References
Ackerly, D. D., D. W. Schwilk, and C. O. Webb. 2006. Niche evolution and adaptive radiation: testing the order of trait divergence. Ecology 87:S50-S61.
Anciães, M., and A. T. Peterson. 2009. Ecological niches and their evolution among Neotropical manakins (Aves: Pipridae). Journal of Avian Biology 40:591-604.
Araújo, M. B., F. Ferri-Yáñez, F. Bozinovic, P. A. Marquet, F. Valladares, and S. L. Chown. 2013. Heat freezes niche evolution. Ecology Letters 16:1206-1219.
Barraclough, T. G., and A. P. Vogler. 2000. Detecting the geographical pattern of speciation from species-level phylogenies. American Naturalist 155:419-434.
Barve, N., V. Barve, A. Jimenez-Valverde, A. Lira-Noriega, S. P. Maher, A. T. Peterson, J. Soberón, and F. Villalobos. 2011. The crucial role of the accessible area in ecological niche modeling and species distribution modeling. Ecological Modelling 222:1810-1819.
Cooper, N., R. P. Freckleton, and W. Jetz. 2011. Phylogenetic conservatism of environmental niches in mammals. Proceedings of the Royal Society B 278:2384-2391.
Coyne, J. A., and H. A. Orr. 2004. Speciation. Sinauer Associates, Sunderland, MA.
Elith, J., M. Kearney, and S. J. Phillips. 2010. The art of modelling range‐shifting species. Methods in Ecology and Evolution 1: 330-342.
Elith, J., S. J. Phillips, T. Hastie, M. Dudík, Y. E. Chee, and C. J. Yates. 2011. A statistical explanation of MaxEnt for ecologists. Diversity and Distribributions 17:43-57.
Evans, M. E., S. A. Smith, R. S. Flynn, and M. J. Donoghue. 2009. Climate, niche evolution, and diversification of the “bird-cage” evening primroses (Oenothera , sections Anogra and Kleinia ). American Naturalist 173:225-240.
Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 125:1-15.
Freckleton, R. P., P. H. Harvey, and M. Pagel. 2002. Phylogenetic analysis and comparative data: a test and review of evidence. American Naturalist 160:712-726.
García-Navas, V., and M. Rodríguez-Rey. 2018. The evolution of climatic niches and its role in shaping diversity patterns in diprotodontid marsupials. Journal of Mammalian Evolution: https://doi.org/10.1007/s10914-10018-19435-z.
Graham, C. H., S. R. Ron, J. C. Santos, C. J. Schneider, and C. Moritz. 2004. Integrating phylogenetics and environmental niche models to explore speciation mechanisms in dendrobatid frogs. Evolution 58:1781-1793.
Guisan, A., B. Petitpierre, O. Broennimann, C. Daehler, and C. Kueffer. 2014. Unifying niche shift studies: insights from biological invasions. Trends in Ecology & Evolution 29:260-269.
Harmon, L. J., J. T. Weir, C. D. Brock, R. E. Glor, and W. Challenger. 2008. GEIGER: investigating evolutionary radiations. Bioinformatics 24:129-131.
Hijmans, R. J. 2019. raster: Geographic Data Analysis and Modeling. R package version 3.0-7. https://CRAN.R-project.org/package=raster
Hijmans, R. J., S. E. Cameron, J. L. Parra, P. G. Jones, and A. Jarvis. 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25:1965-1978.
Hijmans, R. J., and J. Elith. 2015. Species distribution modeling with R. Available: ftp://ctan.math.mun.ca/CRAN/web/packages/dismo/vignettes/sdm.pdf.
Joseph, L., and D. R. B. Stockwell. 2000. Temperature-based models of the migration of Swainson’s Flycatcher (Myiarchus swainsoni ) across South America: a new use for museum specimens of migratory birds. Proceedings of the Academy of Natural Sciences of Philadelphia 150:293-300.
Kadmon, R., O. Farber, and A. Danin. 2004. Effect of roadside bias on the accuracy of predictive maps produced by bioclimatic models. Ecological Applications 14:401-413.
Knouft, J. H., J. B. Losos, R. E. Glor, and J. J. Kolbe. 2006. Phylogenetic analysis of the evolution of the niche in lizards of the Anolis sagrei group. Ecology 87:S29-S38.
