Daversa, D. R., Fenton, A., Dell, A. I., Garner, T. W. J. & Manica, A. Infections on the move: how transient phases of host movement influence disease spread. Proc. R. Soc. B Biol. Sci. 284, 20171807 (2017).
Mazé-Guilmo, E., Blanchet, S., McCoy, K. D. & Loot, G. Host dispersal as the driver of parasite genetic structure: a paradigm lost? Ecol. Lett. 19, 336–347 (2016).
Biek, R. & Real, L. A. The landscape genetics of infectious disease emergence and spread. Mol. Ecol. 19, 3515–3531 (2010).
Kozakiewicz, C. P. et al. Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics. Evol. Appl. https://doi.org/10.1111/eva.12678 (2018).
Brüniche-Olsen, A., Burridge, C. P., Austin, J. J. & Jones, M. E. Disease induced changes in gene flow patterns among Tasmanian devil populations. Biol. Conserv. 165, 69–78 (2013).
Kyle, C. J. et al. Spatial patterns of neutral and functional genetic variations reveal patterns of local adaptation in raccoon (Procyon lotor) populations exposed to raccoon rabies. Mol. Ecol. 23, 2287–2298 (2014).
Schwabl, P. et al. Prediction and prevention of parasitic diseases using a landscape genomics framework. Trends Parasitol. 33, 264–275 (2017).
Streicker, D. G. et al. Host-pathogen evolutionary signatures reveal dynamics and future invasions of vampire bat rabies. Proc. Natl. Acad. Sci. USA 113, 10926–10931 (2016).
Gijsbers, E. F. et al. Low level of HIV-1 evolution after transmission from mother to child. Sci. Rep. 4, 4650–4655 (2014).
Lee, J. S. et al. Gene flow and pathogen transmission among bobcats (Lynx rufus) in a fragmented urban landscape. Mol. Ecol. 21, 1617–1631 (2012).
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).
Brearley, G. et al. Wildlife disease prevalence in human-modified landscapes. Biol. Rev. Camb. Philos. Soc. 88, 427–442 (2013).
Mcdonald, R. I., Kareiva, P. & Forman, R. T. T. The implications of current and future urbanization for global protected areas and biodiversity conservation. Biol. Conserv. 141, 1695–1703 (2008).
Riley, S. P. D. et al. A southern California freeway is a physical and social barrier to gene flow in carnivores. Mol. Ecol. 15, 1733–1741 (2006).
Gaynor, K. M., Hojnowski, C. E., Carter, N. H. & Brashares, J. S. The influence of human disturbance on wildlife nocturnality. Science 360, 1232–1235 (2018).
Riley, S. P. D. et al. Effects of urbanization and habitat fragmentation on bobcats and coyotes in southern California. Conserv. Biol. 17, 566–576 (2003).
Smith, J. A. et al. Fear of the human ‘super predator’ reduces feeding time in large carnivores. Proc. Biol. Sci. 284, 20170433 (2017).
Tracey, J. A., Bevins, S. N., VandeWoude, S. & Crooks, K. R. An agent-based movement model to assess the impact of landscape fragmentation on disease transmission. Ecosphere 5, 119 (2014).
Volz, E. M., Koelle, K. & Bedford, T. Viral phylodynamics. PLoS Comput. Biol. 9, e1002947 (2013).
Ordeñana, M. A. et al. Effects of urbanization on carnivore species distribution and richness. J. Mammal. 91, 1322–1331 (2010).
Crooks, K. R. Relative sensitivities of mammalian carnivores to habitat fragmentation. Conserv. Biol. 16, 488–502 (2002).
Blecha, K. A., Boone, R. B. & Alldredge, M. W. Hunger mediates apex predator’s risk avoidance response in wildland-urban interface. J. Anim. Ecol. 87, 609–622 (2018).
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).
Bradley, C. A. & Altizer, S. Urbanization and the ecology of wildlife diseases. Trends Ecol. Evol. 22, 95–102 (2007).
Cunningham, M. W. et al. Epizootiology and management of feline leukemia virus in the Florida puma. J. Wildl. Dis. 44, 537–552 (2008).
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).
VandeWoude, S. & Apetrei, C. Going wild: lessons from naturally occurring T-lymphotropic lentiviruses. Clin. Microbiol. Rev. 19, 728–762 (2006).
