Philippa Kaur

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

Bolnick, D. I. et al. The ecology of individuals: Incidence and implications of individual specialization. Am. Nat. 161, 1–28. https://doi.org/10.1086/343878 (2003).MathSciNet 
Article 
PubMed 

Google Scholar 
Peterson, A. T., Soberón, J. & Sánchez-Cordero, V. Conservatism of ecological niches in evolutionary time. Science 285, 1265–1267 (1999).CAS 
Article 

Google Scholar 
Wiens, J. J. & Graham, C. H. Niche conservatism: Integrating evolution, ecology, and conservation biology. Annu. Rev. Ecol. Evol. Syst. 36, 519–539 (2005).Article 

Google Scholar 
Bolnick, D. I. et al. Why intraspecific trait variation matters in community ecology. Trends Ecol. Evol. 26, 183–192. https://doi.org/10.1016/j.tree.2011.01.009 (2011).Article 
PubMed 
PubMed Central 

Google Scholar 
Gentile, G., Bonelli, S. & Riva, F. Evaluating intraspecific variation in insect trait analysis. Ecol. Entomol. 46, 11–18 (2021).Article 

Google Scholar 
Ortego, J., Calabuig, G., Cordero, P. J. & Aparicio, J. M. Egg production and individual genetic diversity in lesser kestrels. Mol. Ecol. 16, 2383–2392 (2007).CAS 
Article 

Google Scholar 
Peacor, S. D., Schiesari, L. & Werner, E. E. Mechanisms of nonlethal predator effect on cohort size variation: Ecological and evolutionary implications. Ecology 88, 1536–1547 (2007).Article 

Google Scholar 
Smith, A. B., Godsoe, W., Rodríguez-Sánchez, F., Wang, H.-H. & Warren, D. Niche estimation above and below the species level. Trends Ecol. Evol. 34, 260–273 (2019).Article 

Google Scholar 
Carlson, B. S., Rotics, S., Nathan, R., Wikelski, M. & Jetz, W. Individual environmental niches in mobile organisms. Nat. Commun. 12, 4572. https://doi.org/10.1038/s41467-021-24826-x (2021).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Hutchinson, G. E. Population studies: Animal ecology and demography. Cold Spring Harb. Symp. Quant. Biol. 22, 415–427 (1957).Article 

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

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

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

Google Scholar 
Lowry, H., Lill, A. & Wong, B. B. Behavioural responses of wildlife to urban environments. Biol. Rev. 88, 537–549 (2013).Article 

Google Scholar 
Hällfors, M. H. et al. Combining range and phenology shifts offers a winning strategy for boreal Lepidoptera. Ecol. Lett. 24, 1619–1632 (2021).Article 

Google Scholar 
Joppa, L. N. & Pfaff, A. Global protected area impacts. Proc. R. Soc. B Biol. Sci. 278, 1633–1638. https://doi.org/10.1098/rspb.2010.1713 (2011).Article 

Google Scholar 
Hanson, J. O. et al. Global conservation of species’ niches. Nature 580, 232–234 (2020).ADS 
CAS 
Article 

Google Scholar 
Geldmann, J., Manica, A., Burgess, N. D., Coad, L. & Balmford, A. A global-level assessment of the effectiveness of protected areas at resisting anthropogenic pressures. Proc. Natl. Acad. Sci. 116, 23209–23215. https://doi.org/10.1073/pnas.1908221116 (2019).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Blonder, B. Hypervolume concepts in niche- and trait-based ecology. Ecography 41, 1441–1455 (2018).Article 

Google Scholar 
Mammola, S. & Cardoso, P. Functional diversity metrics using kernel density n-dimensional hypervolumes. Methods Ecol. Evol. 11, 986–995. https://doi.org/10.1111/2041-210X.13424 (2020).Article 

Google Scholar 
Mammola, S. Assessing similarity of n-dimensional hypervolumes: Which metric to use? J. Biogeogr. 46, 2012 (2019).Article 

Google Scholar 
Carvalho, J. C. & Cardoso, P. Decomposing the causes for niche differentiation between species using hypervolumes. Front. Ecol. Evol. https://doi.org/10.3389/fevo.2020.00243 (2020).Article 

Google Scholar 
Pavlek, M. & Mammola, S. Niche-based processes explaining the distributions of closely related subterranean spiders. J. Biogeogr. 48, 118–133. https://doi.org/10.1111/jbi.13987 (2021).Article 

Google Scholar 
Wang, X. et al. Exploring ecological specialization in pipefish using genomic, morphometric and ecological evidence. Divers. Distrib. 27, 1393–1406. https://doi.org/10.1111/ddi.13286 (2021).Article 

Google Scholar 
Jaturapruek, R., Fontaneto, D., Mammola, S. & Maiphae, S. Potential niche displacement in species of aquatic bdelloid rotifers between temperate and tropical areas. Hydrobiologia. https://doi.org/10.1007/s10750-021-04681-z (2021).Article 

Google Scholar 
Hu, Z. M. et al. Intraspecific genetic variation matters when predicting seagrass distribution under climate change. Mol. Ecol. 30, 3840–3855. https://doi.org/10.1111/mec.15996 (2021).Article 
PubMed 

Google Scholar 
Ho, D. E., Imai, K., King, G. & Stuart, E. A. Matching as nonparametric preprocessing for reducing model dependence in parametric causal inference. Polit. Anal. 15, 199–236 (2007).Article 

Google Scholar 
Terraube, J., Van Doninck, J., Helle, P. & Cabeza, M. Assessing the effectiveness of a national protected area network for carnivore conservation. Nat. Commun. 11, 2957. https://doi.org/10.1038/s41467-020-16792-7 (2020).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Chichorro, F., Juslén, A. & Cardoso, P. A review of the relation between species traits and extinction risk. Biol. Conserv. 237, 220–229 (2019).Article 

Google Scholar 
Pearman, P. B., Guisan, A., Broennimann, O. & Randin, C. F. Niche dynamics in space and time. Trends Ecol. Evol. 23, 149–158 (2008).Article 

