Marroquín, S. M. & Knoll, A. H. A new Early Jurassic (ca183 Ma) fossil Lagerstätte from Ya Ha Tinda, Alberta, Canada. Geol. 45, 255–258 (2017).ADS 

    Google Scholar 
    10.Williams, M., Benton, M. J. & Ross, A. The Strawberry Bank Lagerstätte reveals insights into Early Jurassic life. J. Geol. Soc. 172, 683–692 (2015).ADS 

    Google Scholar 
    11.Feldmann, R. M., Villamil, T. & Kauffman, E. G. Decapod and stomatopod crustaceans from mass mortality Lagerstatten: Turonian (Cretaceous) of Colombia. J. Paleontol. 73, 91–101 (1999).
    Google Scholar 
    12.Martill, D. M. et al. A new Plattenkalk Konservat Lagerstätte in the Upper Cretaceous of Gara Sbaa, south-eastern Morocco. Cretac. Res. 32, 433–446 (2011).
    Google Scholar 
    13.Fuchs, D., Ifrim, C. & Stinnesbeck, W. A new Palaeoctopus (Cephalopoda: Coleoidea) from the Late Cretaceous of Vallecillo, north-eastern Mexico, and implications for the evolution of Octopoda. Palaeontology 51, 1129–1139 (2008).
    Google Scholar 
    14.Ifrim, C., Stinnesbeck, W. & Frey, E. Upper Cretaceous (Cenomanian-Turonian and Turonian-Coniacian) open marine plattenkalk deposits in NE Mexico. Neues Jahrbuch für Geologie und Paläontologie – Abhandlungen 245, 71–81 (2007).
    Google Scholar 
    15.Schmid-Röhl, A., Röhl, H. J., Oschmann, W., Frimmel, A. & Schwark, L. Palaeoenvironmental reconstruction of Lower Toarcian epicontinental black shales (Posidonia Shale, SW Germany): Global versus regional control. Geobios 35, 13–20 (2002).
    Google Scholar 
    16.Röhl, H. J., Schmid-Röhl, A., Oschmann, W., Frimmel, A. & Schwark, L. The Posidonia Shale (Lower Toarcian) of SW-Germany: An oxygen-depleted ecosystem controlled by sea level and palaeoclimate. Palaeogeogr. Palaeoclimatol. Palaeoecol. 165, 27–52 (2001).
    Google Scholar 
    17.Allison, P. A. The role of anoxia in the decay and mineralization of proteinaceous macro- fossils. Paleobiology 14, 139–154 (1988).
    Google Scholar 
    18.Muscente, A. D., Martindale, R. C., Schiffbauer, J. D., Creighton, A. L. & Bogan, B. A. Taphonomy of the Lower Jurassic Konservat-Lagerstätte at Ya Ha Tinda (Alberta, Canada) and its significance for exceptional fossil preservation during oceanic anoxic events. Palaios 34, 514–541 (2019).ADS 

    Google Scholar 
    19.Little, C. T. S. & Benton, M. J. Early Jurassic mass extinction: a global long-term event. Geology 23, 495–498 (1995).ADS 

    Google Scholar 
    20.Svensen, H. et al. Hydrothermal venting of greenhouse gases triggering Early Jurassic global warming. Earth Planet. Sci. Lett. 256, 554–566 (2007).ADS 
    CAS 

    Google Scholar 
    21.Ruebsam, W., Reolid, M. & Schwark, L. δ13C of terrestrial vegetation records Toarcian CO2 and climate gradients. Sci. Rep. 10, 1–8 (2020).ADS 

    Google Scholar 
    22.Dera, G. & Donnadieu, Y. Modeling evidences for global warming, Arctic seawater freshening, and sluggish oceanic circulation during the Early Toarcian anoxic event. Paleoceanography 27, 1–15 (2012).
    Google Scholar 
    23.Bailey, T. R., Rosenthal, Y., McArthur, J. M., van de Schootbrugge, B. & Thirlwall, M. F. Paleoceanographic changes of the Late Pliensbachian-Early Toarcian interval: A possible link to the genesis of an Oceanic Anoxic Event. Earth Planet. Sci. Lett. 212, 307–320 (2003).ADS 
    CAS 

    Google Scholar 
    24.Dera, G. et al. Water mass exchange and variations in seawater temperature in the NW Tethys during the Early Jurassic: Evidence from neodymium and oxygen isotopes of fish teeth and belemnites. Earth Planet. Sci. Lett. 286, 198–207 (2009).ADS 
    CAS 

    Google Scholar 
    25.Jenkyns, H. C. The early Toarcian (Jurassic) anoxic event; stratigraphic, sedimentary and geochemical evidence. Am. J. Sci. 288, 101–151 (1988).ADS 
    CAS 

