Philippa Kaur

1.Packer, C. et al. Sport hunting, predator control and conservation of large carnivores. PLoS ONE 4, e5941 (2009).PubMed 
PubMed Central 

Google Scholar 
2.Whitman, K., Starfield, A. M., Quadling, H. S. & Packer, C. Sustainable trophy hunting of African lions. Nature 428, 175–178 (2004).CAS 
PubMed 

Google Scholar 
3.Treves, A. Hunting for large carnivore conservation. J. Appl. Ecol. 46, 1350–1356 (2009).
Google Scholar 
4.Milner-Gulland, E. J. et al. Reproductive collapse in saiga antelope harems. Nature 422, 135 (2003).CAS 
PubMed 

Google Scholar 
5.Bischof, R. et al. Implementation uncertainty when using recreational hunting to manage carnivores. J. Appl. Ecol. 49, 824–832 (2012).PubMed 
PubMed Central 

Google Scholar 
6.Booth, V. R., Masonde, J., Simukonda, C. & Cumming, D. H. M. Managing hunting quotas of African lions (Panthera leo): a case study from Zambia. J. Nat. Conserv. 55, 125817 (2020).
Google Scholar 
7.Potapov, A., Merrill, E. & Lewis, M. A. Wildlife disease elimination and density dependence. Proc. R. Soc. B 279, 3139–3145 (2012).PubMed 
PubMed Central 

Google Scholar 
8.Lloyd-Smith, J. O. et al. Should we expect population thresholds for wildlife disease? Trends Ecol. Evol. 20, 511–519 (2005).
Google Scholar 
9.Beeton, N. & McCallum, H. Models predict that culling is not a feasible strategy to prevent extinction of Tasmanian devils from facial tumour disease. J. Appl. Ecol. 48, 1315–1323 (2011).
Google Scholar 
10.Choisy, M. & Rohani, P. Harvesting can increase severity of wildlife disease epidemics. Proc. R. Soc. B 273, 2025–2034 (2006).PubMed 
PubMed Central 

Google Scholar 
11.Allendorf, F. W. & Hard, J. J. Human-induced evolution caused by unnatural selection through harvest of wild animals. Proc. Natl Acad. Sci. USA 106, 9987–9994 (2009).CAS 
PubMed 
PubMed Central 

Google Scholar 
12.Hamede, R. K., Bashford, J., McCallum, H. & Jones, M. Contact networks in a wild Tasmanian devil (Sarcophilus harrisii) population: using social network analysis to reveal seasonal variability in social behaviour and its implications for transmission of devil facial tumour disease. Ecol. Lett. 12, 1147–1157 (2009).PubMed 

Google Scholar 
13.Woodroffe, R. et al. Culling and cattle controls influence tuberculosis risk for badgers. Proc. Natl Acad. Sci. USA 103, 14713–14717 (2006).CAS 
PubMed 
PubMed Central 

Google Scholar 
14.Carr, A. N. et al. Wildlife Management Practices Associated with Pathogen Exposure in Non-native Wild Pigs in Florida, U.S. (USDA National Wildlife Research Center, 2019).15.Woodroffe, R., Cleaveland, S., Courtenay, O., Laurenson, M. K. & Artois, M. in The Biology and Conservation of Wild Canids 123–142 (Oxford Univ. Press, 2004).16.Carter, S. P. et al. Culling-induced social perturbation in Eurasian badgers Meles meles and the management of TB in cattle: an analysis of a critical problem in applied ecology. Proc. R. Soc. B 274, 2769–2777 (2007).PubMed 
PubMed Central 

Google Scholar 
17.Silk, M. J. et al. Contact networks structured by sex underpin sex-specific epidemiology of infection. Ecol. Lett. 21, 309–318 (2018).PubMed 

Google Scholar 
18.Silk, M. J. et al. The application of statistical network models in disease research. Methods Ecol. Evol. 8, 1026–1041 (2017).
Google Scholar 
19.Morters, M. K. et al. Evidence-based control of canine rabies: a critical review of population density reduction. J. Anim. Ecol. 82, 6–14 (2013).PubMed 

Google Scholar 
20.Lachish, S., McCallum, H., Mann, D., Pukk, C. E. & Jones, M. E. Evaluation of selective culling of infected individuals to control Tasmanian Devil facial tumor disease. Conserv. Biol. 24, 841–851 (2010).PubMed 

Google Scholar 
21.Grubaugh, N. D. et al. Tracking virus outbreaks in the twenty-first century. Nat. Microbiol. 4, 10–19 (2019).CAS 
PubMed 