Google Scholar 
Santangeli, A., Högmander, J. & Laaksonen, T. Returning white-tailed eagles breed as successfully in landscapes under intensive forestry regimes as in protected areas. Anim. Conserv. 16, 500–508. https://doi.org/10.1111/acv.12017 (2013).Article 

Google Scholar 
Broennimann, O. et al. Evidence of climatic niche shift during biological invasion. Ecol. Lett. 10, 701–709 (2007).CAS 
Article 

Google Scholar 
Fitzpatrick, M. C., Weltzin, J. F., Sanders, N. J. & Dunn, R. R. The biogeography of prediction error: Why does the introduced range of the fire ant over-predict its native range? Glob. Ecol. Biogeogr. 16, 24–33 (2007).Article 

Google Scholar 
Dietz, H. & Edwards, P. J. Recognition that causal processes change during plant invasion helps explain conflicts in evidence. Ecology 87, 1359–1367 (2006).Article 

Google Scholar 
Holt, R. D., Keitt, T. H., Lewis, M. A., Maurer, B. A. & Taper, M. L. Theoretical models of species’ borders: Single species approaches. Oikos 108, 18–27 (2005).Article 

Google Scholar 
Zhang, Z., Mammola, S., McLay, C. L., Capinha, C. & Yokota, M. To invade or not to invade? Exploring the niche-based processes underlying the failure of a biological invasion using the invasive Chinese mitten crab. Sci. Total Environ. 728, 138815. https://doi.org/10.1016/j.scitotenv.2020.138815 (2020).ADS 
CAS 
Article 
PubMed 

Google Scholar 
Liu, C., Wolter, C., Xian, W. & Jeschke, J. M. Most invasive species largely conserve their climatic niche. Proc. Natl. Acad. Sci. 117, 23643–23651 (2020).CAS 
Article 

Google Scholar 
Sarasola, J. H., Grande, J. M. & Negro, J. J. Birds of Prey: Biology and Conservation in the XXI Century 63–94 (Springer, 2018).Book 

Google Scholar 
Reif, J., Hořák, D., Krištín, A., Kopsová, L. & Devictor, V. Linking habitat specialization with species’ traits in European birds. Oikos 125, 405–413. https://doi.org/10.1111/oik.02276 (2016).Article 

Google Scholar 
Thornton, D., Branch, L. & Sunquist, M. Passive sampling effects and landscape location alter associations between species traits and response to fragmentation. Ecol. Appl. 21, 817–829. https://doi.org/10.1890/10-0549.1 (2011).Article 
PubMed 

Google Scholar 
Hatfield, J. H., Orme, C. D. L., Tobias, J. A. & Banks-Leite, C. Trait-based indicators of bird species sensitivity to habitat loss are effective within but not across data sets. Ecol. Appl. 28, 28–34. https://doi.org/10.1002/eap.1646 (2018).Article 
PubMed 

Google Scholar 
Kuuluvainen, T. Forest management and biodiversity conservation based on natural ecosystem dynamics in Northern Europe: The complexity challenge. Ambio 38, 309–315 (2009).Article 

Google Scholar 
Niemi, J. & Ahlstedt, J. Finnish Agriculture and Rural Industries 2011 (MTT Economic Research, Agrifood Research Finland, 2011).
Google Scholar 
Lehikoinen, P. et al. Increasing protected area coverage mitigates climate-driven community changes. Biol. Cons. 253, 108892. https://doi.org/10.1016/j.biocon.2020.108892 (2021).Article 

Google Scholar 
Virkkala, R. & Lehikoinen, A. Patterns of climate-induced density shifts of species: Poleward shifts faster in northern boreal birds than in southern birds. Glob. Change Biol. 20, 2995–3003. https://doi.org/10.1111/gcb.12573 (2014).ADS 
Article 

Google Scholar 
Lehikoinen, A. & Virkkala, R. North by north-west: Climate change and directions of density shifts in birds. Glob. Change Biol. 22, 1121–1129. https://doi.org/10.1111/gcb.13150 (2016).ADS 
Article 

Google Scholar 
Santangeli, A., Rajasärkkä, A. & Lehikoinen, A. Effects of high latitude protected areas on bird communities under rapid climate change. Glob. Change Biol. 23, 2241–2249. https://doi.org/10.1111/gcb.13518 (2017).ADS 
Article 

Google Scholar 
Lehikoinen, P., Santangeli, A., Jaatinen, K., Rajasärkkä, A. & Lehikoinen, A. Protected areas act as a buffer against detrimental effects of climate change—Evidence from large-scale, long-term abundance data. Glob. Change Biol. 25, 304–313. https://doi.org/10.1111/gcb.14461 (2019).ADS 
Article 

Google Scholar 
Santangeli, A. & Lehikoinen, A. Are winter and breeding bird communities able to track rapid climate change? Lessons from the high North. Divers. Distrib. 23, 308–316. https://doi.org/10.1111/ddi.12529 (2017).Article 

Google Scholar 
Lindén, H., Helle, E., Helle, P. & Wikman, M. Wildlife triangle scheme in Finland: Methods and aims for monitoring wildlife populations. Finnish Game Res. 49, 4–11 (1996).
Google Scholar 
Blonder, B. Do hypervolumes have holes? Am. Nat. 187, E93–E105. https://doi.org/10.1086/685444 (2016).Article 
PubMed 

Google Scholar 
Fuller, C., Ondei, S., Brook, B. W. & Buettel, J. C. First, do no harm: A systematic review of deforestation spillovers from protected areas. Glob. Ecol. Conserv. 18, e00591. https://doi.org/10.1016/j.gecco.2019.e00591 (2019).Article 

Google Scholar 
Hyvärinen, E., Juslén, A., Kemppainen, E., Uddström, A. & Liukko, U.-M. Suomen lajien uhanalaisuus–Punainen kirja 2019 (2019).Wilman, H. et al. EltonTraits 1.0: Species-level foraging attributes of the world’s birds and mammals. Ecology 95, 2027–2027. https://doi.org/10.1890/13-1917.1 (2014).Article 

