Assessing the effect of sample bias correction in species distribution models

1. Open-source biodiversity databases contain a large number of species occurrence records but are often spatially biased; which affects the reliability of species distribution models based on these records. Sample bias correction techniques require data filtering which comes at the cost of record numbers, or require considerable additional sampling effort. Since independent data is rarely available, assessment of the correction technique often relies solely on performance metrics computed using subsets of the available – biased – data, which may prove misleading. 2. Here, we assess the extent to which an acknowledged sample bias correction technique is likely to improve models’ ability to predict species distributions in the absence of independent data. We assessed variation in model predictions induced by the aforementioned correction and model stochasticity; the variability between model replicates related to a random component (pseudo-absences sets and cross-validation subsets). We present, then, an index of the effect of correction relative to model stochasticity; the Relative Overlap Index (ROI). We investigated whether the ROI better represented the effect of correction than classic performance metrics (Boyce index, cAUC, AUC and TSS) and absolute overlap metrics (Schoener’s D, Pearson’s and Spearman’s correlation coefficients) when considering data related to 64 vertebrate species and 21 virtual species with a generated sample bias. 3. When based on absolute overlaps and cross-validation performance metrics, we found that correction produced no significant effects. When considering its effect relative to model stochasticity, the effect of correction was strong for most species at one of the three sites. The use of virtual species enabled us to verify that the correction technique improved both distribution predictions and the biological relevance of the selected variables at the specific site, when these were not correlated with sample bias patterns. 4. In the absence of additional independent data, the assessment of sample bias correction based on subsample data may be misleading. We propose to investigate both the biological relevance of environmental variables selected, and, the effect of sample bias correction based on its effect relative to model stochasticity. Accessibility maps Cross-validation Performance metrics Overlap Pseudo-absence selection Terrestrial vertebrates Variable selection Virtual speciespublishedVersio

Lovebirds in the air:trade patterns, establishment success and niche shifts of Agapornis parrots within their non-native range

Understanding the factors influencing the establishment of non-native species is pivotal with regards to the development of effective biosecurity policies. In this paper, we aim to assess the role of climate matching, trade patterns and breeding origin as drivers of establishment success of introduced lovebirds (Agapornis species). A comprehensive database on the worldwide distribution of eight species of non-native lovebirds (including establishment success and population size from 21 countries spanning 27 years) was compiled. We combined climate-based species distribution models with environmental niche analyses to evaluate environmental suitability and potential niche shifts in the introduced range of lovebirds. Then, we tested whether combining habitat suitability with information on trade, introduction effort and breeding origin (captive-bred or wild-caught) of imported birds can improve model predictions at the country level. Although climate-based models fit well with the current distribution of non-native lovebirds at 5-arcminute resolution and significant niche similarity was found for 3 species, we also observed successful establishments in areas climatically distinct from those occupied in native ranges. At the country level, only a significant relationship between the number of established populations and both the number of introduction sites and the year of first importation was observed. A significant effect of breeding origin was not found, but most traded birds had a captive-bred origin. Our work contributes to the growing evidence of the complexity of the invasion process and the difficulty of pre-introduction invasion assessments based solely on the characteristics of the recipient environments for the Agapornis species. Surveillance protocols should be applied to both wild-caught and captive-bred lovebirds, as additional data becomes available to better tease apart the role of origin in those species.The realisation of this manuscript was supported by the European Cooperation in Science and Technology COST Action ES1304 (ParrotNet). The contents of this paper are the authors’ responsibility and neither COST nor any person acting on its behalf is responsible for the use that might be made of the information contained in it. Luís Reino was funded by FEDER Funds through the Operational Competitiveness Factors Program “COMPETE”, and by National Funds through the Foundation for Science and Technology (FCT) within the framework of the Project “PTDC/AAG-GLO/0463/2014-POCI-01-0145-FEDER-016583” and FCT Post-doc Grant SFRH/BPD/93079/2013. LC was funded by the H2020-MSCA-IF-2016 fellowship No. 752149.Peer reviewe

Assessing the assessments: evaluation of four impact assessment protocols for invasive alien species