    Google Scholar 
    26.Jenkyns, H. C. Geochemistry of oceanic anoxic events. Geochemistry, Geophysics, Geosystems 11, (2010).27.Caruthers, A. H., Smith, P. L. & Gröcke, D. R. The Pliensbachian-Toarcian (Early Jurassic) extinction, a global multi-phased event. Palaeogeogr. Palaeoclimatol. Palaeoecol. 386, 104–118 (2013).
    Google Scholar 
    28.Caruthers, A. H., Smith, P. L. & Gröcke, D. R. The Pliensbachian-Toarcian (Early Jurassic) extinction: a North American perspective. Geol. Soc. Am. Spec. Papers 505, 225–243 (2014).
    Google Scholar 
    29.Them, T. R. et al. Thallium isotopes reveal protracted anoxia during the Toarcian (Early Jurassic) associated with volcanism, carbon burial, and mass extinction. Proc. Natl. Acad. Sci. U.S.A. 115, 6596–6601 (2018).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    30.Seilacher, A. Posidonia Shales (Toarcian, S. Germany): Stagnant basin model revalidated. in Palaeontology, Essential of Historical Geology (ed. Gallitelli, Motanaro, E.) 279–298 (1982).31.Vincent, P. A re-examination of Hauffiosaurus zanoni, a pliosauroid from the Toarcian (Early Jurassic) of Germany. J. Vertebr. Paleontol. 31, 340–351 (2011).
    Google Scholar 
    32.Littke, R., Leythaeuser, D., Rullkötter, J. & Baker, D. R. Keys to the depositional history of the Posidonia Shale (Toarcian) in the Hils Syncline, northern Germany. Geol. Soc. Spec. Pub. 58, 311–333 (1991).
    Google Scholar 
    33.Golonka, J. Late Triassic and Early Jurassic palaeogeography of the world. Palaeogeogr. Palaeoclimatol. Palaeoecol. 244, 297–307 (2007).
    Google Scholar 
    34.Boomer, I. et al. The biostratigraphy of the Upper Pliensbachian-Toarcian (Lower Jurassic) sequence at Ilminster, Somerset. J. Micropalaeontol. 28, 67–85 (2009).
    Google Scholar 
    35.Boomer, I. et al. Biotic and stable-isotope characterization of the Toarcian Ocean Anoxic Event through a carbonate-clastic sequence from Somerset, UK. Geological Society, London, Special Publications (2021).36.Moore, C. On the Middle and Upper Lias of the South West of England. Proc. Somerset Archaeol. Nat. Hist. Soc. 13, 19–244 (1866).
    Google Scholar 
    37.Rayner, D. H. The structure of certain Jurassic holostean fishes with special reference to their neurocrania. Philos. Trans. R. Soc. Lond. B Biol. Sci. 233, 287–345 (1948).ADS 

    Google Scholar 
    38.Patterson, C. The braincase of pholidophorid and leptolepid fishes, with a review of the actinopterygian braincase. Philos. Trans. R. Soc. Lond. B Biol. Sci. 269, 275–579 (1975).ADS 
    CAS 
    PubMed 

    Google Scholar 
    39.McGowan, C. Further evidence for the wide geographical distribution of ichthyosaur taxa (Reptilia: Ichthyosauria). J. Paleontol. 52, 1155–1162 (1978).
    Google Scholar 
    40.Duffin, C. Pelagosaurus (Mesosuchia, Crocodilia) from the English Toarcian (Lower Jurassic). Neues Jb. Geol. Paläontol. Monat. 1979, 475–485 (1979).
    Google Scholar 
    41.Woodward, A. S. Notes on the collection of fossil fishes from the Upper Lias of Ilminster in the Bath Museum. Proc. Bath Nat. Hist. Antiqu. Field Club 8, 233–242 (1897).
    Google Scholar 
    42.Pierce, S. E. & Benton, M. J. Pelagosaurus typus Bronn, 1841 (Mesoeucrocodylia: Thalattosuchia) from the Upper Lias (Toarcian, Lower Jurassic) of Somerset, England. J. Vertebr. Paleontol. 26, 621–635 (2006).
    Google Scholar 
    43.Caine, H. & Benton, M. J. Ichthyosauria from the Upper Lias of Strawberry Bank, England. Palaeontology 54, 1069–1093 (2011).
    Google Scholar 
    44.Marek, R. D., Moon, B. C., Williams, M. & Benton, M. J. The skull and endocranium of a Lower Jurassic ichthyosaur based on digital reconstructions. Palaeontology 58, 723–742 (2015).
    Google Scholar 
    45.Urlichs, M. The Lower Jurassic in southwestern Germany. Stuttgarter Beitrage zur Naturkunde series b Number 24, 1–45 (1977).
    Google Scholar 
    46.Riegraf, W., Werner, G. & Lörcher, F. Der Posidonienschiefer: Biostratigraphie Fauna und Fazies des südwestdeutschen Untertoarciums (Lias ε). (1984).47.Hauff, B. Untersuchungen der Fossilfundstätten von Holzmaden im Posidonienschiefer des Oberen Lias Württembergs. Palaeontographica 64, 1–42 (1921).
    Google Scholar 
    48.Röhl, H.-J., Schmid-Röhl, A. Lower Toarcian (Upper Liassic) Black Shales of the Central European Epicontinental Basin: A Sequence Stratigraphic Case Study from the SW German Posidonia Shale. in The Deposition of Organic-Carbon-Rich Sediments: Models, Mechanisms, and Consequences: (ed. Harris, N.) 165–189 (Society for Sedimentary Geology Special Publications 82, 2005).49.Parrish, J. T. Climate of the supercontinent Pangaea. J. Geol. 101, 215–233 (1993).ADS 

    Google Scholar 
    50.Hall, R. L. New, biostratigraphically significant ammonities from the Jurassic Fernie Formation, southern Canadian Rocky Mountains. Can. J. Earth Sci. 43, 555–570 (2006).ADS 