Google Scholar 
Morelli, F., Benedetti, Y., Møller, A. P. & Fuller, R. A. Measuring avian specialization. Ecol. Evol. 9, 8378–8386 (2019).Article 

Google Scholar 
Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K. & Mooers, A. O. The global diversity of birds in space and time. Nature 491, 444 (2012).ADS 
CAS 
Article 

Google Scholar 
Cimatti, M. et al. Large carnivore expansion in Europe is associated with human population density and land cover changes. Divers. Distrib. 27, 602–617. https://doi.org/10.1111/ddi.13219 (2021).Article 

Google Scholar 
Laaksonen, T. & Lehikoinen, A. Population trends in boreal birds: Continuing declines in agricultural, northern, and long-distance migrant species. Biol. Conserv. 168, 99–107. https://doi.org/10.1016/j.biocon.2013.09.007 (2013).Article 

Google Scholar 
Blonder, B., Lamanna, C., Violle, C. & Enquist, B. J. The n-dimensional hypervolume. Glob. Ecol. Biogeogr. 23, 595–609. https://doi.org/10.1111/geb.12146 (2014).Article 

Google Scholar 
Cardoso, P. M., Rigal, F. & Carvalho, J. BAT-Biodiversity Assessment Tools (2014).Zuur, A. F. & Ieno, E. N. A protocol for conducting and presenting results of regression-type analyses. Methods Ecol. Evol. 7, 636–645 (2016).Article 

Google Scholar 
Brooks, M. E. et al. glmmTMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling. R J. 9, 378–400 (2017).Article 

Google Scholar 
Zuur, A. F., Ieno, E. N. & Elphick, C. S. A protocol for data exploration to avoid common statistical problems. Methods Ecol. Evol. 1, 3–14. https://doi.org/10.1111/j.2041-210X.2009.00001.x (2010).Article 

Google Scholar 
Sokal, R. R., Rohlf, F. J. & Rohlf, J. F. Biometry (Macmillan, 1995).MATH 

Google Scholar 
Dormann, C. F. et al. Collinearity: A review of methods to deal with it and a simulation study evaluating their performance. Ecography 36, 27–46. https://doi.org/10.1111/j.1600-0587.2012.07348.x (2013).Article 

Google Scholar 
Lüdecke, D., Ben-Shachar, M. S., Patil, I., Waggoner, P. & Makowski, D. performance: An R package for assessment, comparison and testing of statistical models. J. Open Source Softw. https://doi.org/10.21105/joss.03139 (2021).Article 

Google Scholar 
Revell, L. J. phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217–223 (2012).Article 

Google Scholar 
Zuur, A., Ieno, E. N., Walker, N., Saveliev, A. A. & Smith, G. M. Mixed Effects Models and Extensions in Ecology with R 1–552 (Springer, 2009).Book 

Google Scholar 
R Core Development Team. R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, 2021). https://www.R-project.org/. More

Gryseels, S., Bruyn, L. D., Gyselings, R., Leendertz, H. & Leirs, H. Risk of human-to-wildlife transmission of SARS-CoV-2. Mammal Rev. 51, 272–292 (2020).Article 

Google Scholar 
Townsend, A. K., Hawley, D. M., Stephenson, J. F. & Williams, K. E. G. Emerging infectious disease and the challenges of social distancing in human and non-human animals: EIDs and sociality. Proc. R. Soc. B Biol. Sci. 287, 20201039 (2020).CAS 
Article 

Google Scholar 
Dickman, A. J. From Cheetahs to Chimpanzees: A comparative review of the drivers of human–carnivore conflict and human–primate conflict. Folia Primatol. 83, 377–387 (2013).Article 

Google Scholar 
Nyhus, P. J. Human–wildlife conflict and coexistence. Annu. Rev. Environ. Resour. 41, 143–171 (2016).Article 

Google Scholar 
Cunningham, A. A. One health, emerging infectious diseases and wildlife. Philos. Trans. R. Soc. Lond. B Biol. Sci. 372, 4 (2017).
Google Scholar 
Daszak, P., Cunningham, A. A. & Hyatt, A. D. Emerging infectious diseases of wildlife—Threats to biodiversity and human health. Science 287, 443–449 (2000).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Fagre, A. C. et al. Assessing the risk of human-to-wildlife pathogen transmission for conservation and public health. Ecol. Lett. https://doi.org/10.1111/ele.14003 (2022).Article 
PubMed 

Google Scholar 
Messenger, A. M., Barnes, A. N. & Gray, G. C. Reverse zoonotic disease transmission (Zooanthroponosis): A systematic review of seldom-documented human biological threats to animals. PLoS One 9, 1–9 (2014).
Google Scholar 
Craft, M. E. Infectious disease transmission and contact networks in wildlife and livestock. Philos. Trans. R. Soc. B Biol. Sci. 370, 20140107 (2015).Article 

Google Scholar 
Bradley, C. A. & Altizer, S. Urbanization and the ecology of wildlife diseases. Trends Ecol. Evol. 22, 95–102 (2007).PubMed 
Article 

Google Scholar 
Balasubramaniam, K. N., Huffman, M. A., Sueur, C. & Macintosh, A. J. J. Primate infectious disease ecology: Insights and future directions at the human–macaque interface. In The Behavioral Ecology of the Tibetan Macaque. Fascinating Life Sciences (eds Li, J. et al.) 249–284 (Springer, 2020).Chapter 

Google Scholar 
McCabe, C. M., Reader, S. M. & Nunn, C. L. Infectious disease, behavioural flexibility and the evolution of culture in primates. Proc. R. Soc. B Biol. Sci. 282, 20140862 (2014).Article 

Google Scholar 
Silk, M. J. et al. Integrating social behaviour, demography and disease dynamics in network models: Applications to disease management in eclining wildlife populations. Philos. Trans. R. Soc. B Biol. Sci. 374, 20180211 (2019).Article 

