Analysis of the application of ecological niche modeling in phylogeographic studies: contributions, challenges, and future

Carlos Luna-Aranguré, Ella Vázquez-Domínguez


The combined application of ecological niche modeling in phylogeographic studies has contributed to better understanding the relationship between the patterns of genetic variation of species and the abiotic conditions where their populations have evolved.  This has allowed broadening and strengthening the spectrum of phylogeographic questions and hypotheses to be tested, based on the increasing availability of data, algorithms, and models.  However, when these two approaches are combined, some of their limitations are also added, despite taking advantage of their strengths.  This review explores some of the latest contributions of this application.  We found that 44 % of the studies reviewed address the effect of the environment on the diversification and structure of lineages; 20 % of the models concern mammals and 27 %, reptiles; and 34 % of the articles addressed the biota of the Nearctic region.  This review also explores the most important challenges and future perspectives resulting from this synergy.


ecological niche; lineage divergence; niche conservatism; niche modeling; phylogeography; potential distribution.

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Alvarado-Serrano, D. F., y K. L. Lacey. 2014. Ecological Niche Models in Phylogeographic Studies: Applications, Advances and Precautions. Molecular Ecology Resources 14:233-348.

Alvarado-Serrano, D. F., and L. L. Knowles. 2014. Ecological niche models in phylogeographic studies: Applications, advances and precautions. Molecular Ecology Resources 14:233-348.

Ashrafzadeh, M. R., R. Khosravi, M. Ahmadi, and M. Kaboli. 2018. Landscape heterogeneity and ecological niche isolation shape the distribution of spatial genetic variation in Iranian brown bears, Ursus arctos (Carnivora: Ursidae). Mammalian Biology 93:64-75.

Avise, J. C. 2000. Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, U.S.A.

Avise, J. C., B. W. Bowen, and F. J. Ayala. 2016. In the light of evolution X: comparative phylogeography. Proceedings of the National Academy of Sciences 113:7957-7961.

Beaumont, M. A. 2010. Approximate Bayesian computation in evolution and ecology. Annual Review of Ecology. Evolution and Systematics 41:379-406.

Brown, J. L., and L. L. Knowles. 2012. Spatially explicit models of dynamic histories: examination of the genetic consequences of Pleistocene glaciation and recent climate change on the American Pika. Molecular Ecology 21:3757-3775.

Carstens, B. C., and C. L. Richards. 2007. Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution 61:1439-1454.

Chan, L. M., J. L. Brown, and A. D. Yoder. 2011. Integrating statistical genetic and geospatial methods brings new power to phylogeography.  Molecular Phylogenetics and Evolution 59:523-537.

Davis, E. B., J. L. McGuire, and J. D. Orcutt. 2014. Ecological niche models of mammalian glacial refugia show consistent bias. Ecography 37:1133-1138.

de Oliveira, G., T. F. Rangel, M. S. Lima‐Ribeiro, L. C. Terribile, and J. A. F. Diniz‐Filho. 2014. Evaluating, partitioning, and mapping the spatial autocorrelation component in ecological niche modeling: a new approach based on environmentally equidistant records. Ecography 37:637-647.

de Queiroz, K. 2007. S pecies concepts and species delimitation. Systematic Biology 56:879-886.

Diniz‐Filho, J. A. F., H. Rodrigues, M. P. D. C. Telles, G. D. Oliveira, L. C. Terribile, T. N. Soares, and J. C. Nabout. 2015. Correlation between genetic diversity and environmental suitability: taking uncertainty from ecological niche models into account. Molecular Ecology Resources 15:1059-1066.

Elton, C. S. 1927. Animal Ecology. Sidgwick and Jackson. London, UK.

Espindola, S., J. L Parra, and E. Vázquez-Domínguez. 2019. Fundamental niche unfilling and potential invasion risk of the slider turtle Trachemys scripta. PeerJ 7:e7923.

Galbreath, K. E., D. J. Hafner, and K. R. Zamudio. 2009. When cold is better: climate‐driven elevation shifts yield complex patterns of diversification and demography in an alpine specialist (American Pika, Ochotona princeps). Evolution 63:2848-2863.

Gavin, D. G., M. C. Fitzpatrick, P. F. Gugger, K. D. Heath, F. Rodríguez‐Sánchez, S. Z. Dobrowski, and J. L. Blois. 2014. Climate refugia: joint inference from fossil records, species distribution models and phylogeography. New Phytologist 204:37-54.

Grinnell, J. 1917. The niche-relationships of the California thrasher. Auk 34:427-433.