Kozak, K. H., and J. J. Wiens. 2010. Accelerated rates of climatic-niche evolution underlie rapid species diversification. Ecology Letters 13:1378-1389.
Lanyon, S. M. 1993. Phylogenetic frameworks–towards a firmer foundation for the comparative approach. Biological Journal of the Linnaean Society 49:45-61.
Losos, J. B. 2008. Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecology Letters 11:995-1003.
Louca, S., and M. Doebeli. 2018. Efficient comparative phylogenetics on large trees. Bioinformatics 34: 1053-1055.
Maguire, B. 1973. Niche response structure and the analytical potentials of its relationship to the habitat. American Naturalist 107:213-246.
Meyer, A. L. S., and Pie, M. R. 2018. Environmental prevalence and the distribution of species richness across climatic niche space. Journal of Biogeography 45: 2348-2360. https://doi.org/10.1111/jbi.13419
Meseguer, A. S., J. M. Lobo, R. Ree, D. J. Beerling, and I. Sanmartín. 2015. Integrating fossils, phylogenies, and niche models into biogeography to reveal ancient evolutionary history: the case of Hypericum (Hypericaceae). Systematic Biology 64:215-232.
Nakazawa, Y., A. T. Peterson, E. Martínez-Meyer, and A. G. Navarro-Sigüenza. 2004. Seasonal niches of Nearctic-Neotropical migratory birds: Implications for the evolution of migration. Auk 121:610-618.
Nyári, Á. S., and S. Reddy. 2013. Comparative phyloclimatic analysis and evolution of ecological niches in the scimitar babblers (Aves: Timaliidae: Pomatorhinus ). PLoS ONE 8:e55629.
O’Meara, B. C. 2012. Evolutionary inferences from phylogenies: a review of methods. Annual Review of Ecology, Evolution, and Systematics 43:267-285.
O’Meara, B. C., C. Ané, M. J. Sanderson, P. C. Wainwright, and T. Hansen. 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution 60:922-933.
Owens, H. L., L. P. Campbell, L. L. Dornak, E. E. Saupe, N. Barve, J. Soberón, K. Ingenloff, A. Lira-Noriega, C. M. Hensz, C. E. Myers, and A. T. Peterson. 2013. Constraints on interpretation of ecological niche models by limited environmental ranges on calibration areas. Ecological Modelling 263:10-18.
Owens, H. L., D. S. Lewis, J. R. Dupuis, A. L. Clamens, F. A. H. Sperling, A. Y. Kawahara, R. P. Guralnick, and F. L. Condamine. 2017. The latitudinal diversity gradient in New World swallowtail butterflies is caused by contrasting patterns of out-of and into-the-tropics dispersal. Global Ecology and Biogeography 26:1447-1458.
Paradis E., and K. Schliep. 2018. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35: 526-528.
Pagel, M., A. Meade, and D. Barker. 2004. Bayesian estimation of ancestral character states on phylogenies. Systematic Biology 53:673 - 684.
Pearman, P. B., A. Guisan, O. Broennimann, and C. F. Randin. 2008. Niche dynamics in space and time. Trends in Ecology and Evolution 23:149-158.
Peterson, A. T. 2011. Ecological niche conservatism: A time-structured review of evidence. Journal of Biogeography 38:817-827.
Peterson, A. T., J. Soberón, R. G. Pearson, R. P. Anderson, E. Martínez-Meyer, M. Nakamura, and M. B. Araújo. 2011. Ecological Niches and Geographic Distributions. Princeton University Press, Princeton.
Peterson, A. T., J. Soberón, and V. Sánchez-Cordero. 1999. Conservatism of ecological niches in evolutionary time. Science 285:1265-1267.
Phillips, S. J., M. Dudík, J. Elith, C. H. Graham, A. Lehmann, J. Leathwick, and S. Ferrier. 2009. Sample selection bias and presence-only distribution models: implications for background and pseudo-absence data. Ecological Applications 19:181-197.
Powell, A. F., F. K. Barker, S. M. Lanyon, K. J. Burns, J. Klicka, and I. J. Lovette. 2014. A comprehensive species-level molecular phylogeny of the New World blackbirds (Icteridae). Molecular Phylogenetics and Evolution 71:94-112.