Google Scholar 
Engel, G. A. & Jones-Engel, L. The role of Macaca fascicularis in infectious disease transmission. In Monkeys on the Edge: Ecology and Management of Long-Tailed Macaques and Their Interface with Humans (eds Gumert, M. D. et al.) 183–203 (Cambridge University Press, 2011).Chapter 

Google Scholar 
Anderson, R. M. & May, R. M. Infectious Diseases of Humans: Dynamics and Control (Oxford University Press, 1992).
Google Scholar 
Drewe, J. A. & Perkins, S. E. Disease transmission in animal social networks. In Animal Social Networks (eds Krause, J. et al.) 95–110 (Oxford University Press, 2015).
Google Scholar 
Godfrey, S. S. Networks and the ecology of parasite transmission: A framework for wildlife parasitology. Int. J. Parasitol. Parasites Wildl. 2, 235–245 (2013).PubMed 
PubMed Central 
Article 

Google Scholar 
Gomez, J. M., Nunn, C. L. & Verdu, M. Centrality in primate–parasite networks reveals the potential for the transmission of emerging infectious diseases to humans. Proc. Natl. Acad. Sci. 110, 7738–7741 (2013).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Godfrey, S. S., Bull, C. M., James, R. & Murray, K. Network structure and parasite transmission in a group living lizard, the gidgee skink, Egernia stokesii. Behav. Ecol. Sociobiol. 63, 1045–1056 (2009).Article 

Google Scholar 
VanderWaal, K. L., Atwill, E. R., Isbell, L. A. & McCowan, B. Linking social and pathogen transmission networks using microbial genetics in giraffe (Giraffa camelopardalis). J. Anim. Ecol. 83, 406–414 (2014).PubMed 
Article 

Google Scholar 
Drewe, J. A. Who infects whom? Social networks and tuberculosis transmission in wild meerkats. Proc. R. Soc. B Biol. Sci. 277, 633–642 (2010).Article 

Google Scholar 
MacIntosh, A. J. J. et al. Monkeys in the middle: Parasite transmission through the social network of a wild primate. PLoS One 7, 15–21 (2012).
Google Scholar 
Epstein, J. & Axtell, R. Growing Artificial Societies: Social Science from the Bottom Up (MIT Press, 1996).Book 

Google Scholar 
Bansal, S., Grenfell, B. T. & Meyers, L. A. When individual behaviour matters: Homogeneous and network models in epidemiology. J. R. Soc. Interface 4, 879–891 (2007).PubMed 
PubMed Central 
Article 

Google Scholar 
Brauer, F. Compartmental models in epidemiology, chapter 2. In Mathematical Epidemiology (eds Brauer, F. et al.) (Springer, 2008).MATH 
Chapter 

Google Scholar 
Carne, C., Semple, S., MacLarnon, A., Majolo, B. & Maréchal, L. Implications of tourist–macaque interactions for disease transmission. EcoHealth 14, 704–717 (2017).PubMed 
PubMed Central 
Article 

Google Scholar 
Rushmore, J. et al. Network-based vaccination improves prospects for disease control in wild chimpanzees. J. R. Soc. Interface 11, 20140349 (2014).PubMed 
PubMed Central 
Article 

Google Scholar 
Sah, P., Mann, J. & Bansal, S. Disease implications of animal social network structure: A synthesis across social systems. J. Anim. Ecol. 87, 546–558 (2018).PubMed 
Article 

Google Scholar 
Griffin, R. H. & Nunn, C. L. Community structure and the spread of infectious disease in primate social networks. Evol. Ecol. 26, 779–800 (2012).Article 

Google Scholar 
Hasegawa, M., Kishino, H. & Yano, T. Dating of the human–ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22, 160–174 (1985).ADS 
CAS 
PubMed 
Article 

Google Scholar 
Fuentes, A. & Hockings, K. J. The ethnoprimatological approach in primatology. Am. J. Primatol. 72, 841–847 (2010).PubMed 
Article 

Google Scholar 
Lappan, S., Malaivijitnond, S., Radhakrishna, S., Riley, E. P. & Ruppert, N. The human–primate interface in the new normal: Challenges and opportunities for primatologists in the COVID-19 era and beyond. Am. J. Primatol. 82, 1–12 (2020).Article 
CAS 

Google Scholar 
Mckinney, T. A classification system for describing anthropogenic influence on nonhuman primate populations. Am. J. Primatol. 77, 715–726 (2015).PubMed 
Article 

Google Scholar 
Devaux, C. A., Mediannikov, O., Medkour, H. & Raoult, D. Infectious disease risk across the growing human–non human primate interface: A review of the evidence. Front. Public Health 7, 1–22 (2019).Article 

Google Scholar 
Kaur, T. & Singh, J. Primate-parasitic zoonoses and anthropozoonoses: A literature review. In Primate Parasite Ecology: The Dynamics and Study of Host–Parasite Relationships (eds Huffman, M. A. & Chapman, C. A.) 199–230 (Cambridge University Press, 2009).
Google Scholar 
Melin, A. D., Janiak, M. C., Marrone, F., Arora, P. S. & Higham, J. P. Comparative ACE2 variation and primate COVID-19 risk. Commun. Biol. 3, 641 (2020).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Klegarth, A. Synanthropy. In The International Encyclopedia of Primatology (Wiley, 2017). https://doi.org/10.1002/9781119179313.wbprim0448.Chapter 

Google Scholar 
Gumert, M. D. A common monkey of Southeast Asia: Longtailed macaque populations, ethnophoresy, and their occurrence in human environments. In Monkeys on the Edge: Ecology and Management of Longtailed Macaques and Their Interface with Humans (eds Gumert, M. D. et al.) 3–43 (Cambridge University Press, 2011).Chapter 

Google Scholar 
Riley, E. P. The human–macaque interface: Conservation implications of current and future overlap and conflict in Lore Lindu National Park, Sulawesi, Indonesia. Am. Anthropol. 109, 473–484 (2007).Article 

Google Scholar 
Thierry, B. Unity in diversity: Lessons from macaque societies. Evol. Anthropol. 16, 224–238 (2007).Article 