    Google Scholar 
    51.Hall, R. L., McNicoll, V., Grocke, D. R., Craig, J. & Johnston, K. Integrated stratigraphy of the lower and middle Fernie Formation in Alberta and British Columbia, Western Canada. Riv. Ital. Paleontol. Stratigr. 110, 61–68 (2004).
    Google Scholar 
    52.Them, T. R. et al. High-resolution carbon isotope records of the Toarcian Oceanic Anoxic Event (Early Jurassic) from North America and implications for the global drivers of the Toarcian carbon cycle. Earth Planet. Sci. Lett. 459, 118–126 (2017).ADS 
    CAS 

    Google Scholar 
    53.Hall, R.L., Poulton, T.P., and Monger, J. W. H. Field Trip A1: Calgary–Vancouver. in Field Guide for the Fifth International Symposium on the Jurassic System (ed. Smith, P. L.) 29–61 (International Union of Geological Sciences Subcommission on Jurassic Stratigraphy, 1998).54.Hall, R. L. New lower jurassic ammonite faunas from the fernie formation, southern Canadian Rocky Mountains. Can. J. Earth Sci. 24, 1688–1704 (1987).ADS 

    Google Scholar 
    55.Stronach, N. J. Depositional environments and cycles in the Jurassic Fernie Formation, southern Canadian Rocky Mountains. Can. Soc. Pet. Geol. Memoir 9, 43–67 (1984).
    Google Scholar 
    56.Maxwell, E. E. & Martindale, R. C. New Saurorhynchus (Actinopterygii: Saurichthyidae) material from the Early Jurassic of Alberta, Canada. Can. J. Earth Sci. 54, 714–719 (2017).ADS 

    Google Scholar 
    57.Hall, R. L. Seirocrinus subangularis (Miller, 1821), a Pliensbachian (Lower Jurassic) crinoid from the Fernie Formation, Alberta, Canada. J. Paleontol. 65, 300–307 (1991).
    Google Scholar 
    58.Feldman, R. M. & Copeland, M. J. A new species of erymid lobster from Lower Jurassic strata (Sinemurian/Pliensbachian), Fernie Formation, southwestern Alberta. Geol. Surv. Can. Bull. 379, 93–101 (1988).
    Google Scholar 
    59.Schweigert, G., Garassino, A., Hall, R. L., Hauff, R. B. & Karasawa, H. The lobster genus Uncina Quenstedt, 1851 (Crustacea: Decapoda: Astacidea: Uncinidae) from the Lower Jurassic. Stuttgarter Beiträge zur Naturkunde Serie B (Geologie und Paläontologie) 332, 1–43 (2003).
    Google Scholar 
    60.Martindale, R. C. & Aberhan, M. Response of macrobenthic communities to the Toarcian Oceanic Anoxic Event in northeastern Panthalassa (Ya Ha Tinda, Alberta, Canada). Palaeogeogr. Palaeoclimatol. Palaeoecol. 478, 103–120 (2017).
    Google Scholar 
    61.Hall, R. L. Paraplesioteuthis hastata (Munster), the first teuthid squid recorded from the Jurassic of North America. J. Paleontol. 59, 870–874 (1985).
    Google Scholar 
    62.Marroquín, S. M., Martindale, R. C. & Fuchs, D. New records of the late Pliensbachian to early Toarcian (Early Jurassic) gladius-bearing coleoid cephalopods from the Ya Ha Tinda Lagerstätte, Canada. Papers Palaeontol. 4, 245–276 (2018).
    Google Scholar 
    63.Muscente, A. D. & Xiao, S. Resolving three-dimensional and subsurficial features of carbonaceous compressions and shelly fossils using backscattered electron scanning electron microscopy (BSE-SEM). Palaios 30, 462–481 (2015).ADS 

    Google Scholar 
    64.Lindgren, J. et al. Soft-tissue evidence for homeothermy and crypsis in a Jurassic ichthyosaur. Nature 564, 359–365 (2018).ADS 
    CAS 
    PubMed 

    Google Scholar 
    65.Seilacher, A., Andalib, F., Dietl, G. & Gocht, H. Preservational history of compressed Jurassic ammonites from Southern Germany. Neues Jahrbuch für Geologie und Paläontologie – Abhandlungen 152, 307–356 (1976).
    Google Scholar 
    66.Them, T. R. et al. Evidence for rapid weathering response to climatic warming during the Toarcian Oceanic Anoxic Event. Earth Planet. Sci. Lett. 7, 1–10 (2017).CAS 

    Google Scholar 
    67.Szpak, P. Fish bone chemistry and ultrastructure: Implications for taphonomy and stable isotope analysis. J. Archaeol. Sci. 38, 3358–3372 (2011).
    Google Scholar 
    68.Kunkel, J. G., Nagel, W. & Jercinovic, M. J. Mineral fine structure of the American lobster cuticle. J. Shellfish Res. 31, 515–526 (2012).
    Google Scholar 
    69.Doguzhaeva, L. A. & Mutvei, H. Gladius composition and ultrastructure in extinct squid-like coleoids: Loligosepia, Trachyteuthis and Teudopsis. Rev. Paleobiol. 22, 877–894 (2003).
    Google Scholar 
    70.Glass, K. et al. Direct chemical evidence for eumelanin pigment from the Jurassic period. Proc. Natl. Acad. Sci. U.S.A. 109, 10218–10223 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    71.Schiffbauer, J. D., Wallace, A. F., Broce, J. & Xiao, S. Exceptional fossil conservation through phosphatization. The Paleontol. Soc. Papers 20, 59–82 (2014).
    Google Scholar 
    72.Muscente, A. D., Hawkins, A. D. & Xiao, S. Fossil preservation through phosphatization and silicification in the Ediacaran Doushantuo Formation (South China): a comparative synthesis. Palaeogeogr. Palaeoclimatol. Palaeoecol. 434, 46–62 (2015).
    Google Scholar 
    73.Glenn, C. R. Phosphorus and phosphorites: sedimentology and environments of formation. Eclogae Geol. Helv. 87, 747–788 (1994).
    Google Scholar 
    74.Arning, E. T., Birgel, D., Brunner, B. & Peckmann, J. Bacterial formation of phosphatic laminites off Peru. Geobiology 7, 295–307 (2009).CAS 
    PubMed 