Aim: Effective policy and management responses to the multiple threats posed by invasive alien species (IAS) rely on the ability to assess their impacts before conclusive empirical evidence is available. A plethora of different IAS risk and/or impact assessment protocols have been proposed, but it remains unclear whether, how and why the outcomes of such assessment protocols may differ. Location: Europe. Methods: Here, we present an in-depth evaluation and informed assessment of the consistency of four prominent protocols for assessing IAS impacts (EICAT, GISS, Harmonia and NNRA), using two non-native parrots in Europe: the widespread ring-necked parakeet (Psittacula krameri) and the rapidly spreading monk parakeet (Myiopsitta monachus). Results: Our findings show that the procedures used to assess impacts may influence assessment outcomes. We find that robust IAS prioritization can be obtained by assessing species based on their most severe documented impacts, as all protocols yield consistent outcomes across impact categories. Additive impact scoring offers complementary, more subtle information that may be especially relevant for guiding management decisions regarding already established invasive alien species. Such management decisions will also strongly benefit from consensus approaches that reduce disagreement between experts, fostering the uptake of scientific advice into policy-making decisions. Main conclusions: Invasive alien species assessments should take advantage of the capacity of consensus assessments to consolidate discussion and agreement between experts. Our results suggest that decision-makers could use the assessment protocol most fit for their purpose, on the condition they apply a precautionary approach by considering the most severe impacts only. We also recommend that screening for high-impact IAS should be performed on a more robust basis than current ad hoc practices, at least using the easiest assessment protocols and reporting confidence scores.This study is a joint effort from a workshop organized under COST European Cooperation in Science and Technology Actions Parrotnet (ES1304) and Alien Challenge (TD1209). We would also like to thank two anonymous referees for helpful comments on an earlier version of this manuscript. D.S is currently funded by a Marie Skłodowska‐Curie Action under the Horizon 2020 call (H2020‐MSCA‐IF‐2015, grant number 706318) and acknowledges the Danish National Research Foundation for support to the Center for Macroecology, Evolution and Climate (grant number DNRF96). J.C.S. was supported by funds from the Ministry of Economy and Competitivity, Spanish Research Council (CGL‐2016‐79568‐C3‐3‐P)

Habitat selection of an exotic species in urban areas : the case of the ring-necked parakeet Psittacula krameri

L’étude des mécanismes qui régissent le succès d’établissement et d’expansion des espèces exotiques apparait primordial pour l’appréhension de leurs potentiels impacts. Ce travail de thèse a pour objet d’étude la Perruche à collier \textit{Psittacula krameri}, un Psittacidé largement introduit en Europe. Les objectifs de ces travaux relèvent de l’étude des facteurs qui peuvent influencer le succès d’établissement de cette espèce en milieu urbain, par l’analyse de la sélection de l’habitat à l’étude des traits comportementaux. Les résultats montrent que la sélection de l’habitat est associée aux activités humaines, de par la préférence de l’espèce pour les zones urbanisées dans lesquelles l’espèce semble être attirée par les lumières artificielles et les espèces végétales exotiques. La comparaison de la sélection de l’habitat avec une espèce native en expansion, le Choucas des tours \textit{Corvus monedula}, a permis de montrer que la Perruche à collier est contrainte spatialement aux zones suburbaines tandis que le Choucas pourrait être capable de s’étendre aux zones les plus urbanisées. Une approche expérimentale et éthologique a mis en lumière le comportement agressif de la Perruche à collier et une monopolisation passive des ressources alimentaires, suggérant un avantage compétitif sur les espèces natives. L’ensemble des résultats de cette thèse laisse présager un potentiel de forte croissance démographique des populations et contribue aux connaissances nécessaires pour comprendre les mécanismes qui régissent l’établissement et le succès des espèces en expansion, native et exotique, tant au travers de l’étude spatiale que comportementale.Identifying the mechanisms which may allow invasive species to establish and spread is not only a scientific question of interest but also a crucial knowledge to acquire for the management of these species. This thesis work focuses on the ring-necked parakeet, \textit{Psittacula krameri},, a Psittacine species widely introduced throughout Europe.This thesis aimed to study factors underlying the spatiotemporal distribution and which may explain the urban success of this species, from the analysis of habitat selection to behavioral traits. Results showed that habitat selection is closely related to anthropic activities, the species showing a clear preference for suburban zones and green urban areas in which the species seems to be attracted by artificial lights and exotic tree species. Using the Western jackdaw, a native range-expanding and co-occurring species, distribution modelling allowed to predict the potential future distribution and showed that, while the jackdaw may spatially expand in the more urbanized part of the city, the ring-necked parakeet may be restricted to suburban areas in the future. An ethological experiment highlighted the agonistic behavior of the ring-necked parakeet and a passive monopolization of resources, suggesting a competitive advantage over native species, exacerbated by temporal niche overlap and avoidance behavior by native species. This thesis suggests that parakeets have the potential to reach high numbers in urban areas and the overall findings provide further insight into the mechanisms allowing the establishment and spread of expanding species, native and exotic, through spatial and behavioral factors

Sélection de l'habitat d'une espèce exotique en milieu urbain : le cas de la perruche à collier Psittacula krameri