Google Scholar 
Balasubramaniam, K. N. et al. The influence of phylogeny, social style, and sociodemographic factors on macaque social network structure. Am. J. Primatol. 80, e227227 (2018).Article 

Google Scholar 
Sueur, C. et al. A comparative network analysis of social style in macaques. Anim. Behav. 82(4), 845–852 (2011).Article 

Google Scholar 
Balasubramaniam, K. N. et al. Implementing social network analysis to understand the socioecology of wildlife co-occurrence and joint interactions with humans in anthropogenic environments. J. Anim. Ecol. 90, 2819–2833 (2021).PubMed 
Article 

Google Scholar 
Henzi, S. P. & Barrett, L. The value of grooming to female primates. Primates 40, 47–59 (1999).Article 

Google Scholar 
Schino, G. & Aureli, F. Trade-offs in primate grooming reciprocation: Testing behavioural flexibility and correlated evolution. Biol. J. Linn. Soc. 95, 439–446 (2008).Article 

Google Scholar 
Radhakrishna, S. & Sinha, A. Less than wild? Commensal primates and wildlife conservation. J. Biosci. 36, 749–753 (2011).PubMed 
Article 

Google Scholar 
Balasubramaniam, K. N. et al. Impact of individual demographic and social factors on human–wildlife interactions: A comparative study of three macaque species. Sci. Rep. 10, 21991 (2020).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Marty, P. R. et al. Time constraints imposed by anthropogenic environments alter social behaviour in long-tailed macaques. Anim. Behav. 150, 157–165 (2019).Article 

Google Scholar 
Kaburu, S. S. K. et al. Interactions with humans impose time constraints on urban-dwelling rhesus macaques (Macaca mulatta). Behaviour 156, 1255–1282 (2019).Article 

Google Scholar 
Altmann, J. Observational study of behavior: Sampling methods. Behaviour 49, 227–267 (1974).CAS 
PubMed 
Article 

Google Scholar 
Kaburu, S. S. K. et al. Rates of human–monkey interactions affect grooming behaviour among urban-dwelling rhesus macaques (Macaca mulatta). Am. J. Phys. Anthropol. 168, 92–103 (2019).PubMed 
Article 

Google Scholar 
Martin, P. & Bateson, P. Measuring Behaviour (Cambridge University Press, 1993).Book 

Google Scholar 
Farine, D. R. & Whitehead, H. Constructing, conducting and interpreting animal social networks. J. Anim. Ecol. 84, 1144–1163 (2015).PubMed 
PubMed Central 
Article 

Google Scholar 
Rozins, C. et al. Social structure contains epidemics and regulates individual roles in disease transmission in a group-living mammal. Ecol. Evol. 8, 12044–12055 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Fujii, K., Jin, J., Shev, A., Beisner, B., McCowan, B. & Fushing, H. Perc: Using percolation and conductance to find information flow certainty in a direct network (R Package Version 0.1.2.) https://rdrr.io/cran/Perc/ (2016).Funkhouser, J. A., Mayhew, J. A., Sheeran, L. K. & Mulcahy, J. B. comparative investigations of social context-dependent dominance in captive chimpanzees (Pan troglodytes) and wild Tibetan macaques (Macaca thibetana). Sci. Rep. 8, 1–15 (2018).CAS 
Article 

Google Scholar 
McCowan, B. J. et al. Measuring dominance certainty and assessing its impact on individual and societal health in a nonhuman primate: A network approach. Philos. Trans. R. Soc. B 377, 20200438 (2022).Article 

Google Scholar 
Bjornstad, O. N. Package ‘epimdr’ (2020).Tuite, A. R. et al. Estimated epidemiologic parameters and morbidity associated with pandemic H1N1 influenza. CMAJ 182, 131–136 (2010).PubMed 
PubMed Central 
Article 

Google Scholar 
Arienzo, M. D. & Coniglio, A. Assessment of the SARS-CoV-2 basic reproduction number, R0, based on the early phase of COVID-19 outbreak in Italy. Biosaf. Health 2, 57–59 (2020).PubMed 
PubMed Central 
Article 

Google Scholar 
Bailey, N. T. The Mathematical Theory of Epidemics (Griffin, 1957).
Google Scholar 
Magnusson, A., Skaug, H., Nielsen, A., Berg, C., Kristensen, K., Maechler, M., van Bentham, K., Sadat, N., Bolker, B. & Brooks, M. Package ‘glmmTMB’. https://cran.r-project.org/web/packages/glmmTMB/glmmTMB.pdf (2019).Quinn, G. P. & Keough, M. J. Experimental Designs and Data Analysis for Biologists (Cambridge University Press, 2002).Book 

Google Scholar 
Lüdecke, D., Ben-Shachar, M., Patil, I., Waggoner, P. & Makowski, D. Performance: An R package for assessment, comparison and testing of statistical models. J. Open Source Softw. 6, 3139 (2021).ADS 
Article 

Google Scholar 
Chiyo, P. I., Moss, C. J. & Alberts, S. C. The influence of life history milestones and association networks on crop-raiding behavior in male African elephants. PLoS One 7, e31382 (2012).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
VanderWaal, K. L., Atwill, E. R., Isbell, L. A. & McCowan, B. Quantifying microbe transmission networks for wild and domestic ungulates in Kenya. Biol. Conserv. 169, 136–146 (2014).Article 

Google Scholar 
Berman, C. M. Primate kinship: Contributions from Cayo Santiago. Am. J. Primatol. 78, 63–77 (2016).PubMed 
Article 

Google Scholar 
Balasubramaniam, K. N. et al. Social network community structure and the contact-mediated sharing of commensal E. coli among captive rhesus macaques (Macaca mulatta). PeerJ 6, e4271 (2018).PubMed 
PubMed Central 
Article 

Google Scholar 
Marty, P. R. et al. Individuals in urban dwelling primate species face unequal benefits associated with living in an anthropogenic environment. Primates 61, 245–259 (2020).Article 