    Google Scholar 
    75.Dera, G. et al. Distribution of clay minerals in Early Jurassic Peritethyan seas: Palaeoclimatic significance inferred from multiproxy comparisons. Palaeogeogr. Palaeoclimatol. Palaeoecol. 271, 39–51 (2009).
    Google Scholar 
    76.Fantasia, A. et al. Global versus local processes during the Pliensbachian-Toarcian transition at the Peniche GSSP, Portugal: A multi-proxy record. Earth-Sci. Rev. 198, 102932 (2019).CAS 

    Google Scholar  More

  • in

    Ontogenetic shifts from social to experiential learning drive avian migration timing

    1.Bauer, S. & Hoye, B. J. Migratory animals couple biodiversity and ecosystem functioning worldwide. Science 344, 1242552–1242552 (2014).CAS 
    PubMed 

    Google Scholar 
    2.Abrahms, B. et al. Emerging perspectives on resource tracking and animal movement ecology. Trends Ecol. Evol. 36, 308–320 (2021).PubMed 

    Google Scholar 
    3.Armstrong, J. B., Takimoto, G., Schindler, D. E., Hayes, M. M. & Kauffman, M. J. Resource waves: phenological diversity enhances foraging opportunities for mobile consumers. Ecology 97, 1099–1112 (2016).PubMed 

    Google Scholar 
    4.Middleton, A. D. et al. Green-wave surfing increases fat gain in a migratory ungulate. Oikos 20, 741–749 (2018).
    Google Scholar 
    5.Fryxell, J. M., Greever, J. & Sinclair, A. Why are migratory ungulates so abundant. Am. Nat. 131, 781–798 (1988).
    Google Scholar 
    6.Wilcove, D. S. & Wikelski, M. Going, going, gone: is animal migration disappearing. PLoS Biol. 6, e188–4 (2008).PubMed 
    PubMed Central 

    Google Scholar 
    7.Mueller, T., O’Hara, R. B., Converse, S. J., Urbanek, R. P. & Fagan, W. F. Social learning of migratory performance. Science 341, 999–1002 (2013).ADS 
    CAS 
    PubMed 

    Google Scholar 
    8.Berdahl, A. M. et al. Collective animal navigation and migratory culture: from theoretical models to empirical evidence. Philos. Trans. R. Soc. B Biol. Sci. 373, 20170009–20170016 (2018).
    Google Scholar 
    9.Campioni, L., Dias, M. P., Granadeiro, J. P. & Catry, P. An ontogenetic perspective on migratory strategy of a long‐lived pelagic seabird: timings and destinations change progressively during maturation. J. Anim. Ecol. 89, 29–43 (2020).PubMed 

    Google Scholar 
    10.Sergio, F. et al. Individual improvements and selective mortality shape lifelong migratory performance. Nature 515, 1–17 (2014).MathSciNet 

    Google Scholar 
    11.Thorup, K. et al. Evidence for a navigational map stretching across the continental U.S. in a migratory songbird. Proc. Natl Acad. Sci. USA 104, 18115–18119 (2007).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    12.Teitelbaum, C. S. et al. Experience drives innovation of new migration patterns of whooping cranes in response to global change. Nat. Commun. 7, 12793 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    13.Teitelbaum, C. S., Converse, S. J. & Mueller, T. The importance of early life experience and animal cultures in reintroductions. Conserv. Lett. 34, e12599–7 (2018).
    Google Scholar 
    14.Jesmer, B. R. et al. Is ungulate migration culturally transmitted? Evidence of social learning from translocated animals. Science 361, 1023–1025 (2018).ADS 
    CAS 
    PubMed 

    Google Scholar 
    15.Kendal, R. L., Coe, R. L. & Laland, K. N. Age differences in neophilia, exploration, and innovation in family groups of callitrichid monkeys. Am. J. Primatol. 66, 167–188 (2005).CAS 
    PubMed 

    Google Scholar 
    16.French, J. B. et al. Whooping cranes past and present. in Whooping Cranes (eds. French, J. B. Jr, Conserve, S. J. & Austin, J. E.) (Academic Publisher, 2019).17.Urbanek, R. P., Fondow, L. E. A., Zimorski, S. E., Wellington, M. A. & Nipper, M. A. Winter release and management of reintroduced migratory Whooping Cranes Grus americana. Bird. Conserv. Int. 20, 43–54 (2009).
    Google Scholar 
    18.Sorte, F. A. L. & Graham, C. H. Phenological synchronization of seasonal bird migration with vegetation greenness across dietary guilds. J. Anim. Ecol. 90, 343–355 (2021).PubMed 

    Google Scholar 
    19.Pettorelli, N. et al. Using the satellite-derived NDVI to assess ecological responses to environmental change. Trends Ecol. Evol. 20, 503–510 (2005).PubMed 