Urban areas are human-dominated systems, with specific characteristics, from abiotic to biotic components, and a privileged place for the introduction of exotic species. Identifying the mechanisms which may allow invasive species to establish and spread is not only a scientific question of interest but also a crucial knowledge to acquire for the management of these species. This thesis work focuses on the ring-necked parakeet, Psittacula krameri, a Psittacine species widely introduced throughout Europe and for which the spatial expansion and demographic growth have raised concerns about its potential impacts in the introduced range. This thesis aimed to study factors underlying the spatiotemporal distribution and which may explain the urban success of this species, from the analysis of habitat selection to behavioral traits, and by the exploration of the recent technological and statistical improvements in the acquisition and analysis of spatiotemporal data. Results showed that habitat selection is closely related to anthropic activities, the species showing a clear preference for suburban zones and green urban areas in which the species seems to be attracted by artificial lights and exotic tree species. Using the Western jackdaw, a native range-expanding and co-occurring species, distribution modelling allowed to predict the potential future distribution and showed that, while the jackdaw may spatially expand in the more urbanized part of the city, the ring-necked parakeet may be restricted to suburban areas in the future. An ethological experiment highlighted the agonistic behavior of the ring-necked parakeet and a passive monopolization of resources, suggesting a competitive advantage over native species, exacerbated by temporal niche overlap and avoidance behavior by native species. This thesis suggests that parakeets have the potential to reach high numbers in urban areas and the overall findings provide further insight into the mechanisms allowing the establishment and spread of expanding species, native and exotic, through spatial and behavioral factors.Les milieux urbanisés constituent des systèmes particuliers, sous dominance anthropique, aux caractéristiques spécifiques tant en termes de composantes biotiques qu’abiotiques. Lieu privilégié d’introduction d’espèces exotiques, l’étude des mécanismes qui régissent le succès d’établissement et d’expansion de ces espèces apparait primordial pour l’appréhension de leurs potentiels impacts et la compréhension de ces néo-systèmes. Ce travail de thèse a pour objet d’étude la Perruche à collier Psittacula krameri, un Psittacidé largement introduit en Europe et dont l’expansion spatiale et démographique soulève des interrogations quant à ses impacts potentiels dans les zones d’introductions. Les objectifs de ces travaux relèvent de l’étude des facteurs qui peuvent influencer le succès d’établissement de cette espèce en milieu urbain, par l’analyse de la sélection de l’habitat à l’étude des traits comportementaux, et par l’exploration des récentes avancées technologiques et statistiques dans l’acquisition de données spatiales et temporelles. Les résultats montrent que la sélection de l’habitat est associée aux activités humaines, de par la préférence de l’espèce pour les zones urbanisées et les espaces verts urbains, dans lesquels l’espèce semble être attirée par les lumières artificielles et les espèces végétales exotiques. La comparaison de la sélection de l’habitat avec une espèce native en expansion, le Choucas des tours Corvus monedula, a permis d’étayer cette hypothèse, la Perruche à collier étant contrainte spatialement aux zones suburbaines dans sa distribution potentielle future tandis que le Choucas pourrait être capable de s’étendre aux zones les plus urbanisées. Une approche expérimentale et éthologique a permis de mettre en lumière le comportement agressif de la Perruche à collier et une monopolisation passive des ressources alimentaires, suggérant un avantage compétitif sur les espèces natives, accentué par un chevauchement de niche temporelle et un comportement d’évitement des espèces natives face à la Perruche à collier. L’ensemble des résultats de cette thèse laisse présager un potentiel de forte croissance démographique des populations de perruches à collier et contribue aux connaissances nécessaires pour comprendre les mécanismes qui régissent l’établissement et le succès des espèces en expansion, native et exotique, tant au travers de l’étude spatiale que comportementale

“Kill Two Birds with One Stone”: Urban Tree Species Classification Using Bi-Temporal Pléiades Images to Study Nesting Preferences of an Invasive Bird

This study presents the results of object-based classifications assessing the potential of bi-temporal Pléiades images for mapping broadleaf and coniferous tree species potentially used by the ring-necked parakeet Psittacula krameri for nesting in the urban area of Marseille, France. The first classification was performed based solely on a summer Pléiades image (acquired on 28 July 2015) and the second classification based on bi-temporal Pléiades images (a spring image acquired on 24 March 2016 and the summer image). An ensemble of spectral and textural features was extracted from both images and two machine-learning classifiers were used, Random Forest (RF) and Support Vector Machine (SVM). Regardless of the classifiers, model results suggest that classification based on bi-temporal Pléiades images produces more satisfying results, with an overall accuracy 11.5–13.9% higher than classification using the single-date image. Textural and spectral features extracted from the blue and the NIR bands were consistently ranked among the most important features. Regardless of the classification scheme, RF slightly outperforms SVM. RF classification using bi-temporal Pléiades images allows identifying 98.5% of the tree species used by the ring-necked parakeet for nesting, highlighting the promising value of remote sensing techniques to assess the ecological requirements of fauna in urban areas

“Kill Two Birds with One Stone”: Urban Tree Species Classification Using Bi-Temporal Pléiades Images to Study Nesting Preferences of an Invasive Bird