Google Scholar 
22.Didelot, X., Fraser, C., Gardy, J. & Colijn, C. Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks. Mol. Biol. Evol. 34, msw075 (2017).
Google Scholar 
23.Smith, M. D. et al. Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Mol. Biol. Evol. 32, 1342–1353 (2015).CAS 
PubMed 
PubMed Central 

Google Scholar 
24.Logan, K. A. & Runge, J. P. et al. Effects of hunting on a puma population in Colorado. Wildl. Monogr. 209, 1–35 (2020).
Google Scholar 
25.Biek, R., Pybus, O. G., Lloyd-Smith, J. O. & Didelot, X. Measurably evolving pathogens in the genomic era. Trends Ecol. Evol. 30, 306–313 (2015).PubMed 
PubMed Central 

Google Scholar 
26.Pybus, O. G., Tatem, A. J. & Lemey, P. Virus evolution and transmission in an ever more connected world. Proc. R. Soc. B 282, 20142878 (2015).PubMed 
PubMed Central 

Google Scholar 
27.Woolhouse, M. E. J., Adair, K. & Brierley, L. RNA viruses: a case study of the biology of emerging infectious diseases. Microbiol. Spectr. https://doi.org/10.1128/microbiolspec.oh-0001-2012 (2021).28.Pybus, O. G. & Rambaut, A. Evolutionary analysis of the dynamics of viral infectious disease. Nat. Rev. Genet. 10, 540–550 (2009).CAS 
PubMed 
PubMed Central 

Google Scholar 
29.Fountain-Jones, N. M. et al. Towards an eco-phylogenetic framework for infectious disease ecology. Biol. Rev. 93, 950–970 (2018).PubMed 

Google Scholar 
30.Webb, C. O. Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. Am. Nat. 156, 145–155 (2000).PubMed 

Google Scholar 
31.Biek, R. et al. Epidemiology, genetic diversity, and evolution of endemic feline immunodeficiency virus in a population of wild cougars. J. Virol. 77, 9578–9589 (2003).CAS 
PubMed 
PubMed Central 

Google Scholar 
32.Pedersen, N. C., Yamamoto, J. K., Ishida, T. & Hansen, H. Feline immunodeficiency virus infection. Vet. Immunol. Immunopathol. 21, 111–129 (1989).CAS 
PubMed 

Google Scholar 
33.Malmberg, J. L. et al. Altered lentiviral infection dynamics follow genetic rescue of the Florida panther. Proc. R. Soc. B 286, 20191689 (2019).PubMed 
PubMed Central 

Google Scholar 
34.Elbroch, L. M., Levy, M., Lubell, M., Quigley, H. & Caragiulo, A. Adaptive social strategies in a solitary carnivore. Sci. Adv. 3, e1701218 (2017).PubMed 
PubMed Central 

Google Scholar 
35.Sweanor, L. L., Logan, K. A. & Hornocker, M. G. Cougar dispersal patterns, metapopulation dynamics, and conservation. Conserv. Biol. 14, 798–808 (2000).
Google Scholar 
36.Fountain-Jones, N. M. et al. Linking social and spatial networks to viral community phylogenetics reveals subtype-specific transmission dynamics in African lions. J. Anim. Ecol. 86, 1469–1482 (2017).PubMed 

Google Scholar 
37.Gilbertson, M. L. J. et al. Transmission of one predicts another: apathogenic proxies for transmission dynamics of a fatal virus. Preprint at bioRxiv https://doi.org/10.1101/2021.01.09.426055 (2021).38.Fountain-Jones, N. M. et al. Host relatedness and landscape connectivity shape pathogen spread in a large secretive carnivore. Commun. Biol. 4, 12 (2021).PubMed 
PubMed Central 

Google Scholar 
39.Hornocker, M. G. & Negri, S. Cougar: Ecology and Conservation (Univ. Chicago Press, 2010).40.Moss, W. E., Alldredge, M. W. & Pauli, J. N. Quantifying risk and resource use for a large carnivore in an expanding urban-wildland interface. J. Appl. Ecol. 53, 371–378 (2016).
Google Scholar 
41.Trumbo, D. et al. Urbanization impacts apex predator gene flow but not genetic diversity across an urban-rural divide. Mol. Ecol. 28, 4926–4940 (2019).CAS 
PubMed 

Google Scholar 
42.VandeWoude, S. & Apetrei, C. Going wild: lessons from naturally occurring T-lymphotropic lentiviruses. Clin. Microbiol. Rev. 19, 728–762 (2006).CAS 
PubMed 
PubMed Central 