Brown, E. W., Yuhki, N., Packer, C. & O’Brien, S. J. A lion lentivirus related to feline immunodeficiency virus: epidemiologic and phylogenetic aspects. J. Virol. 68, 5953–5968 (1994).
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).
Biek, R., Ruth, T. K., Murphy, K. M., Anderson, C. R. Jr. & Poss, M. Examining effects of persistent retroviral infection on fitness and pathogen susceptibility in a natural feline host. Can. J. Zool. 84, 365–373 (2006).
Reynolds, J. J. H. et al. Feline immunodeficiency virus in puma: estimation of force of infection reveals insights into transmission. Ecol. Evol. ece3.5584, https://doi.org/10.1002/ece3.5584 (2019).
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).
Fountain-Jones, N. M. et al. Towards an eco-phylogenetic framework for infectious disease ecology. Biol. Rev. 93, 950–970 (2018).
Smith, J. A. et al. Fear of the human ‘super predator’ reduces feeding time in large carnivores. Proc. R. Soc. London B Biol. Sci. 284, 20170433 (2017).
Ferrier, S., Manion, G., Elith, J. & Richardson, K. Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment. Divers. Distrib. 13, 252–264 (2007).
Clarke, R. T., Rothery, P. & Raybould, A. F. Condence limits for regression relationships between distance matrices: estimating gene flow with distance. J. Agric. Biol. Environ. Stat. https://doi.org/10.1198/108571102320 (2002).
Chou, J. et al. A comparative study of SVDquartets and other coalescent-based species tree estimation methods. BMC Genomics 16, S2 (2015).
Shirk, A. J., Landguth, E. L. & Cushman, S. A. A comparison of regression methods for model selection in individual-based landscape genetic analysis. Mol. Ecol. Resour. 18, 55–67 (2018).
Smouse, P. E. & Peakall, R. Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure. Heredity (Edinb.) 82, 561–573 (1999).
Kass, R. E. & Raftery, A. E. Bayes factors. J. Am. Stat. Assoc. 90, 773–795 (1995).
Logan, K. A. & Sweanor, L. L. Desert Puma: Evolutionary Ecology and Conservation of an Enduring Carnivore (Island Press, 2001).
Biek, R. et al. Genetic consequences of sex-biased dispersal in a solitary carnivore: yellowstone cougars. Biol. Lett. 2, 312–315 (2006).
Dickson, B. G., Jenness, J. S. & Beier, P. Influence of vegetation, topography, and roads on cougar movement in Southern California. J. Wildl. Manag. 69, 264–276 (2005).
Kerr, T. J. et al. Viruses as indicators of contemporary host dispersal and phylogeography: an example of feline immunodeficiency virus (FIV Ple) in free-ranging African lion (Panthera leo). J. Evol. Biol. https://doi.org/10.1111/jeb.13348 (2018).
Epps, C. W. & Keyghobadi, N. Landscape genetics in a changing world: disentangling historical and contemporary influences and inferring change. Mol. Ecol. 24, 6021–6040 (2015).
Hornocker, M. G. & Negri, S. Cougar: Ecology and Conservation (University of Chicago Press, 2010).
Sweanor, L. L., Logan, K. A. & Hornocker, M. G. Cougar dispersal patterns, metapopulation dynamics, and conservation. Conserv. Biol. 14, 798–808 (2000).
Suraci, J. P., Clinchy, M., Zanette, L. Y. & Wilmers, C. C. Fear of humans as apex predators has landscape‐scale impacts from mountain lions to mice. Ecol. Lett. ele.13344 https://doi.org/10.1111/ele.13344 (2019).
Tian, H. et al. Transmission dynamics of re-emerging rabies in domestic dogs of rural China. PLOS Pathog. 14, e1007392 (2018).
Carver, S. et al. Pathogen exposure varies widely among sympatric populations of wild and domestic felids across the United States. Ecol. Appl. 26, 367–381 (2016).
Di Pietro, F., Ortenzi, F., Tilio, M., Concetti, F. & Napolioni, V. Genomic DNA extraction from whole blood stored from 15- to 30-years at −20 °C by rapid phenol–chloroform protocol: a useful tool for genetic epidemiology studies. Mol. Cell. Probes 25, 44–48 (2011).
Lee, J. S. et al. Targeted enrichment for pathogen detection and characterization in three felid species. J. Clin. Microbiol. 55, 1658–1670 (2017).