This study presents the results of object-based classifications assessing the potential of bi-temporal Pléiades images for mapping broadleaf and coniferous tree species potentially used by the ring-necked parakeet Psittacula krameri for nesting in the urban area of Marseille, France. The first classification was performed based solely on a summer Pléiades image (acquired on 28 July 2015) and the second classification based on bi-temporal Pléiades images (a spring image acquired on 24 March 2016 and the summer image). An ensemble of spectral and textural features was extracted from both images and two machine-learning classifiers were used, Random Forest (RF) and Support Vector Machine (SVM). Regardless of the classifiers, model results suggest that classification based on bi-temporal Pléiades images produces more satisfying results, with an overall accuracy 11.5–13.9% higher than classification using the single-date image. Textural and spectral features extracted from the blue and the NIR bands were consistently ranked among the most important features. Regardless of the classification scheme, RF slightly outperforms SVM. RF classification using bi-temporal Pléiades images allows identifying 98.5% of the tree species used by the ring-necked parakeet for nesting, highlighting the promising value of remote sensing techniques to assess the ecological requirements of fauna in urban areas

Interference competition between an invasive parakeet and native bird species at feeding sites

International audienceno abstrac

El gusto por lo exótico: la depredación de la cotorra de Kramer invasora por el búho chico en una zona urbana

[EN] Predation pressure by native species may limit the spread of alien invasive species, thus playing a pivotal role in the impact and implementation of management strategies. The ring–necked parakeet Psittacula krameri is one of the most widespread alien bird species in Europe, with nearly 70 established populations. Predators of this species include diurnal raptors, synanthropic corvids, and rodents. Here we report for the first time that long–eared owls Asio otus might have preyed upon parakeets in their night roosts. Analysis of 167 owl pellets showed that ring–necked parakeets made up over 10 % of the total volume of the diet of these owls in winter (32.93 % of absolute frequency), representing the most important prey species after murid rodents and passerine birds. Further studies are needed to investigate whether parakeet consumption by long–eared owls is only a local occurrence or whether it is widespread in European cities. If so, predation by long–eared owl may eventually lead to a form of parakeet control and may limit the impact of this introduced parakeet on native biodiversity.[ES] La presión predatoria que ejercen las especies nativas puede limitar la propagación de especies invasoras exóticas y, en consecuencia, tener un papel decisivo en los efectos y la aplicación de estrategias de gestión. La cotorra de Kramer, Psittacula krameri, es una de las especies de aves exóticas más extendida de Europa, donde tiene cerca de 70 po-blaciones establecidas. Entre los depredadores de esta especie se encuentran rapaces diurnas, córvidos sinantrópicos y roedores. En este estudio observamos por primera vez que el búho chico, Asio otus, puede cazar cotorras en sus dormideros. El análisis de 167 excrementos de búho chico mostró que las cotorras de Kramer constituyen el 10 % de volumen total de la dieta de estos búhos en invierno (32,93 % de frecuencia absoluta) y son la presa más importante después de los roedores múridos y las aves paseriformes. Es necesario seguir estudiando esta cuestión para analizar si el consumo de cotorras de Kramer por el búho chico es solo un fenómeno local o si se ha generalizado en las ciudades europeas. En ese caso, es posible que, la depredación por el búho chico termine suponiendo una forma de control de la cotorra y limite el impacto de esta especie introducida en la biodiversidad autóctona.We thank COST (European Cooperation in Science and Technology Actions) ES1304 “ParrotNet” for their support in the development of this manuscript.Peer reviewe

Dispersal-based species pools as sources of connectivity area mismatches

International audienceContext Prioritising is likely to differ depending on the species considered for connectivity assessments, leading to a lack of consensual decisions for territorial planning. Objectives The objective was to assess the relevance of identifying priority areas for connectivity for groups of species based on common dispersal abilities. We aimed to assess the impact of target groups choices on predicted priority areas. Method The study was located at the Thau Lagoon territory to demonstrate the methodological approach. Ecological niche modelling was used to quantify species resistance and to identify suitable habitat patches. We coupled the least-cost path methodology with circuit theory to assess species connectivity. We classified connectivity from high to low levels and averaged the results by dispersal groups. Results We found important differences in identified priority areas between groups with dissimilar dispersal abilities, with little overlap between highly connected areas. We identified a gap between the level of protection of low dispersal species and highly connected areas. We found mismatches between existing corridors and connectivity in low dispersal species, and a greater impact in areas of expected urban sprawl projects on favourably connected areas for species with high dispersal capabilities. Conclusion We have demonstrated that a diversity of dispersal capacity ranges must be accounted for in order to identify ecological corridors in programmes that aim to restore habitat connectivity at territorial levels. Our findings are oriented to support the decisions of planning initiatives, at both local and regional scale