QGIS Development Team. 2019. QGIS Geographic Information System . Open Source Geospatial Foundation Project. http://qgis.osgeo.org
Qiao, H., J. Soberón, and A. T. Peterson. 2015. No silver bullets in correlative ecological niche modeling: Insights from testing among many potential algorithms for niche estimation. Methods in Ecology and Evolution 6:1126-1136.
R Core Team. 2019. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
Revell, L. J. 2012. phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution 3:217-223.
Revell, L. J., L. J. Harmon, and D. C. Collar. 2008. Phylogenetic signal, evolutionary process, and rate. Systematic Biology 57:591-601.
Ribeiro, V., A. T. Peterson, F. P. Werneck, and R. B. Machado. 2016. Ecological and historical views of the diversification of Geositta miners (Aves: Furnariidae: Sclerurinae). Journal of Ornithology 158:15-23.
Rice, N. H., E. Martínez-Meyer, and A. T. Peterson. 2003. Ecological niche differentiation in theAphelocoma jays: A phylogenetic perspective. Biological Journal of the Linnaean Society 80:369-383.
Saupe, E. E., V. Barve, C. E. Myers, J. Soberón, N. Barve, C. M. Hensz, A. T. Peterson, H. L. Owens, and A. Lira-Noriega. 2012. Variation in niche and distribution model performance: The need for a priori assessment of key causal factors. Ecological Modelling 237:11-22.
Saupe, E. E., N. Barve, H. L. Owens, J. C. Cooper, P. A. Hosner, and A. T. Peterson. 2017. Reconstructing ecological niche evolution when niches are incompletely characterized. Systematic Biology 67:428-438.
Smith, S. A., and M. J. Donoghue. 2010. Combining historical biogeography with niche modeling in theCaprifolium clade of Lonicera (Caprifoliaceae, Dipsacales). Systematic Biology 59:322-341.
Soberón, J. 2007. Grinnellian and Eltonian niches and geographic distributions of species. Ecology Letters 10:1115-1123.
Swofford, D. L., and W. P. Maddison. 1987. Reconstructing ancestral character states under Wagner parsimony. Mathematical Biosciences 87:199-229.
Turelli, M., N. H. Barton, and J. A. Coyne. 2001. Theory and speciation. Trends in Ecology & Evolution 16:330-343.
VanDerWal, J, L. P. Shoo, C. Graham, and S. E. Williams SE. 2009. Selecting pseudo- absence data for presence-only distribution modeling: how far should you stray from what you know? Ecological Modelling 220:589-594.
Veloz, S. D., J. W. Williams, J. L. Blois, F. He, B. Otto-Bliesner, and Z. Liu. 2012. No-analog climates and shifting realized niches during the late quaternary: implications for 21st-century predictions by species distribution models. Global Change Biology 18:1698-1713.
Vieites, D. R., S. Nieto-Román, and D. B. Wake. 2009. Reconstruction of the climate envelopes of salamanders and their evolution through time. Proceedings of the National Academy of Sciences USA 106:19715-19722.
Warren, D. L., M. Cardillo, D. F. Rosauer, and D. I. Bolnick. 2014. Mistaking geography for biology: inferring processes from species distributions. Trends in Ecology & Evolution 29:572-580.
Wiens, J. J., and C. H. Graham. 2005. Niche conservatism: Integrating evolution, ecology, and conservation biology. Annual Review of Ecology, Evolution and Systematics 36:519-539.
Yesson, C., and A. Culham. 2006. Phyloclimatic modeling: combining phylogenetics and bioclimatic modeling. Systematic Biology 55:785-802.
Figure 1. Coding scheme for different model configurations in bins spanning the variation in an environmental dimension. Dark gray indicates environments associated with the overall area of interest; light gray indicates environments associated with M (i.e.η (M )); black bar indicates conditions known to be occupied by the species. Two scenarios are presented: under “well-characterized,” occupied conditions are completely contained within η (M ), so coding is without uncertainty. Under “partially characterized,” occupied conditions abut the limits ofη (M ), such that true upper limit is unknown, and is coded as such. The white vertical lines delimit the set of bins across the spectrum of environmental values.