Google Scholar 
Zinsstag, J., Schelling, E., Waltner-Toews, D. & Tanner, M. From ‘one medicine’ to ‘one health’ and systemic approaches to health and well-being. Prev. Vet. Med. 101, 148–156 (2011).CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Lloyd-Smith, J. O., Schreiber, S. J., Kopp, P. E. & Getz, W. M. Superspreading and the effect of individual variation on disease emergence. Nature 438, 355–359 (2005).ADS 
CAS 
PubMed 
PubMed Central 
Article 

Google Scholar 
Schülke, O. et al. Quantifying within-group variation in sociality—covariation among metrics and patterns across primate groups and species. Behav. Ecol. Sociobiol. 76, 50 (2022).Article 

Google Scholar 
Romano, V., Shen, M., Pansanel, J., MacIntosh, A. J. J. & Sueur, C. Social transmission in networks: Global efficiency peaks with intermediate levels of modularity. Behav. Ecol. Sociobiol. 72, 154 (2018).Article 

Google Scholar  More

Dickie, M., Serrouya, R., McNay, R. S. & Boutin, S. Faster and farther: wolf movement on linear features and implications for hunting behaviour. J. Appl. Ecol. 54, 253–263 (2017).Article 

Google Scholar 
Owen-Smith, N., Fryxell, J. M. & Merrill, E. H. Foraging theory upscaled: The behavioural ecology of herbivore movement. Philos. Trans. R. Soc. B Biol. Sci. 365, 2267–2278. https://doi.org/10.1098/rstb.2010.0095 (2010).CAS 
Article 

Google Scholar 
Holling, C. S. The functional response of predators to prey density and its role in mimicry and population regulation. Mem. Entomol. Soc. Can. 97, 5–60 (1965).Article 

Google Scholar 
Holling, C. The components of predation as revealed by a study of small-mammal predation of the European pine sawfly (1959).Dickie, M., McNay, S. R., Sutherland, G. D., Cody, M. & Avgar, T. Corridors or risk? Movement along, and use of, linear features varies predictably among large mammal predator and prey species. J. Anim. Ecol. https://doi.org/10.1111/1365-2656.13130 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
DeCesare, N. J. Separating spatial search and efficiency rates as components of predation risk. Proc. Biol. Sci. 279, 4626–4633. https://doi.org/10.1098/rspb.2012.1698 (2012).Article 
PubMed 
PubMed Central 

Google Scholar 
Muhly, T. B., Semeniuk, C., Massolo, A., Hickman, L. & Musiani, M. Human activity helps prey win the predator-prey space race. PLoS ONE 6, e17050. https://doi.org/10.1371/journal.pone.0017050 (2011).ADS 
CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Fleming, P. A. & Bateman, P. W. Novel predation opportunities in anthropogenic landscapes. Anim. Behav. 138, 145–155. https://doi.org/10.1016/j.anbehav.2018.02.011 (2018).Article 

Google Scholar 
Whittington, J. et al. Caribou encounters with wolves increase near roads and trails: A time-to-event approach. J. Appl. Ecol. 48, 1535–1542. https://doi.org/10.1111/j.1365-2664.2011.02043.x (2011).Article 

Google Scholar 
Larivière, S. & Messier, F. Effect of density and nearest neighbours on simulated waterfowl nests: Can predators recognize high-density nesting patches?. Oikos 83, 12–20. https://doi.org/10.2307/3546541 (1998).Article 

Google Scholar 
Taitt, M. J. & Krebs, C. J. Predation, cover, and food manipulations during a spring decline of Microtus townsendii. J. Anim. Ecol. 52, 837–848. https://doi.org/10.2307/4458 (1983).Article 

Google Scholar 
Fisher, J. T. & Wilkinson, L. The response of mammals to forest fire and timber harvest in the North American boreal forest. Mammal. Rev. 35, 51–81 (2005).Article 

Google Scholar 
Fisher, J. T. & Burton, A. C. Wildlife winners and losers in an oil sands landscape. Front. Ecol. Environ. 16, 323–328. https://doi.org/10.1002/fee.1807 (2018).Article 

Google Scholar 
Francis, A. L., Procter, C., Kuzyk, G. & Fisher, J. T. Female Moose Prioritize Forage Over Mortality Risk in Harvested Landscapes. J. Wildl. Manag. (2021).Hebblewhite, M., Munro, R. H. & Merrill, E. H. Trophic consequences of postfire logging in a wolf–ungulate system. For. Ecol. Manag. 257, 1053–1062. https://doi.org/10.1016/j.foreco.2008.11.009 (2009).Article 

Google Scholar 
Pulliam, H. R. Sources, sinks, and population regulation. Am. Nat. 132, 652–661 (1988).Article 

Google Scholar 
Battin, J. When good animals love bad habitats: Ecological traps and the conservation of animal populations. Conserv. Biol. 18, 1482–1491 (2004).Article 

Google Scholar 
Nielsen, S. E., Stenhouse, G. B. & Boyce, M. S. A habitat-based framework for grizzly bear conservation in Alberta. Biol. Conserv. 130, 217–229 (2006).Article 

Google Scholar 
Bentz, B. et al. Salt Lake City 42 (University of Utah Press, 2005).
Google Scholar 
Carroll, A. L., Taylor, S. W., Régnière, J. & Safranyik, L. in Mountain pine beetle symposium: challenges and solutions. 223–232 (Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre).Lindenmayer, D. B. & Noss, R. F. Salvage logging, ecosystem processes, and biodiversity conservation. Conserv. Biol. 20, 949–958. https://doi.org/10.1111/j.1523-1739.2006.00497.x (2006).CAS 
Article 
PubMed 

Google Scholar 
Leverkus, A. B., Lindenmayer, D. B., Thorn, S. & Gustafsson, L. Salvage logging in the world’s forests: Interactions between natural disturbance and logging need recognition. Glob. Ecol. Biogeogr. 27, 1140–1154. https://doi.org/10.1111/geb.12772 (2018).Article 

