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Parveen S, Kaur S, Baishya R, Goel S. Predicting the potential suitable habitats of genus Nymphaea in India using MaxEnt modeling. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:853. [PMID: 36203117 DOI: 10.1007/s10661-022-10524-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Modeling and mapping the distribution of suitable habitats of aquatic plants are critical for assessing the impact of factors like changing climate on species habitat range shifts, declines, and expansions. Nymphaea is an aquatic perennial herb considered valuable because of its ornamental, economic, medicinal, and ecological importance. In India, the geographical distribution of Nymphaea is diverse, and the suitable habitats of individual species are vulnerable to the changing climate and global warming effects. Despite its increased vulnerability, only a few limited conservation efforts in aquatic environments are being made to date. In several places, the distribution of Nymphaea has been impacted by both anthropogenic and climate-related disturbances. A comprehensive strategy will be needed to meet the socio-ecological challenge of Nymphaea conservation. In this study, we employed maximum entropy (MaxEnt) method to assess how climate change affects the distribution of Nymphaea suitable habitat. The occurrence records of Nymphaea were collected from primary surveys, Global Biodiversity Information Facility (GBIF), and published works. Bioclimatic variables obtained from the Coupled Model Intercomparison Project (CMIP6) were employed as predictor variables in distribution modeling. The projections were made using three SSPs (stringent mitigation scenarios) for the future period of 2050. Our results showed shifts in the suitability ranges of Nymphaea under different projection scenarios. The study provides information about the distribution of suitable habitats for Nymphaea in India, which may be helpful for ongoing efforts to conserve and manage the aquatic plants, particularly in areas that are losing suitable climate conditions.
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Affiliation(s)
- Seema Parveen
- Department of Botany, University of Delhi, Delhi-110007, India
| | - Sharanjeet Kaur
- Department of Botany, University of Delhi, Delhi-110007, India
| | - Ratul Baishya
- Department of Botany, University of Delhi, Delhi-110007, India
| | - Shailendra Goel
- Department of Botany, University of Delhi, Delhi-110007, India.
- Genetics and Genomics Laboratory, Department of Botany, University of Delhi, Chattra Marg, Delhi-110007, India.
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Wang Y, Samarasekara CL, Stone L. A machine learning method for estimating the probability of presence using presence‐background data. Ecol Evol 2022; 12:e8998. [PMID: 35784023 PMCID: PMC9203590 DOI: 10.1002/ece3.8998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Yan Wang
- School of Science RMIT University Melbourne Victoria Australia
| | | | - Lewi Stone
- School of Science RMIT University Melbourne Victoria Australia
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Ocampo CB, Guzmán-Rodríguez L, Moreno M, Castro MDM, Valderrama-Ardila C, Alexander N. Integration of phlebotomine ecological niche modelling, and mapping of cutaneous leishmaniasis surveillance data, to identify areas at risk of under-estimation. Acta Trop 2021; 224:106122. [PMID: 34480871 PMCID: PMC9017289 DOI: 10.1016/j.actatropica.2021.106122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/13/2021] [Accepted: 08/25/2021] [Indexed: 12/01/2022]
Abstract
INTRODUCTION Passive surveillance systems are thought to under-estimate the true incidence of American cutaneous leishmaniasis (ACL) by two- to five-fold. Ecological niche models based on remotely sensed data can identify environmental factors which favor phlebotomine vectors. Here we report an integrated approach to identifying areas at risk of cutaneous leishmaniasis by applying spatial analysis methods to niche model results, and local surveillance data, in two locations in Colombia with differing vector ecology. The objective was to identify townships in which later phases of the project could implement community-based surveillance to obtain direct estimates of under-reporting. MATERIALS AND METHODS The study was carried out in one municipality in each of two departments of the Andean region of Colombia: Pueblo Rico in Risaralda, and Rovira in Tolima. Niche mapping by maximum entropy, based on published and unpublished existing locations of Pintomyia (Pifanomyia) longiflocosa and Psychodopygus panamensis, and using variables on land cover, climate and elevation. Field catches were done in each municipality to test predictions of high relative probability of presence. The niche model results were included as a predictor in a conditional autoregressive spatial model, in which the outcome variable was the number of cases by township, as detected by passive surveillance. RESULTS Having rarefied 173 geolocated records, 46 of Pi. longiflocosa and 57 of Ps. panamensis were used for the niche modelling. At the national level, both species had high relative probability of presence on parts of the slopes of the three Andean cordilleras. Pi. longiflocosa also has a high relative probability of presence in the higher parts of the Magdalena valley, as does Ps. panamensis in some areas close to the Caribbean coast. At the local level, field catches confirmed that Pi. longiflocosa was the most abundant species in Rovira, and likewise Ps. panamensis in Pueblo Rico. The spatial regression showed that the incidence of ACL, according to surveillance, was positively, but not statistically significantly, associated with the relative probability of presence from the risk model. CONCLUSIONS These niche maps bring together published and unpublished results on phlebotomine species which are important vectors in Colombia. Maps of the fitted values of incidence were used to guide the selection of townships in which further phases of the study will attempt to quantify the extent of under-estimation of ACL incidence.
