Essay: Chromosome counts

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Chromosome counts for 1364 accessions of 801 vascular plants endemic to Italy have been extracted from Chrobase.it (http://bot.biologia.unipi.it/chrobase/ last accessed 12 May 2016). Chrobase. It is the largest online dataset of chromosome counts for the Italian vascular flora (Peruzzi & Bedini, 2014), hosting cytogenetic data for endemic and non-endemic species. For this study we only selected counts of endemic plants because they are one of the most sensitive components of a flora, being often restricted to ecologically selective habitats (Thompson, 2005), for which we are confident that the environmental variables calculated in the present study can be a good proxy for the total ecological requirements of the species. Most counts have been associated to an exact geographic locality in the database. For those chromosome counts lacking precise information (< 10%), we identified an approximate locality based on the restricted distribution range of the species (Peruzzi et al., 2015).
 
Mean chromosome numbers were estimated for each species, while within species variation to be incorporated into the phylogenetic analysis was not estimated separately for each species, because within species samples are limited to few counts (Garamsegi, 2014). Hence, we estimated the pooled variance across the species and used it, weighted by sample size, to estimate the observation variance of the individual species, as recommended by Hansen & Bartoszek (2012). Trial analyses revealed that log transformation improved model fit by over 500 log-likelihood units relative to untransformed data, thus mean chromosome numbers were log transformed prior to analysis.
Chromosome number evolution was analysed in 6 major angiosperm clades (Monocots, Fabids, Malvids, Caryophyllales, Lamiids, Campanulids; APG IV, 2016) including a minimum of 67 and a maximum of 200 taxa per clade. The whole dataset is listed in the Supporting Information Table S2.

Phylogeny

The topology of the phylogentic tree is based on the backbone phylogeny of European flora (Durka & Michalski 2012). Subsequently, lower level nodes and species were resolved and assembled onto the backbone tree, using more than 90 phylogenetic and systematic studies (see Supporting information Table S1 and Figure S1).
Mean diploid (2n) and basic (x, see Peruzzi, 2013) chromosome numbers for each taxon were visualized on the phylogenetic tree (Fig. 1) with the plotsimmap function in the package phytools (Revell, 2012) of R (R Core Team, 2015).

Climatic, ecological and morphological data

Climatic data associated with the sampling sites were acquired from the Worldclim database at 2.5 min scale (http://www.worldclim.org; Hijmans et al., 2005) The considered climate data are: mean annual temperature (”C), temperature seasonality (SD ” 100), temperature continentality (”C), mean annual precipitation (mm) and precipitation seasonality (coefficient of variation). Means and standard deviations were estimated for each species within a buffer of 10 min over georeferenced sites using Qgis v. 2.18 (Quantum Gis, http://www.qgis.org).
Data about morphological traits and habitat characteristics, for each of the considered species, were retrieved from literature (Pignatti, 1982 and Table S1). To characterise the relevant features of vegetative morphology and reproductive strategies, we considered the growth form (annual herb, geophytes, perennial herb and woody),

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