Assessing the extinction risk of the spontaneous flora in urban tree bases

As the spatial arrangement of trees planted along streets in cities makes their bases potential ecological corridors for the flora, urban tree bases may be a key contributor to the overall connectivity of the urban ecosystem. However, these tree bases are also a highly fragmented environment in which extinctions are frequent. The goal of this study was to assess the plant species’ ability to survive and spread through urban tree bases. To do so, we developed a Bayesian framework to assess the extinction risk of a plant metapopulation using presence/absence data, assuming that the occupancy dynamics was described by a Hidden Markov Model. The novelty of our approach is to take into account the combined effect of low-distance dispersal and the potential presence of a seed bank on the extinction risk. We introduced a metric of the extinction risk and examined its performance over a wide range of metapopulation parameters. We applied our framework to yearly floristic inventories carried out in 1324 tree bases in Paris, France. While local extinction risks were generally high, extinction risks at the street scale varied greatly from one species to another. We identified 10 plant species that could survive and spread through urban tree bases, and three plant traits correlated with the extinction risk at the metapopulation scale: the maximal height, and the beginning and end of the flowering period. Our results suggest that some plant species can use urban tree bases as ecological corridors despite high local extinction risks by forming a seed bank. We also identified other plant traits correlated with the ability to survive in tree bases, related to the action of gardeners. Moreover, our findings demonstrate that our Bayesian estimation framework based on percolation theory has the potential to be extended to more general metapopulations.

See Table 1 for more details on the plant traits and the correlation tests used.

Stellaria media
Yes 22  Table E: Summary of the results of the regression of LER on species and portions of streets.For the species, estimates are expressed relative to Bromus sterilis.For the streets, estimates are expressed relative to BARO-1.The species in grey are the ones for which a significantly lower LER was identified.
The portions of streets in bold are the ones for which a significantly higher LER was identified.We recall that the SMD measures the difference between two probability distributions.Therefore, a quotient smaller than one indicates that posterior distributions of patch extinction probabilities are on average closer between portions of a same street than between portions of different streets, while a quotient larger than one indicates the opposite.

Figure A :
Figure A: Map of the study area.The full street names are listed in Table A. Map from OpenStreetMap (openstreetmap.org/copyright),adapted to add the locations of tree bases.
(b) Distribution of the quotients of the average SMDs inside a street and between streets, grouped by street.

Figure C :
Figure C: Comparison of the average Standardised Mean Differences (SMDs) of the posterior distributions of patch extinction probabilities computed between portions of the same streets or of different streets.The plots correspond to the distribution of the quotients of the mean SMDs inside a street and between streets, grouped by species (a) or by street (b).We recall that the SMD measures the difference between two probability distributions.Therefore, a quotient smaller than one indicates that posterior distributions of patch extinction probabilities are on average closer between portions of a same street than between portions of different streets, while a quotient larger than one indicates the opposite.

Table A :
List of the portions of streets taken into account in this study

Table C :
Summary of the results of the regression of MaxGER on species and portions of streets.For the species, estimates are expressed relative to Bromus sterilis.For the streets, estimates are expressed relative to BARO-1.The species in bold are the ones for which a significantly higher extinction risk was identified.

Table D :
Summary of the results of the correlation tests of the global extinction risk (as quantified by the MaxGER metric and averaged over all streets for each species) with the species traits listed in Table1.The traits in bold are the ones for which a significant correlation was identified (when accounting for multiple testing using the Holm-Bonferroni method).

Table F :
Summary of the results of the correlation tests of the local extinction risk (as quantified by the LER metric and averaged over all streets for each species) with the species traits listed in Table1.No significant correlation was identified when accounting for multiple testing (using the Holm-Bonferroni method).

Table G :
Value of H inf = min{h ∈ 0, H max : P(H ≤ h|Obs) ≥ 0.05} for each species listed in TableB.The posterior distribution of H was obtained by performing parameter inference simultaneously on all portions of streets listed in TableB, assuming that only p ext and s differed from one portion of street to another.Species in bold are species for which the absence of a seed bank was identified (that Distribution of the quotients of the average SMDs inside a street and between streets, grouped by species. is, for which P(H = 0|Obs) ≥ 0.95).The asterisk indicates species for which neither the absence (see above) nor the presence (defined as P(H ≥ 1|Obs) ≥ 0.95) of a seed bank was identified.