    Google Scholar 
    20.Xu, F. & Si, Y. The frost wave hypothesis: how the environment drives autumn departure of migratory waterfowl. Ecol. Indic. 101, 1018–1025 (2019).
    Google Scholar 
    21.Nuijten, R. J. M. et al. The exception to the rule: retreating ice front makes Bewick’s swans Cygnus columbianus bewickii migrate slower in spring than in autumn. J. Avian Biol. 45, 113–122 (2013).
    Google Scholar 
    22.Barrett, B., Zepeda, E., Pollack, L., Munson, A. & Sih, A. Counter-culture: does social learning help or hinder adaptive response to human-induced rapid environmental change? Front. Ecol. Evol. 7, 485–18 (2019).
    Google Scholar 
    23.Schmaljohann, H. & Both, C. The limits of modifying migration speed to adjust to climate change. Nat. Clim. Change 7, 573–576 (2017).ADS 

    Google Scholar 
    24.Rotics, S. et al. The challenges of the first migration: movement and behaviour of juvenile vs. adult white storks with insights regarding juvenile mortality. J. Anim. Ecol. 85, 938–947 (2016).PubMed 

    Google Scholar 
    25.Thurfjell, H., Ciuti, S. & Boyce, M. S. Learning from the mistakes of others: How female elk (Cervus elaphus) adjust behaviour with age to avoid hunters. PLoS ONE 12, e0178082–20 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    26.Reader, S. M. & Laland, K. N. Primate innovation: sex, age and social rank differences. Int. J. Primatol. 22, 787–805 (2001).
    Google Scholar 
    27.Brent, L. J. N. et al. Ecological knowledge, leadership, and the evolution of menopause in killer whales. Curr. Biol. 25, 746–750 (2015).CAS 
    PubMed 

    Google Scholar 
    28.Aplin, L. M. et al. Experimentally induced innovations lead to persistent culture via conformity in wild birds. Nature 518, 538–541 (2015).ADS 
    CAS 
    PubMed 

    Google Scholar 
    29.Gill, J. A. et al. Why is timing of bird migration advancing when individuals are not? Proc. R. Soc. B Biol. Sci. 281, 20132161 (2014).
    Google Scholar 
    30.Dall, S. R. X., Bell, A. M., Bolnick, D. I. & Ratnieks, F. L. W. An evolutionary ecology of individual differences. Ecol. Lett. 15, 1189–1198 (2012).PubMed 
    PubMed Central 

    Google Scholar 
    31.Shaw, A. K. Causes and consequences of individual variation in animal movement. Mov. Ecol. 8, 1–12 (2020).
    Google Scholar 
    32.van de Pol, M. & Wright, J. A simple method for distinguishing within- versus between-subject effects using mixed models. Anim. Behav. 77, 753–758 (2009).
    Google Scholar 
    33.Gurarie, E. et al. Tactical departures and strategic arrivals: divergent effects of climate and weather on caribou spring migrations. Ecosphere 10, 407–432 (2019).
    Google Scholar 
    34.Burnside, R. J., Salliss, D., Collar, N. J. & Dolman, P. M. Birds use individually consistent temperature cues to time their migration departure. Proc. Natl Acad. Sci. USA 118, e2026378118 (2021).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    35.Whitehead, H. Conserving and managing animals that learn socially and share cultures. Learn. Behav. 38, 329–336 (2010).PubMed 

    Google Scholar 
    36.Vilhunen, S., Hirvonen, H. & Laakkonen, M. V.-M. Less is more: social learning of predator recognition requires a low demonstrator to observer ratio in Arctic charr (Salvelinus alpinus). Behav. Ecol. Sociobiol. 57, 275–282 (2004).
    Google Scholar 
    37.Roth, T. C. II & Krochmal, A. R. The role of age-specific learning and experience for turtles navigating a changing landscape. Curr. Biol. 25, 333–337 (2015).CAS 
    PubMed 

    Google Scholar 
    38.Vitasse, Y., Signarbieux, C. & Fu, Y. H. Global warming leads to more uniform spring phenology across elevations. Proc. Natl Acad. Sci. 115, 1004–1008 (2018).CAS 
    PubMed 

    Google Scholar 
    39.Aikens, E. O. et al. Drought reshuffles plant phenology and reduces the foraging benefit of green‐wave surfing for a migratory ungulate. Glob. Change Biol. 23, 239–11 (2020).
    Google Scholar 
    40.Douglas, D. C. et al. Moderating Argos location errors in animal tracking data. Methods Ecol. Evol. 3, 999–1007 (2012).
    Google Scholar 
    41.Dodge, S. et al. Environmental drivers of variability in the movement ecology of turkey vultures (Cathartes aura) in North and South America. Philos. Trans. R. Soc. B Biol. Sci. 369, 20130195–20130195 (2014).
    Google Scholar 
    42.Aikens, E. O. et al. The greenscape shapes surfing of resource waves in a large migratory herbivore. Ecol. Lett. 65, 502–510 (2017).
    Google Scholar 
    43.Bunnefeld, N. et al. A model-driven approach to quantify migration patterns: individual, regional and yearly differences. J. Anim. Ecol. 80, 466–476 (2010).PubMed 

    Google Scholar 
    44.Paradis, E., Claude, J. & Strimmer, K. Ape: analyses of phylogenetics and evolution in {R} language. Bioinformatics 20, 289–290 (2004).CAS 