Google Scholar 
Kuzyk, G. et al. Moose population dynamics during 20 years of declining harvest in British Columbia. Alces 54, 101–119 (2018).
Google Scholar 
Kuzyk, G. W. Provincial population and harvest estimates of moose in British Columbia. Alces J. Devot. Biol. Manag. Moose 52, 1–11 (2016).Procter, C. et al. Factors affecting moose population declines in British Columbia. 2020 Progress Report: February 2012-May 2020. B.C. Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Victoria, B.C., Wildlife Working Report No. WR-128. Pp. 89. https://www2.gov.bc.ca/gov/content/environment/plants-animals-ecosystems/wildlife/wildlife-conservation/moose/moose-conservation/moose-research. (2020).Wittmer, H. U., Sinclair, A. R. E. & McLellan, B. N. The role of predation in the decline and extirpation of woodland caribou. Oecologia 144, 257–267. https://doi.org/10.1007/s00442-005-0055-y (2005).ADS 
Article 
PubMed 

Google Scholar 
Latham, A. D. M., Latham, M. C., Boyce, M. S. & Boutin, S. Movement responses by wolves to industrial linear features and their effect on woodland caribou in northeastern Alberta. Ecol. Appl. 21, 2854–2865 (2011).Article 

Google Scholar 
James, A. R. C. & Stuart-Smith, A. K. Distribution of caribou and wolves in relation to linear corridors. J. Wildl. Manag. 64, 154–159. https://doi.org/10.2307/3802985 (2000).Article 

Google Scholar 
DeMars, C. A. & Boutin, S. Nowhere to hide: Effects of linear features on predator–prey dynamics in a large mammal system. J. Anim. Ecol. 87, 274–284. https://doi.org/10.1111/1365-2656.12760 (2018).Article 
PubMed 

Google Scholar 
McKenzie, H. W., Merrill, E. H., Spiteri, R. J. & Lewis, M. A. How linear features alter predator movement and the functional response. Interface Focus 2, 205–216. https://doi.org/10.1098/rsfs.2011.0086 (2012).Article 
PubMed 
PubMed Central 

Google Scholar 
Houle, M., Fortin, D., Dussault, C., Courtois, R. & Ouellet, J.-P. Cumulative effects of forestry on habitat use by gray wolf (Canis lupus) in the boreal forest. Landsc. Ecol. 25, 419–433. https://doi.org/10.1007/s10980-009-9420-2 (2010).Article 

Google Scholar 
Kuzyk, G. W., Kneteman, J. & Schmiegelow, F. K. Winter habitat use by wolves, Canis lupus, in relation to forest harvesting in west-central Alberta. Can. Field Nat. 118, 368–375 (2004).Article 

Google Scholar 
Mumma, M. A. et al. Regional moose (Alces alces) responses to forestry cutblocks are driven by landscape-scale patterns of vegetation composition and regrowth. For. Ecol. Manag. 481, 118763 (2021).Article 

Google Scholar 
Scheideman, M. Use and selection at two spatial scales by female moose (Alces alces) across central British Columbia following a mountain pine beetle outbreak MSc thesis, University of Northern British Columbia (2018).Alfaro, R. I., van Akker, L. & Hawkes, B. Characteristics of forest legacies following two mountain pine beetle outbreaks in British Columbia Canada. Can. J. For. Res. 45, 1387–1396 (2015).Article 

Google Scholar 
Dhar, A., Parrott, L. & Hawkins, C. D. B. Aftermath of mountain pine beetle outbreak in British Columbia: Stand dynamics, management response and ecosystem resilience. Forests 7, 171 (2016).Article 

Google Scholar 
Shackelford, N., Standish, R. J., Ripple, W. & Starzomski, B. M. Threats to biodiversity from cumulative human impacts in one of North America’s last wildlife frontiers. Conserv. Biol. 32, 672–684 (2018).Article 

Google Scholar 
Corbett, L. J., Withey, P., Lantz, V. A. & Ochuodho, T. O. The economic impact of the mountain pine beetle infestation in British Columbia: Provincial estimates from a CGE analysis. For. Int. J. For. Res. 89, 100–105. https://doi.org/10.1093/forestry/cpv042 (2015).Latham, A. D. M. Wolf ecology and caribou-primary prey-wolf spatial relationships in low productivity peatland complexes in northeastern Alberta PhD thesis, University of Alberta, (2009).Person, D. K. & Russell, A. L. Reproduction and den site selection by wolves in a disturbed landscape. Northw. Sci. 83, 211–224. https://doi.org/10.3955/046.083.0305 (2009).Article 

Google Scholar 
Gillingham, M. Documentation for using Find Points Cluster Identification Program (Version 2) (University of Northern British Columbia, 2009).
Google Scholar 
Avgar, T., Potts, J. R., Lewis, M. A. & Boyce, M. S. Integrated step selection analysis: Bridging the gap between resource selection and animal movement. Methods Ecol. Evol. 7, 619–630. https://doi.org/10.1111/2041-210X.12528 (2016).Article 

Google Scholar 
Signer, J., Fieberg, J. & Avgar, T. Animal movement tools (amt): R package for managing tracking data and conducting habitat selection analyses. Ecol. Evol. 9, 880–890 (2019).Article 

Google Scholar 
Thurfjell, H., Ciuti, S. & Boyce, M. S. Applications of step-selection functions in ecology and conservation. Mov. Ecol. 2, 4. https://doi.org/10.1186/2051-3933-2-4 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Benson, J. F. & Patterson, B. R. Spatial overlap, proximity, and habitat use of individual wolves within the same packs. Wildl. Soc. Bull. (2011-) 39, 31–40 (2015).Fieberg, J., Matthiopoulos, J., Hebblewhite, M., Boyce, M. S. & Frair, J. L. Correlation and studies of habitat selection: problem, red herring or opportunity?. Philos. Trans. R. Soc. B Biol. Sci. 365, 2233–2244 (2010).Article 

Google Scholar 
Ladle, A. et al. Grizzly bear response to spatio-temporal variability in human recreational activity. J. Appl. Ecol. 56, 375–386. https://doi.org/10.1111/1365-2664.13277 (2019).Article 