Gutiérrez-García, T.A., and E. Vázquez-Domínguez. 2011. Comparative phylogeography: designing studies while surviving the process. BioScience 61:857-868.

Hardy, M. E., J. M. Grady, and E. J. Routman. 2002. Intraspecific phylogeography of the slender madtom: the complex evolutionary history of the Central Highlans of United States. Molecular Ecology 11:2393-2403.

He, Q., D. L.Edwards, and L. L. Knowles. 2013. Integrative testing of how environments from the past to the present shape genetic structure across landscapes. Evolution 67:3386-3402.

Holt, R. D. 2014. Evolution of the Ecological Niche. The Princeton Guide to Evolution. Princeton University Press. Princeton, U.S.A.

Hugall, A., C. Moritz, A. Moussalli, and J. Stanisic. 2002. Reconciling paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875). Proceedings of the National Academy of Sciences 99:6112-6117.

Hutchinson, G. E. 1957. Concluding Remarks. Cold Spring Harbor Symposia on Quantitative Biology 22:415-427.

Igea, J., P. Aymerich, A. Fernández-González, J. González-Esteban, A. Gómez, R. Alonso, and J. Castresana. 2013. Phylogeography and postglacial expansion of the endangered semi-aquatic mammal Galemys pyrenaicus. BMC Evolutionary Biology 13:115-134.

Kalkvik, H. M., I. J. Stout, T. J. Doonan, and C. L. Parkinson. 2012. Investigating niche and lineage diversification in widely distributed taxa: phylogeography and ecological niche modeling of the Peromyscus maniculatus species group.  Ecography 35:54-64.

Kozak, K. H., C. H. Graham, and J. J. Wiens. 2008. Integrating GIS-based environmental data into evolutionary biology. Trends in Ecology and Evolution 23:141-148.

Lobo, J. M., A. Jiménez‐Valverde, and R. Real. 2008. AUC: a misleading measure of the performance of predictive distribution models. Global ecology and Biogeography 17:145-151.

Luna-Aranguré, C., J. Soberón, and E. Vázquez-Domínguez. 2019. A tale of four bears: Environmental signal on the phylogeographical patterns within the extant Ursus species. Journal of Biogeography Early vew 10.1111/jbi.13752

Martínez-Méndez, N., O. Mejía, and F. R. M. de la Cruz. 2015. The past, present and future of a lizard: The phylogeography and extinction risk of Sceloporus serrifer (Squamata: Phrynosomatidae) under a global warming scenario. Zoologischer Anzeiger 254:86-98.

McCormack, J. E., A. J. Zellmer, and L. L. Knowles. 2010. Does niche divergence accompany allopatric divergence in Aphelocoma jays as predicted under ecological speciation?: insights from tests with niche models.  Evolution: International Journal of Organic Evolution 64:1231-1244.

Mizerovská, D., V. Nicolas, T. C. Demos, D. Akaibe, M. Colyn, C. Denys, and A. Laudisoit. 2019. Genetic variation of the most abundant forest‐dwelling rodents in Central Africa (Praomys jacksoni complex): Evidence for Pleistocene refugia in both montane and lowland forests. Journal of Biogeography 46:1466-1478.

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.

Perktaş, U., H. Gur, and E. Ada. 2015. Historical demography of the Eurasian green woodpecker: integrating phylogeography and ecological niche modelling to test glacial refugia hypothesis. Folia Zoologica 64:284-296.

Peterson, A. T., and N. Vargas. 1993. Ecological diversity in scrub jays, Aphelocoma coerulescens. Pp. 309-317 in Biological Diversity of Mexico: Origins and Distribution (Ramamoorthy T. P., R. Bye, A. Lot, and J. Fa, eds.). Oxford University Press, New York, U.S.A.

Peterson, A. T. 2011. Ecological niche conservatism: A time‐structured review of evidence. Journal of Biogeography 38:817-827.

Peterson, A. T., J. Soberon, R. G. Pearson, R. P. Anderson, E. Martinez-Meyer, M. Nakamura, and M. B. Araujo. 2011. Ecological niches and geographic distributions. Princeton University Press, New Jersey, U.S.A.

Peterson, A. T., M. Papeş, and J. Soberón. 2015. Mechanistic and correlative models of ecological niches. European Journal of Ecology 1:28-38.

Pulliam, H. R. 2000. On the relationship between niche and distribution. Ecology letters 3:349-361.

Pyron, R. A., G.C. Costa, M. A. Patten, and F. T. Burbrink. 2015. Phylogenetic niche conservatism and the evolutionary basis of ecological speciation. Biological Reviews 90:1248-1262.