    Google Scholar 
    45.Burnham, K. P. & Anderson, D. R. Model Selection and Inference: A Practical Information-Theoretic Approach Vol. 72 (Springer, 1998).46.Nally, R. M., Duncan, R. P., Thomson, J. R. & Yen, J. D. L. Model selection using information criteria, but is the “best” model any good? J. Appl. Ecol. 55, 1441–1444 (2017).
    Google Scholar 
    47.Bates, D., Mächler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).
    Google Scholar 
    48.Fox, J. & Weisberg, S. Visualizing fit and lack of fit in complex regression models with predictor effect plots and partial residuals. J. Stat. Softw. 87, 1–27 (2018).
    Google Scholar 
    49.“R Core Team”. R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, 2021).50.Abrahms, B., Teitelbaum, C., Mueller, T. & Converse, S. Data from: ontogenetic shifts from social to experiential learning drive avian migration timing. Movebank Data Repository https://doi.org/10.5441/001/1.t23vm852 (2021).51.Abrahms, B. Code from: ontogenetic shifts from social to experiential learning drive avian migration timing. Github Repository. https://doi.org/10.5281/zenodo.5719357 (2021). More

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    Outcrossing rates in an experimentally admixed population of self-compatible and self-incompatible Arabidopsis lyrata

    Study speciesArabidopsis lyrata subsp. lyrata (Brassicaceae) is a small, insect-pollinated, short-lived perennial native to the Great Lakes region of North America. It grows in relatively dry habitats with porous soils, such as sand dunes and rocky outcrops (Mable et al. 2005). Like many other Brassicaceae, this plant is usually characterized by sporophytic SI (Mable et al. 2003) and thus obligately outcrossing, although hand-pollinations have indicated that SC individuals occur at low frequencies in otherwise SI populations (Mable et al. 2005). A few populations consist of only SC plants and are characterized by a mating system with high selfing rates (Foxe et al. 2010) and shorter-life spans (Gorman et al. 2020b). Evidence suggests that there have been at least two relatively recent ( More

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    Genomic landscape of a relict fir-associated fungus reveals rapid convergent adaptation towards endophytism

    1.Tigano A, Colella JP, MacManes MD. Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent. Mol Ecol. 2020;29:1300–14.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    2.Gladieux P, Ropars J, Badouin H, Branca A, Aguileta G, de Vienne DM, et al. Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes. Mol Ecol. 2014;23:753–73.PubMed 

    Google Scholar 
    3.Martin F, Aerts A, Ahrén D, Brun A, Danchin EG, Duchaussoy F, et al. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature. 2008;452:88–92.CAS 
    PubMed 

    Google Scholar 
    4.Weiß M, Waller F, Zuccaro A, Selosse MA. Sebacinales-one thousand and one interactions with land plants. New Phytol. 2016;211:20–40.PubMed 

    Google Scholar 
    5.Knapp DG, Németh JB, Barry K, Hainaut M, Henrissat B, Johnson J, et al. Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi. Sci Rep. 2018;8:6321.PubMed 
    PubMed Central 

    Google Scholar 
    6.Martino E, Morin E, Grelet GA, Kuo A, Kohler A, Daghino S, et al. Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists. New Phytol. 2018;217:1213–29.CAS 
    PubMed 

    Google Scholar 
    7.Arnold AE. Understanding the diversity of foliar endophytic fungi: progress, challenges, and frontiers. Fungal Biol Rev. 2007;21:51–66.
    Google Scholar 
    8.Carroll G. Fungal endophytes in stems and leaves: from latent pathogen to mutualistic symbiont. Ecology. 1988;69:2–9.
    Google Scholar 
    9.Miller JD, Sumarah MW, Adams GW. Effect of a rugulosin-producing endophyte in Picea glauca on Choristoneura fumiferana. J Chem Ecol. 2008;34:362–8.CAS 
    PubMed 

    Google Scholar 
    10.White JF Jr, Torres MS. Is plant endophyte-mediated defensive mutualism the result of oxidative stress protection? Physiol Plant. 2010;138:440–6.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    11.May G, Nelson P. Defensive mutualisms: do microbial interactions within hosts drive the evolution of defensive traits? Funct Ecol. 2014;28:356–63.
    Google Scholar 
    12.Carroll G. The foraging ascomycete, in: Abstracts of the 16th International Botanical Congress. St Louis, Missouri, USA, 1999.13.Müller MM, Valjakka R, Suokko A, Hantula J. Diversity of endophytic fungi of single Norway spruce needles and their role as pioneer decomposers. Mol Ecol. 2001;10:1801–10.PubMed 

    Google Scholar 
    14.Thomas DC, Vandegrift R, Ludden A, Carroll GC, Roy BA. Spatial ecology of the fungal genus Xylaria in a tropical cloud forest. Biotropica. 2016;48:381–93.
    Google Scholar 
    15.Naranjo-Ortiz MA, Gabaldón T. Fungal evolution: major ecological adaptations and evolutionary transitions. Biol Rev Camb Philos Soc. 2019;94:1443–76.PubMed 
    PubMed Central 

    Google Scholar 
    16.Oono R, Lutzoni F, Arnold AE, Kaye L, U’Ren JM, May G, et al. Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species. Am J Bot. 2014;101:1362–74.PubMed 

    Google Scholar 
    17.Shao S, Jin Z. In Species Diversity and Extinction (ed. Tepper, GH) Ch. 15. Nova Science Publishers. 2010.18.Yuan ZL, Rao LB, Chen YC, Zhang CL, Wu YG. From pattern to process: species and functional diversity in fungal endophytes of Abies beshanzuensis. Fungal Biol. 2011;115:197–213.PubMed 