Google Scholar 
43.Logan, K. A. & Sweanor, L. L. Desert Puma: Evolutionary Ecology and Conservation of an Enduring Carnivore (Island Press, 2001).44.Krakoff, E., Gagne, R. B., VandeWoude, S. & Carver, S. Variation in intra-individual lentiviral evolution rates: a systematic review of human, nonhuman primate, and felid species. J. Virol. https://doi.org/10.1128/JVI.00538-19 (2019).45.Volz, E. M. & Didelot, X. Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance. Syst. Biol. 67, 719–728 (2018).PubMed 
PubMed Central 

Google Scholar 
46.Murrell, B. et al. Detecting individual sites subject to episodic diversifying selection. PLoS Genet. 8, e1002764 (2012).CAS 
PubMed 
PubMed Central 

Google Scholar 
47.Kenyon, J. C. & Lever, A. M. L. The molecular biology of feline immunodeficiency virus (FIV). Viruses 3, 2192–2213 (2011).CAS 
PubMed 
PubMed Central 

Google Scholar 
48.Tamuri, A. U., dos Reis, M., Hay, A. J. & Goldstein, R. A. Identifying changes in selective constraints: host shifts in influenza. PLoS Comput. Biol. 5, e1000564 (2009).PubMed 
PubMed Central 

Google Scholar 
49.Forni, D., Cagliani, R., Clerici, M. & Sironi, M. Molecular evolution of human coronavirus genomes. Trends Microbiol. 25, 35–48 (2017).CAS 
PubMed 

Google Scholar 
50.Fountain-Jones, N. M. et al. Urban landscapes can change virus gene flow and evolution in a fragmentation-sensitive carnivore. Mol. Ecol. 26, 6487–6498 (2017).PubMed 

Google Scholar 
51.Kozakiewicz, C. P. et al. Pathogens in space: advancing understanding of pathogen dynamics and disease ecology through landscape genetics. Evol. Appl. 11, 1763–1778 (2018).PubMed 
PubMed Central 

Google Scholar 
52.McDonald, J. L., Smith, G. C., McDonald, R. A., Delahay, R. J. & Hodgson, D. Mortality trajectory analysis reveals the drivers of sex-specific epidemiology in natural wildlife–disease interactions. Proc. R. Soc. B 281, 20140526 (2014).PubMed 
PubMed Central 

Google Scholar 
53.Gilbertson, M. L. J., Fountain-Jones, N. M. & Craft, M. E. Incorporating genomic methods into contact networks to reveal new insights into animal behaviour and infectious disease dynamics. Behaviour 155, 759–791 (2018).PubMed 

Google Scholar 
54.Alldredge, M. W., Blecha, T. & Lewis, J. H. Less invasive monitoring of cougars in Colorado’s front range. Wildl. Soc. Bull. 43, 222–230 (2019).
Google Scholar 
55.Lewis, J. S. et al. The effects of urbanization on population density, occupancy, and detection probability of wild felids. Ecol. Appl. 25, 1880–1895 (2015).PubMed 

Google Scholar 
56.Csárdi, G. & Nepusz, T. The igraph software package for complex network research. InterJournal Complex Syst. 1695, 1–9 (2006).57.Didelot, X., Kendall, M., Xu, Y., White, P. J. & McCarthy, N. Genomic epidemiology analysis of infectious disease outbreaks using TransPhylo. Curr. Protoc. 1, e60 (2021).PubMed 
PubMed Central 

Google Scholar 
58.Handcock, M. S., Hunter, D. R., Butts, C. T., Goodreau, S. M. & Morris, M. statnet: software tools for the representation, visualization, analysis and simulation of network data. J. Stat. Softw. 24, 1548 (2008).PubMed 
PubMed Central 

Google Scholar 
59.Wertheim, J. O., Murrell, B., Smith, M. D., Pond, S. L. K. & Scheffler, K. RELAX: detecting relaxed selection in a phylogenetic framework. Mol. Biol. Evol. 32, 820–832 (2015).CAS 
PubMed 

Google Scholar 
60.Kosakovsky Pond, S. L. et al. A random effects branch-site model for detecting episodic diversifying selection. Mol. Biol. Evol. 28, 3033–3043 (2011).CAS 
PubMed 
PubMed Central 

Google Scholar 
61.Weaver, S. et al. Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes. Mol. Biol. Evol. 35, 773–777 (2018).CAS 
PubMed 
PubMed Central 

Google Scholar 
62.Gill, M. S., Lemey, P., Bennett, S. N., Biek, R. & Suchard, M. A. Understanding past population dynamics: Bayesian coalescent-based modeling with covariates. Syst. Biol. 65, 1041–1056 (2016).PubMed 
PubMed Central 