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Affiliation(s)
- Clara B Ocampo
- Centro Internacional de Entrenamiento e Investigaciones Médicas, CIDEIM. Cali, Colombia; Universidad Icesi., Cali, Colombia; Ministerio de Ciencia Tecnología e Innovación (Minciencias), Bogotá, Colombia
| | - Lina Guzmán-Rodríguez
- Centro Internacional de Entrenamiento e Investigaciones Médicas, CIDEIM. Cali, Colombia
| | - Mabel Moreno
- Centro Internacional de Entrenamiento e Investigaciones Médicas, CIDEIM. Cali, Colombia
| | - María Del Mar Castro
- Centro Internacional de Entrenamiento e Investigaciones Médicas, CIDEIM. Cali, Colombia; Universidad Icesi., Cali, Colombia
| | | | - Neal Alexander
- Centro Internacional de Entrenamiento e Investigaciones Médicas, CIDEIM. Cali, Colombia; Universidad Icesi., Cali, Colombia.
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Liu S, Yu T. Kernel density estimation in mixture models with known mixture proportions. Stat Med 2021; 40:6360-6372. [PMID: 34474504 DOI: 10.1002/sim.9187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 06/18/2021] [Accepted: 08/17/2021] [Indexed: 11/11/2022]
Abstract
In this article, we consider the density estimation for data with a mixture structure, where the component densities are assumed unknown, but for each observation, the probabilities of its membership to the subpopulations are known or estimable from other resources. Data of this kind arise from practice and have wide applications. Motivated from the classical kernel density estimation method for a single population, we propose a weighted kernel density estimation method to estimate the component density functions nonparametrically. Within the framework of the EM algorithm, we derive an algorithm that computes our proposed estimates effectively. Via extensive simulation studies, we demonstrate that our methods outperform the existing methods in most occasions. We further compare our methods with existing methods by real data examples.
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Affiliation(s)
- Siyun Liu
- Department of Statistics and Data Science, National University of Singapore, Singapore
| | - Tao Yu
- Department of Statistics and Data Science, National University of Singapore, Singapore
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Hogg SE, Wang Y, Stone L. Effectiveness of joint species distribution models in the presence of imperfect detection. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Yan Wang
- Mathematics School of Science RMIT Melbourne Australia
| | - Lewi Stone
- Mathematics School of Science RMIT Melbourne Australia
- Biomathematics Unit School of Zoology Faculty of Life Science Tel Aviv University Tel Aviv Israel
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Feldman MJ, Imbeau L, Marchand P, Mazerolle MJ, Darveau M, Fenton NJ. Trends and gaps in the use of citizen science derived data as input for species distribution models: A quantitative review. PLoS One 2021; 16:e0234587. [PMID: 33705414 PMCID: PMC7951830 DOI: 10.1371/journal.pone.0234587] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 02/11/2021] [Indexed: 11/19/2022] Open
Abstract
Citizen science (CS) currently refers to the participation of non-scientist volunteers in any discipline of conventional scientific research. Over the last two decades, nature-based CS has flourished due to innovative technology, novel devices, and widespread digital platforms used to collect and classify species occurrence data. For scientists, CS offers a low-cost approach of collecting species occurrence information at large spatial scales that otherwise would be prohibitively expensive. We examined the trends and gaps linked to the use of CS as a source of data for species distribution models (SDMs), in order to propose guidelines and highlight solutions. We conducted a quantitative literature review of 207 peer-reviewed articles to measure how the representation of different taxa, regions, and data types have changed in SDM publications since the 2010s. Our review shows that the number of papers using CS for SDMs has increased at approximately double the rate of the overall number of SDM papers. However, disparities in taxonomic and geographic coverage remain in studies using CS. Western Europe and North America were the regions with the most coverage (73%). Papers on birds (49%) and mammals (19.3%) outnumbered other taxa. Among invertebrates, flying insects including Lepidoptera, Odonata and Hymenoptera received the most attention. Discrepancies between research interest and availability of data were as especially important for amphibians, reptiles and fishes. Compared to studies on animal taxa, papers on plants using CS data remain rare. Although the aims and scope of papers are diverse, species conservation remained the central theme of SDM using CS data. We present examples of the use of CS and highlight recommendations to motivate further research, such as combining multiple data sources and promoting local and traditional knowledge. We hope our findings will strengthen citizen-researchers partnerships to better inform SDMs, especially for less-studied taxa and regions. Researchers stand to benefit from the large quantity of data available from CS sources to improve global predictions of species distributions.
