The paper describes rich, a new R package to perform species richness estimation and comparison. Species richness is the simplest surrogate for the more complex concept of species biodiversity. It is relatively easy to assess although estimations strongly depend on sampling intensity with the consequence that richness estimations should be standardized to perform valid comparisons. The R package rich allows such corrections as well as the computation of various statistics and implements different randomization tests to compare cumulative and average species richness of two communities. These tests are useful for ranking sites or communities which is a classical goal in restoration ecology and conservation biology.
We sampledca2500 specimens ofPhilaenus spumarius(Hemiptera: Aphrophoridae) throughout Corsica withouta prioriknowledge on the presence of symptoms on plants. We screened 448 specimens for the presence ofXylella fastidiosa (Xf)using qPCR and a custom nested PCR. qPCR appeared versatile and under-estimated the prevalence ofXf. Nested PCR showed thatXfwas present in all populations. Molecular results were validated by prediction on the distribution ofXfmade from tests conducted on plants, which shows the pertinence of using vectors in risk assessment studies.Xfwas detected in tenerals and adults. Thus,P.spumariuscould acquireXffrom its host plant, mostlyCistus monspeliensisin Corsica, which may act as reservoir for the next season. This contrasts with other observations and suggests that management strategies may have to be adapted on a case-by-case basis. At least two genetic entities and several variants ofXfnot yet identified on plants were present in the insects, which suggests ancient introductions ofXfand a probable underestimation of the current diversity of the strains present in Corsica. Interestingly 6% of the specimens carried two subspecies ofXf. Studies are required to better characterize the strains present in Corsica and to determine how the disease was introduced, spread and why no sign of a potential epidemic was detected earlier. This study shows that, when sensitive enough methods are implemented, spittlebugs (and more specificallyP.spumariusfor which species distribution modelling shows it could be a good sentinel for Europe) can be used to predict and better assess the exact distribution ofXf. Furthermore,Xfmultiply only in their foregut and does not become circulative, which facilitates its detection.
The bacteriumXylella fastidiosa (Xf)is a plant endophyte native to the Americas that causes diseases in many crops of economic importance (grapevine,Citrus, Olive trees etc).Xfhas been recently detected in several regions outside of its native range including Europe where little is known about its potential geographical expansion. We collected data documenting the native and invaded ranges of theXfsubspeciesfastidiosa,paucaand multiplex and fitted bioclimatic species distribution models (SDMs) to assess the potential climate suitability of European continent for those pathogens. According to model predictions, the currently reported distribution ofXfin Europe is small compared to the large extent of climatically suitable areas. The regions at high risk encompass the Mediterranean coastal areas of Spain, Greece, Italy and France, the Atlantic coastal areas of France, Portugal and Spain as well as the southwestern regions of Spain and lowlands in southern Italy. The extent of predicted climatically suitable conditions for the different subspecies are contrasted. The subspeciesmultiplex, and to a certain extent the subspeciesfastidiosa, represent a threat to most of Europe while the climatically suitable areas for the subspeciespaucaare mostly limited to the Mediterranean basin. These results provide crucial information for the design of a spatially informed European-scale integrated management strategy, including early detection surveys in plants and insect vectors and quarantine measures.