Google Scholar 
63.Faith, D. P. Conservation evaluation and phylogenetic diversity. Biol. Conserv. 61, 1–10 (1992).
Google Scholar 
64.Tsirogiannis, C. & Sandel, B. PhyloMeasures: a package for computing phylogenetic biodiversity measures and their statistical moments. Ecography 39, 709–714 (2016).
Google Scholar 
65.Fountain-Jones, N. nfj1380/Transmission-dynamics_huntingPumaFIV: (Puma-FIV_transmissionDynamics) (Zenodo, 2021); https://doi.org/10.5281/zenodo.560216266.Fountain-Jones, N. et al. Emerging phylogenetic structure of the SARS-CoV-2 pandemic. Virus Evol. 6, veaa082 (2020).PubMed 
PubMed Central 

Google Scholar 
67.Karcher, M. D., Palacios, J. A., Bedford, T., Suchard, M. A. & Minin, V. N. Quantifying and mitigating the effect of preferential sampling on phylodynamic inference. PLoS Comput. Biol. 12, e1004789 (2016).PubMed 
PubMed Central 

Google Scholar  More

1.Wobeser, G. Rev. Sci. Tech. 21, 159–178 (2002).CAS 
Article 

Google Scholar 
2.Fountain-Jones, N. M. et al. Nat. Ecol. Evol. https://doi.org/10.1038/10.1038/s41559-021-01635-5 (2021).Article 

Google Scholar 
3.Lloyd-Smith, J. O. et al. Trends Ecol. Evol. 20, 511–519 (2005).Article 

Google Scholar 
4.Woodroffe, R. et al. Proc. Natl Acad. Sci. USA 103, 14713–14717 (2006).CAS 
Article 

Google Scholar 
5.Ham, C., Donnelly, C. A., Astley, K. L., Jackson, S. Y. B. & Woodroffe, R. J. Appl. Ecol. 56, 2390–2399 (2019).Article 

Google Scholar 
6.Logan, K. A. & Runge, J. P. Wildl. Monogr. 209, 1–35 (2021).Article 

Google Scholar 
7.Fountain-Jones, N. M. et al. Commun. Biol. 4, 12 (2021).Article 

Google Scholar  More

1.Loreau, M. et al. Do not downplay biodiversity loss. Nature https://doi.org/10.1038/s41586-021-04179-7 (2022).2.Leung, B. et al. Clustered versus catastrophic global vertebrate declines. Nature 588, 267–271 (2020).ADS 
CAS 
Article 

Google Scholar 
3.Antão, L. H. et al. Temperature-related biodiversity change across temperate marine and terrestrial systems. Nat. Ecol. Evol. 4, 927–933 (2020).Article 

Google Scholar 
4.Leung, B., Greenberg, D. A. & Green, D. M. Trends in mean growth and stability in temperate vertebrate populations. Divers. Distrib. 23, 1372–1380 (2017).Article 

Google Scholar 
5.Daskalova, G. N., Myers-Smith, I. H. & Godlee, J. L. Rare and common vertebrates span a wide spectrum of population trends. Nat. Commun. 11, 4394 (2020).ADS 
CAS 
Article 

Google Scholar 
6.Murali, G. et al. Emphasizing declining populations in the Living Planet Report. Nature https://doi.org/10.1038/s41586-021-04165-z (2022).7.Leung, B., et al. Reply to: Emphasizing declining populations in the Living Planet Report. Nature https://doi.org/10.1038/s41586-021-04166-y (2022).8.Dornelas, M., et al. A balance of winners and losers in the Anthropocene. Ecol. Lett. 22, 847–854 (2019).Article 

Google Scholar 
9.Hilborn, R. Faith based fisheries. Fisheries 31, 554–555 (2006).
Google Scholar  More

Department of Biology, McGill University, Montreal, Quebec, CanadaBrian Leung & Anna L. HargreavesBieler School of Environment, McGill University, Montreal, Quebec, CanadaBrian LeungDepartment of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, CanadaDan A. GreenbergSchool of Biology and Ecology and Mitchell Center for Sustainability Solutions, University of Maine, Orono, ME, USABrian McGillCentre for Biological Diversity, University of St Andrews, St Andrews, UKMaria DornelasIndicators and Assessments Unit, Institute of Zoology, Zoological Society of London, London, UKRobin FreemanB.L. wrote the response. A.C.H. and D.A.G. helped with writing, editing and discussing ideas. B.M. and M.D. discussed ideas with some editing. R.F. contributed discussions to the original manuscript2. More