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).
Lee, J. S. et al. Evolution of puma lentivirus in bobcats (Lynx rufus) and mountain lions (Puma concolor) in North America. J. Virol. 88, 7727–7737 (2014).
Martin, D. P., Murrell, B., Golden, M., Khoosal, A. & Muhire, B. RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol. 1, vev003 (2015).
Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).
Stöver, B. C. & Müller, K. F. TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinforma. 11, 7 (2010).
Rambaut, A., Lam, T. T., Max Carvalho, L. & Pybus, O. G. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2, vew007 (2016).
Suchard, M. A. et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 4 (2018).
Ayres, D. L. et al. BEAGLE 3: Improved performance, scaling, and usability for a high-performance computing library for statistical phylogenetics. Syst. Biol. 68, 1052–1061, https://doi.org/10.1093/sysbio/syz020 (2019).
Lemey, P., Rambaut, A., Welch, J. J. & Suchard, M. A. Phylogeography takes a relaxed random walk in continuous space and time. Mol. Biol. Evol. 27, 1877–1885 (2010).
Lefort, V., Longueville, J.-E. & Gascuel, O. SMS: Smart model selection in PhyML. Mol. Biol. Evol. 34, 2422–2424 (2017).
Gill, M. S. et al. Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Mol. Biol. Evol. 30, 713–724 (2013).
Baele, G. et al. Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol. Biol. Evol. 29, 2157–2167 (2012).
Lartillot, N. & Philippe, H. Computing Bayes factors using thermodynamic integration. Syst. Biol. 55, 195–207 (2006).
Xie, W., Lewis, P. O., Fan, Y., Kuo, L. & Chen, M.-H. Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst. Biol. 60, 150–160 (2011).
Baele, G., Lemey, P. & Vansteelandt, S. Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution. BMC Bioinforma. 14, 85 (2013).
Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67, 901–904 (2018).
Volz, E. M. et al. Identification of hidden population structure in time-scaled phylogenies. Syst. Biol. 69, 884–896, https://doi.org/10.1093/sysbio/syaa009 (2019).
Karcher, M. D., Palacios, J. A., Lan, S. & Minin, V. N. phylodyn: an R package for phylodynamic simulation and inference. Mol. Ecol. Resour. 17, 96–100 (2017).
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).
Bowcock, A. M. et al. High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368, 455–457 (1994).
McRae, B. H. Isolation by resistance. Evolution 60, 1551–1561 (2006).
Chifman, J. & Kubatko, L. Quartet inference from SNP data under the coalescent model. Bioinformatics 30, 3317–3324 (2014).
Swofford, D. L. PAUP* Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4.0b10 (Sinauer Associates, 2002).
Peterman, W. E. ResistanceGA: an R package for the optimization of resistance surfaces using genetic algorithms. Methods Ecol. Evol. 9, 1638–1647 (2018).
Pierce, B. M., Bleich, V. C. & Bowyer, R. T. Social organization of mountain lions: does a land-tenure system regulate population size? Ecology 81, 1533–1543 (2000).
Fitzpatrick, M. C. & Keller, S. R. Ecological genomics meets community-level modelling of biodiversity: mapping the genomic landscape of current and future environmental adaptation. Ecol. Lett. 18, 1–16 (2015).
Fitzpatrick, M. C. et al. Forecasting the future of biodiversity: a test of single- and multi-species models for ants in North America. Ecography 34, 836–847 (2011).
Dellicour, S., Rose, R., Faria, N. R., Lemey, P. & Pybus, O. G. SERAPHIM: studying environmental rasters and phylogenetically informed movements. Bioinformatics 32, 3204–3206 (2016).
Dellicour, S. et al. Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data. BMC Bioinforma. 17, 82–94 (2016).
Laenen, L. et al. Spatio-temporal analysis of Nova virus, a divergent hantavirus circulating in the European mole in Belgium. Mol. Ecol. 25, 5994–6008 (2016).
Dijkstra, E. W. A note on two problems in connexion with graphs. Numer. Math. 1, 269–271 (1959).
Dellicour, S. et al. Using viral gene sequences to compare and explain the heterogeneous spatial dynamics of virus epidemics. Mol. Biol. Evol. 34, 2563–2571 (2017).
Source: Ecology - nature.com