Rangel, T. F., N. R. Edwards, P. B. Holden, J. A. F. Diniz-Filho, W. D. Gosling, M. T. P. Coelho, and R. K. Colwell. 2018. Modeling the ecology and evolution of biodiversity: Biogeographical cradles, museums, and graves. Science 361:eaar5452.

Raxworthy, C. J., C. M. Ingram, N. Rabibisoa, and R. G. Pearson. 2007. Applications of ecological niche modeling for species delimitation: a review and empirical evaluation using day geckos (Phelsuma) from Madagascar. Systematic Biology 56:907-923.

Rolland, J., D. Silvestro, D. Schluter, A. Guisan, O. Broennimann, and N. Salamin. 2018. The impact of endothermy on the climatic niche evolution and the distribution of vertebrate diversity. Nature Ecology and Evolution 2:459-464.

Rosauer, D. F., R. A. Catullo, J. VanDerWal, A. Moussalli, and C. Moritz. 2015. Lineage range estimation method reveals fine-scale endemism linked to Pleistocene stability in Australian rainforest herpetofauna. PloS One 10:e0126274.

Smith, A. B., W. Godsoe, F. Rodríguez-Sánchez, H. H. Wang, and D. Warren. 2018. Niche estimation above and below the species level. Trends in Ecology and Evolution 34:260-273.

Soberón, J. 2007. Grinnellian and Eltonian niches and geographic distributions of species. Ecology Letters 10:1115-1123.

Soberón, J., and A. T. Peterson. 2005. Interpretation of models of fundamental ecological niches and species’ distributional areas. Biodiversity Informatics 2:1-10.

Soberón, J., and A. T. Peterson. 2011. Ecological niche shifts and environmental space anisotropy: a cautionary note. Revista Mexicana de Biodiversidad 82:1348-1355.

Suárez‐Atilano, M., O. Rojas‐Soto, J. L. Parra, and E. Vázquez-Domínguez. 2017. The role of the environment on the genetic divergence between two Boa imperator lineages. Journal of Biogeography 44:2045-2056.

Svenning, J. C., C. Fløjgaard, K. A. Marske, D. Nógues-Bravo, and S. Normand. 2011. Applications of species distribution modeling to paleobiology. Quaternary Science Reviews 30:2930-2947.

Terribile, L. C., and J. A. F. Diniz-Filho. 2010. How many studies are necessary to compare niche-based models for geographic distributions? Inductive reasoning may fail at the end. Brazilian Journal of Biology 70:263-269.

Varela, S., J. M. Lobo, and J. Hortal. 2011. Using species distribution models in paleobiogeography: a matter of data, predictors and concepts. Palaeogeography, Palaeoclimatology, Palaeoecology 310:451-463.

Varela, S., M. S. Lima-Ribeiro, and L. C. Terribile. 2015. A short guide to the climatic variables of the Last Glacial Maximum for biogeographers. PloS One 10:e0129037.

Vázquez-Domínguez, E. 2007. Filogeografía y vertebrados. Pp. 441-466 in La ecología molecular de plantas y animales. (Eguiarte L., V. Souza, and X. Aguirre, eds.). INE. Ciudad de México, México.

Velasco, J. A., F. Villalobos, J. A. Diniz-Filho, A. C. Algar, O. Flores-Villela, G. Köhler, and E. Martínez-Meyer. 2018. Climatic and evolutionary factors shaping geographical gradients of species richness in Anolis lizards. Biological Journal of the Linnean Society 123:615-627.

Warren, D. L., R. E. Glor, and M. Turelli. 2008. Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution 62:2868-2883.

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 and Evolution 29:572-580.

Wiens, J. J. 2011. The niche, biogeography and species interactions. Philosophical Transactions of the Royal Society B: Biological Sciences 366:2336-2350.

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.

Williams, J. W., and S. T. Jackson. 2007. Novel climates, no‐analog communities, and ecological surprises.  Frontiers in Ecology and the Environment 5:475-482.

Worth, J. R., G. J. Williamson, S. Sakaguchi, P. G. Nevill, and G. J. Jordan. 2014. Environmental niche modelling fails to predict Last Glacial Maximum refugia: niche shifts, microrefugia or incorrect palaeoclimate estimates? Global Ecology and Biogeography 23:1186-1197.

Worton, B. J. 1989. Kernel methods for estimating the utilization distribution in home-range studies. Ecology 70:164-168.

Zink, R. M. 2014. Homage to Hutchinson, and the role of ecology in lineage divergence and speciation. Journal of Biogeography 41:999-1006.


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