Department of Biology, McGill University, Montreal, Quebec, CanadaBrian Leung & Anna L. HargreavesBieler School of Environment, McGill University, Montreal, Quebec, CanadaBrian LeungDepartment of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, CanadaDan A. GreenbergSchool of Biology and Ecology and Mitchell Center for Sustainability Solutions, University of Maine, Orono, ME, USABrian McGillCentre for Biological Diversity, University of St Andrews, St Andrews, UKMaria DornelasIndicators and Assessments Unit, Institute of Zoology, Zoological Society of London, London, UKRobin FreemanB.L. wrote the response. A.L.H. and D.A.G. helped with writing, editing and discussing ideas. B.M., M.D. and R.F. discussed ideas and did some editing. More

Cite this articleLeung, B., Hargreaves, A.L., Greenberg, D.A. et al. Reply to: Shifting baselines and biodiversity success stories.
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1.Leung, B. et al. Clustered versus catastrophic global vertebrate declines. Nature 588, 267–271 (2020).CAS 
Article 
ADS 

Google Scholar 
2.McRae, L., Deinet, S. & Freeman, R. The diversity-weighted Living Planet Index: controlling for taxonomic bias in a global biodiversity indicator. PLoS ONE 12, e0169156 (2017).Article 

Google Scholar 
3.Koricheva, J. & Gurevitch, J. Uses and misuses of meta-analysis in plant ecology. J. Ecol. 102, 828–844 (2014).Article 

Google Scholar 
4.Cardinale, B. J., Gonzalez, A., Allington, G. R. H. & Loreau, M. Is local biodiversity in decline or not? A summary of the debate over analysis of species richness time trends. Biol. Conserv. 219, 175–183 (2018).Article 

Google Scholar 
5.Inger, R. et al. Common European birds are declining rapidly while less abundant species’ numbers are rising. Ecol. Lett. 18, 28–36 (2015).Article 

Google Scholar 
6.Rosenberg, K. V. et al. Decline of the North American avifauna. Science 366, 120–124 (2019).CAS 
Article 
ADS 

Google Scholar 
7.Gonzalez, A. et al. Estimating local biodiversity change: a critique of papers claiming no net loss of local diversity. Ecology 97, 1949–1960 (2016).Article 

Google Scholar 
8.Scholes, R. J. et al. Toward a global biodiversity observing system. Science 321, 1044–1045 (2008).CAS 
Article 

Google Scholar  More

1.Almond, R. E. A., Grooten, M. & Petersen, T. (eds) Living Planet Report 2020 – Bending the Curve of Biodiversity Loss (WWF, 2020).2.Leung, B. et al. Clustered versus catastrophic global vertebrate declines. Nature 588, 267–271 (2020).CAS 
Article 
ADS 

Google Scholar 
3.Buckland, S. T., Studeny, A. C., Magurran, A. E., Illian, J. B. & Newson, S. E. The geometric mean of relative abundance indices: a biodiversity measure with a difference. Ecosphere 2, 1–15 (2011).Article 

Google Scholar 
4.McRae, L., Deinet, S. & Freeman, R. The diversity-weighted living planet index: controlling for taxonomic bias in a global biodiversity indicator. PLoS ONE 12, e0169156 (2017).Article 

Google Scholar 
5.Leung, B., Greenberg, D. A. & Green, D. M. Trends in mean growth and stability in temperate vertebrate populations. Divers. Distrib. 23, 1372–1380 (2017).Article 

Google Scholar 
6.Marconi, V., McRae, L., Deinet, S., Ledger, S. & Freeman, F. in Living Planet Report 2020 – Bending the Curve of Biodiversity Loss (eds Almond, R. E. A., Grooten, M. & Petersen, T.) (WWF, 2020).7.Daskalova, G. N., Myers-Smith, I. H. & Godlee, J. L. Rare and common vertebrates span a wide spectrum of population trends. Nat. Commun. 11, 4394 (2020).CAS 
Article 
ADS 

Google Scholar 
8.Daskalova, G. N. et al. Landscape-scale forest loss as a catalyst of population and biodiversity change. Science 368, 1341–1347 (2020).CAS 
Article 
ADS 

Google Scholar 
9.IPBES. Summary for Policymakers of the Global Assessment Report on Biodiversity and Ecosystem Services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES Secretariat, 2019).10.van Strien, A. J., Soldaat, L. L. & Gregory, R. D. Desirable mathematical properties of indicators for biodiversity change. Ecol. Indic. 14, 202–208 (2012).Article 

Google Scholar  More