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Affiliation(s)
- Mariano J. Feldman
- Centre d’étude de la forêt, Institut de Recherche sur les Forêts (IRF), Université du Québec en Abitibi-Témiscamingue (UQAT), Rouyn-Noranda, Québec, Canada
| | - Louis Imbeau
- Centre d’étude de la forêt, Institut de Recherche sur les Forêts (IRF), Université du Québec en Abitibi-Témiscamingue (UQAT), Rouyn-Noranda, Québec, Canada
| | - Philippe Marchand
- Centre d’étude de la forêt, Institut de Recherche sur les Forêts (IRF), Université du Québec en Abitibi-Témiscamingue (UQAT), Rouyn-Noranda, Québec, Canada
| | - Marc J. Mazerolle
- Département des sciences du bois et de la forêt, Centre d’étude de la forêt, Faculté de foresterie, de géographie et de géomatique, Université Laval, Québec City, Québec City, Canada
| | - Marcel Darveau
- Département des sciences du bois et de la forêt, Centre d’étude de la forêt, Faculté de foresterie, de géographie et de géomatique, Université Laval, Québec City, Québec City, Canada
- Ducks Unlimited Canada, Québec City, Québec City, Canada
| | - Nicole J. Fenton
- Centre d’étude de la forêt, Institut de Recherche sur les Forêts (IRF), Université du Québec en Abitibi-Témiscamingue (UQAT), Rouyn-Noranda, Québec, Canada
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Van Eupen C, Maes D, Herremans M, Swinnen KR, Somers B, Luca S. The impact of data quality filtering of opportunistic citizen science data on species distribution model performance. Ecol Modell 2021. [DOI: 10.1016/j.ecolmodel.2021.109453] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Sherpa S, Renaud J, Guéguen M, Besnard G, Mouyon L, Rey D, Després L. Landscape does matter: Disentangling founder effects from natural and human-aided post-introduction dispersal during an ongoing biological invasion. J Anim Ecol 2020; 89:2027-2042. [PMID: 32597498 DOI: 10.1111/1365-2656.13284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/19/2020] [Indexed: 11/28/2022]
Abstract
Environmental features impacting the spread of invasive species after introduction can be assessed using population genetic structure as a quantitative estimation of effective dispersal at the landscape scale. However, in the case of an ongoing biological invasion, deciphering whether genetic structure represents landscape connectivity or founder effects is particularly challenging. We examined the modes of dispersal (natural and human-aided) and the factors (landscape or founders history) shaping genetic structure in range edge invasive populations of the Asian tiger mosquito, Aedes albopictus, in the region of Grenoble (Southeast France). Based on detailed occupancy-detection data and environmental variables (climatic, topographic and land-cover), we modelled A. albopictus potential suitable area and its expansion history since first introduction. The relative role of dispersal modes was estimated using biological dispersal capabilities and landscape genetics approaches using genome-wide SNP dataset. We demonstrate that both natural and human-aided dispersal have promoted the expansion of populations. Populations in diffuse urban areas, representing highly suitable habitat for A. albopictus, tend to disperse less, while roads facilitate long-distance dispersal. Yet, demographic bottlenecks during introduction played a major role in shaping the genetic variability of these range edge populations. The present study is one of the few investigating the role of founder effects and ongoing expansion processes in shaping spatial patterns of genetic variation in an invasive species at the landscape scale. The combination of several dispersal modes and large proportions of continuous suitable habitats for A. albopictus promoted range filling of almost its entire potential distribution in the region of Grenoble only few years after introduction.
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Affiliation(s)
- Stéphanie Sherpa
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, CNRS, Grenoble, France
| | - Julien Renaud
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, CNRS, Grenoble, France
| | - Maya Guéguen
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, CNRS, Grenoble, France
| | - Gilles Besnard
- Entente Interdépartementale Rhône Alpes pour la Démoustication (EID), Chindrieux, France
| | - Loic Mouyon
- Entente Interdépartementale Rhône Alpes pour la Démoustication (EID), Chindrieux, France
| | - Delphine Rey
- Entente Interdépartementale Rhône Alpes pour la Démoustication (EID), Chindrieux, France
| | - Laurence Després
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, CNRS, Grenoble, France
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