    Google Scholar 
    19.Yuan ZL, Verkley GJM. Pezicula neosporulosa sp. nov. (Helotiales, Ascomycota), an endophytic fungus associated with Abies spp. in China and Europe. Mycoscience. 2014;56:205–13.
    Google Scholar 
    20.Sieber T. Endophytic fungi in forest trees: are they mutualists? Fungal Biol Rev. 2007;21:75–89.
    Google Scholar 
    21.Levis NA, Martin RA, O’Donnell KA, Pfennig DW. Intraspecific adaptive radiation: competition, ecological opportunity, and phenotypic diversification within species. Evolution. 2017;71:2496–509.PubMed 

    Google Scholar 
    22.Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, Otillar R, et al. MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res. 2014;42:D699–D704.CAS 
    PubMed 

    Google Scholar 
    23.Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42:D490–D495.CAS 
    PubMed 

    Google Scholar 
    24.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–W101.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    25.Blin K, Wolf T, Chevrette MG, Lu XW, Schwalen CJ, Kautsar SA, et al. antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res. 2017;45:W36–W41.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    26.Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 2015;16:157.PubMed 
    PubMed Central 

    Google Scholar 
    27.Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    28.Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000;17:540–52.CAS 
    PubMed 

    Google Scholar 
    29.Enright AJ, Dongen SV, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002;30:1575–84.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    30.Han MV, Thomas GW, Lugo-Martinez J, Hahn MW. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Mol Biol Evol. 2013;30:1987–97.CAS 
    PubMed 

    Google Scholar 
    31.Walkowiak S, Rowland O, Rodrigue N, Subramaniam R. Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum. BMC Genomics. 2016;17:1014.PubMed 
    PubMed Central 

    Google Scholar 
    32.Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589–95.PubMed 
    PubMed Central 

    Google Scholar 
    33.Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.PubMed 
    PubMed Central 

    Google Scholar 
    34.Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;43:11.10.1–11.10.33.
    Google Scholar 
    35.Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123:585–95.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    36.Fu YX, Li WH. Statistical tests of neutrality of mutations. Genetics. 1993;133:693–709.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    37.Hutter S, Vilella AJ, Rozas J. Genome-wide DNA polymorphism analyses using VariScan. BMC Bioinform. 2006;7:409.
    Google Scholar 
    38.Richards JK, Stukenbrock EH, Carpenter J, Liu Z, Cowger C, Faris JD, et al. Local adaptation drives the diversification of effectors in the fungal wheat pathogen Parastagonospora nodorum in the United States. PLoS Genet. 2019;15:e1008223.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    39.Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006;23:254–67.CAS 
    PubMed 

    Google Scholar 
    40.Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210–2.PubMed 

    Google Scholar 
    41.Looney B, Miyauchi S, Morin E, Drula E, Courty PE, Kohler A, et al. Evolutionary priming and transition to the ectomycorrhizal habit in an iconic lineage of mushroom-forming fungi: is preadaptation a requirement? bioRxiv. 2021. https://doi.org/10.1101/2021.02.23.432530.42.Wey T, Schlegel M, Stroheker S, Gross A. MAT-gene structure and mating behavior of Hymenoscyphus fraxineus and Hymenoscyphus albidus. Fungal Genet Biol. 2016;87:54–63.CAS 
    PubMed 

    Google Scholar 
    43.Zijlstra JD, Van’t Hof P, Baar J, Verkley GJM, Summerbell RC, Paradi I, et al. Diversity of symbiotic root endophytes of the Helotiales in ericaceous plants and the grass, Deschampsia flexuosa. Stud Mycol. 2005;53:147–62.
    Google Scholar 
    44.Almario J, Jeena G, Wunder J, Langen G, Zuccaro A, Zuccaro A, et al. Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition. Proc Natl Acad Sci USA. 2017;114:E9403–E9412.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    45.Gazis R, Kuo A, Riley R, LaButti K, Lipzen A, Lin J, et al. The genome of Xylona heveae provides a window into fungal endophytism. Fungal Biol. 2016;120:26–42.CAS 
    PubMed 

    Google Scholar 
    46.Perotto S, Daghino S, Martino E. Ericoid mycorrhizal fungi and their genomes: another side to the mycorrhizal symbiosis? New Phytol. 2018;220:1141–7.PubMed 

    Google Scholar 
    47.Wrzosek M, Ruszkiewicz-Michalska M, Sikora K, Damszel M, Sierota Z. The plasticity of fungal interactions. Mycol Prog. 2017;16:101–8.
    Google Scholar 
    48.Parrent JL, James TY, Vasaitis R, Taylor AF. Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses. BMC Evol Biol. 2009;9:148.PubMed 
    PubMed Central 

    Google Scholar 
    49.Zhang F, Anasontzis GE, Labourel A, Champion C, Haon M, Kemppainen M, et al. The ectomycorrhizal basidiomycete Laccaria bicolor releases a secreted β-1,4 endoglucanase that plays a key role in symbiosis development. New Phytol. 2018;220:1309–21.CAS 
    PubMed 

    Google Scholar 
    50.Mesny F, Miyauchi S, Thiergart T, Pickel B, Atanasova L, Karlsson M, et al. Genetic determinants of endophytism in the Arabidopsis root mycobiome. Nat Commun. 2021;12:7227.CAS 
    PubMed 