Google Scholar 
Kohl, M. T. et al. Diel predator activity drives a dynamic landscape of fear. Ecol. Monogr. 88, 638–652 (2018).Article 

Google Scholar 
Scrafford, M. A., Avgar, T., Heeres, R. & Boyce, M. S. Roads elicit negative movement and habitat-selection responses by wolverines (Gulo gulo luscus). Behav. Ecol. 29, 534–542. https://doi.org/10.1093/beheco/arx182 (2018).Article 

Google Scholar 
Prokopenko, C. M., Boyce, M. S. & Avgar, T. Characterizing wildlife behavioural responses to roads using integrated step selection analysis. J. Appl. Ecol. 54, 470–479. https://doi.org/10.1111/1365-2664.12768 (2017).Article 

Google Scholar 
Avgar, T., Lele, S. R., Keim, J. L. & Boyce, M. S. Relative selection strength: Quantifying effect size in habitat- and step-selection inference. Ecol. Evol. 7, 5322–5330. https://doi.org/10.1002/ece3.3122 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Boyce, M. S., Vernier, P. R., Nielsen, S. E. & Schmiegelow, F. K. A. Evaluating resource selection functions. Ecol. Model. 157, 281–300. https://doi.org/10.1016/S0304-3800(02)00200-4 (2002).Article 

Google Scholar 
Visscher, D. R. & Merrill, E. H. Temporal dynamics of forage succession for elk at two scales: Implications of forest management. For. Ecol. Manag. 257, 96–106. https://doi.org/10.1016/j.foreco.2008.08.018 (2009).Article 

Google Scholar 
Stelfox, J. G., Lynch, G. M. & McGillis, J. R. Effects of clearcut logging on wild ungulates in the Central Albertan foothills. For. Chron. 52, 65–70. https://doi.org/10.5558/tfc52065-2 (1976).Article 

Google Scholar 
Gagné, C., Mainguy, J. & Fortin, D. The impact of forest harvesting on caribou–moose–wolf interactions decreases along a latitudinal gradient. Biol. Conserv. 197, 215–222. https://doi.org/10.1016/j.biocon.2016.03.015 (2016).Article 

Google Scholar 
Potvin, F., Breton, L. & Courtois, R. Response of beaver, moose, and snowshoe hare to clear-cutting in a Quebec boreal forest: a reassessment 10 years after cut. Can. J. For. Res. 35, 151–160 (2005).Article 

Google Scholar 
Rempel, R. S., Elkie, P. C., Rodgers, A. R. & Gluck, M. J. Timber-management and natural-disturbance effects on moose habitat: landscape evaluation. J. Wildl. Manag. 61, 517–524. https://doi.org/10.2307/3802610 (1997).Article 

Google Scholar 
Kunkel, K. E. & Pletscher, D. H. Habitat factors affecting vulnerability of moose to predation by wolves in southeastern British Columbia. Can. J. Zool. 78, 150–157. https://doi.org/10.1139/z99-181 (2000).Article 

Google Scholar 
Mech, L. D. & Boitani, L. Wolves: behavior, ecology, and conservation. (University of Chicago Press, 2007).Charnov, E. L. Optimal foraging, the marginal value theorem. (1976).Hebblewhite, M. & Merrill, E. H. Trade-offs between predation risk and forage differ between migrant strategies in a migratory ungulate. Ecology 90, 3445–3454. https://doi.org/10.1890/08-2090.1 (2009).Article 
PubMed 

Google Scholar 
Lendrum, P. E., Anderson Jr, C. R., Long, R. A., Kie, J. G. & Bowyer, R. T. Habitat selection by mule deer during migration: effects of landscape structure and natural-gas development. Ecosphere 3, art82. https://doi.org/10.1890/ES12-00165.1 (2012).Mumma, M. & Gillingham, M. Determining factors that affect survival of moose in Central British Columbia. Technical report to the Habitat Conservation Trust Foundation for Grant Agreement CAT19-0-522 (1 April 2017 through 31 March 2019). 56 (2019).Roffler, G. H., Gregovich, D. P. & Larson, K. R. Resource selection by coastal wolves reveals the seasonal importance of seral forest and suitable prey habitat. For. Ecol. Manag. 409, 190–201. https://doi.org/10.1016/j.foreco.2017.11.025 (2018).Article 

Google Scholar 
Lesmerises, F., Dussault, C. & St-Laurent, M.-H. Wolf habitat selection is shaped by human activities in a highly managed boreal forest. For. Ecol. Manag. 276, 125–131. https://doi.org/10.1016/j.foreco.2012.03.025 (2012).Article 

Google Scholar 
Muhly, T. B. et al. Functional response of wolves to human development across boreal North America. Ecol. Evol. 9, 10801–10815. https://doi.org/10.1002/ece3.5600 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Mladenoff, D. J., Sickley, T. A. & Wydeven, A. P. Predicting gray wolf landscape recolonization: logistic regression models vs. new field data. Ecol. Appl. 9, 37–44. https://doi.org/10.1890/1051-0761(1999)009[0037:PGWLRL]2.0.CO;2 (1999).Rogala, J. K. et al. Human activity differentially redistributes large mammals in the Canadian Rockies National Parks. Ecol. Soc. 16 (2011).Robertson, B. A. & Hutto, R. L. A framework for understanding ecological traps and an evaluation of existing evidence. Ecology 87, 1075–1085. https://doi.org/10.1890/0012-9658(2006)87[1075:AFFUET]2.0.CO;2 (2006).Article 
PubMed 

Google Scholar 
Finnegan, L. et al. Natural regeneration on seismic lines influences movement behaviour of wolves and grizzly bears. PLoS ONE 13, e0195480. https://doi.org/10.1371/journal.pone.0195480 (2018).CAS 
Article 
PubMed 
PubMed Central 

Google Scholar 
Dickie, M., Serrouya, R., DeMars, C., Cranston, J. & Boutin, S. Evaluating functional recovery of habitat for threatened woodland caribou. Ecosphere 8, e01936. https://doi.org/10.1002/ecs2.1936 (2017).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

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

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

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