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The diversification and evolution of niche breadth across spatial scales in western North American monkeyflowers

Cite this dataset

Li, Qin (2020). The diversification and evolution of niche breadth across spatial scales in western North American monkeyflowers [Dataset]. Dryad.


Species show remarkable variation in ecological niche breadth, but the directionality of niche breadth evolution remains a question for niche axes across spatial scales. Testing the association between niche breadth evolution and the process of diversification could shed light on the role of ecology in the formation and maintenance of biodiversity. Here we applied Cladogenetic State change Speciation and Extinction models in western North American monkeyflowers (Mimulus sensu lato), with two states of niche breadth (generalist and specialist). We aimed to estimate the effects of niche breadth along broad-scale bioclimatic and local-scale microhabitat axes on diversification rate, and the evolutionary trend and mode of niche breadth. We found opposite patterns across spatial scales, with higher speciation rates detected for generalists along broad-scale bioclimatic axes and for specialists along local-scale microhabitat axes. Furthermore, we found weak trends towards specialization for bioclimatic niche breadth, but generalization for microhabitat niche breadth. Both cladogenetic and anagenetic changes were comparable and thus important in the evolution of niche breadth in this group. Together, these findings suggest that the underlying mechanisms of niche breadth evolution might differ across spatial scales, and that change in niche breadth could be tightly associated with the diversification process.


We compiled locality data for 82 species mainly from the Global Biodiversity Information Facility (, and additional data were collected from several local databases: the Consortium of California Herbaria (, the Consortium of Pacific Northwest Herbaria ( and the Southwest Environmental Information Network (; all accessed January 2017). We cleaned the locality data and filter out mistmatch records. Next, we estimated niche breadth across broad and local spacial scales. On the one hand, we extracted bioclimatic values: precipitation seasonality, the synchronicity of temperature and precipitation and the first PC axis of two highly correlated axes (the minimum temperature of the coldest month, and growing degree days above 0 celsius degree). Niche breadths of biolimatic niches were done along normalized gradients with kernel densities. On the other hand, we applied text mining technique to count word frequencies based on specimen habitat records, and estimated niche breadths for two microhabitat axes: habitat water affinity and substrate type. Countinuous niche breadths were converted into binary states, generalists and specialists based on the threshold of mean values. We used Cladogenetic State change Speciation and Extinction models (ClaSSE) to estimate state-dependent diversification rate, niche breadth evolutionary trend, and evolutionary mode.

Usage notes

See Readme.txt for details of raw data, processed data, and codes for analysis and generating figures.