    Google Scholar 
    51.Schulz B, Sucker J, Aust HJ. Biologically active secondary metabolites of endophytic Pezicula species. Mycol Res. 1995;99:1007–15.CAS 

    Google Scholar 
    52.Tanney JB, McMullin DR, Miller JD. Toxigenic Foliar Endophytes from the Acadian Forest. In: Pirttilä A, Frank A (eds) Endophytes of Forest Trees. Forestry Sciences, vol 86. Springer, Cham. 2018;343–81.53.Yue Q, Li Y, Chen L, Zhang X, Liu X, An Z, et al. Genomics-driven discovery of a novel self-resistance mechanism in the echinocandin-producing fungus Pezicula radicicola. Environ Microbiol. 2018;20:3154–67.CAS 
    PubMed 

    Google Scholar 
    54.Rogers RL, Grizzard SL, Titus-McQuillan JE, Bockrath K, Patel S, Wares JP, et al. Gene family amplification facilitates adaptation in freshwater unionid bivalve Megalonaias nervosa. Mol Ecol. 2021;30:1155–73.CAS 
    PubMed 

    Google Scholar 
    55.Mäkinen M, Kuuskeri J, Laine P, Smolander OP, Kovalchuk A, Zeng Z, et al. Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi. BMC Genomics. 2019;20:430.PubMed 
    PubMed Central 

    Google Scholar 
    56.Yang Y, Liu X, Cai J, Chen Y, Li B, Guo Z, et al. Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae. BMC Genomics. 2019;20:782.PubMed 
    PubMed Central 

    Google Scholar 
    57.Franco MEE, Wisecaver JH, Arnold AE, Ju YM, Slot JC, Ahrendt S, et al. Secondary metabolism drives ecological breadth in the Xylariaceae. bioRxiv. 2021. https://doi.org/10.1101/2021.06.01.446356.58.Matsuda Y, Yamakawa M, Inaba T, Obase K, Ito S. Intraspecific variation in mycelial growth of Cenococcum geophilum isolates in response to salinity gradients. Mycoscience. 2017;58:369–77.
    Google Scholar 
    59.Taylor JW, Branco S, Gao C, Hann-Soden C, Montoya L, Sylvain I, et al. Sources of fungal genetic variation and associating it with phenotypic diversity. Microbiol Spectr. 2017;5:1–21.CAS 

    Google Scholar 
    60.Chen ECH, Morin E, Beaudet D, Noel J, Yildirir G, Ndikumana S, et al. High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis. New Phytol. 2018;220:1161–71.CAS 
    PubMed 

    Google Scholar 
    61.McCutcheon TL, Carroll GC, Schwab S. Genotypic diversity in populations of a fungal endophyte from Douglas Fir. Mycologia. 1993;85:180–6.
    Google Scholar 
    62.Perotto S, Girlanda M, Martino E. Ericoid mycorrhizal fungi: some new perspectives on old acquaintances. Plant Soil. 2002;244:41–53.CAS 

    Google Scholar 
    63.Müller MM, Valjakka R, Hantula J. Genetic diversity of Lophodermium piceae in South Finland. For Pathol. 2007;37:329–37.
    Google Scholar 
    64.Morgenstern K, Polster J-U, Krabel D. Genetic variation between and within two populations of Rhabdocline pseudotsugae in Germany. Can J Res. 2016;46:716–24.CAS 

    Google Scholar 
    65.Atwell S, Corwin JA, Soltis NE, Subedy A, Denby KJ, Kliebenstein DJ. Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity. Front Microbiol. 2015;6:996.PubMed 
    PubMed Central 

    Google Scholar 
    66.Gasca-Pineda J, Velez P, Hosoya T. Phylogeography of post-Pleistocene population expansion in Dasyscyphella longistipitata (Leotiomycetes, Helotiales), an endemic fungal symbiont of Fagus crenata in Japan. MycoKeys. 2020;65:1–24.PubMed 
    PubMed Central 

    Google Scholar 
    67.Groenewald M, Linde CC, Groenewald JZ, Crous PW. Indirect evidence for sexual reproduction in Cercospora beticola populations from sugar beet. Plant Pathol. 2008;57:25–32.CAS 

    Google Scholar 
    68.Nordborg M, Charlesworth B, Charlesworth D. Increased levels of polymorphism surrounding selectively maintained sites in highly selfing species. Proc R Soc B. 1996;263:1033–9.
    Google Scholar 
    69.Koenig D, Hagmann J, Li R, Bemm F, Slotte T, Neuffer B, et al. Long-term balancing selection drives evolution of immunity genes in Capsella. Elife. 2019;8:e43606.PubMed 
    PubMed Central 

    Google Scholar 
    70.Carbone I, Jakobek JL, Ramirez-Prado JH, Horn BW. Recombination, balancing selection and adaptive evolution in the aflatoxin gene cluster of Aspergillus parasiticus. Mol Ecol. 2007;16:4401–17.CAS 
    PubMed 

    Google Scholar 
    71.Drott MT, Debenport T, Higgins SA, Buckley DH, Milgroom MG. Fitness cost of aflatoxin production in Aspergillus flavus when competing with soil microbes could maintain balancing selection. mBio. 2019;10:e02782–18.CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    72.Chen F, Goodwin PH, Khan A, Hsiang T. Population structure and mating-type genes of Colletotrichum graminicola from Agrostis palustris. Can J Microbiol. 2002;48:427–36.CAS 
    PubMed 

    Google Scholar  More