DOI: 10.5061/dryad.gqnk98skk
title: The diversification and evolution of niche breadth across spatial scales in western North American monkeyflowers

description: 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.
description: We compiled
 locality data for 82 species mainly from the Global Biodiversity
 Information Facility (http://www.gbif.org), and additional data were
 collected from several local databases: the Consortium of California
 Herbaria (http://ucjeps.berkeley.edu/consortium), the Consortium of
 Pacific Northwest Herbaria (http://www.pnwherbaria.org) and the Southwest
 Environmental Information Network (http://swbiodiversity.org; 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.
description: See Readme.txt for
 details of raw data, processed data, and codes for analysis and generating
 figures.