1
|
Feng X, Peterson AT, Aguirre-López LJ, Burger JR, Chen X, Papeş M. Rethinking ecological niches and geographic distributions in face of pervasive human influence in the Anthropocene. Biol Rev Camb Philos Soc 2024; 99:1481-1503. [PMID: 38597328 DOI: 10.1111/brv.13077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Species are distributed in predictable ways in geographic spaces. The three principal factors that determine geographic distributions of species are biotic interactions (B), abiotic conditions (A), and dispersal ability or mobility (M). A species is expected to be present in areas that are accessible to it and that contain suitable sets of abiotic and biotic conditions for it to persist. A species' probability of presence can be quantified as a combination of responses to B, A, and M via ecological niche modeling (ENM; also frequently referred to as species distribution modeling or SDM). This analytical approach has been used broadly in ecology and biogeography, as well as in conservation planning and decision-making, but commonly in the context of 'natural' settings. However, it is increasingly recognized that human impacts, including changes in climate, land cover, and ecosystem function, greatly influence species' geographic ranges. In this light, historical distinctions between natural and anthropogenic factors have become blurred, and a coupled human-natural landscape is recognized as the new norm. Therefore, B, A, and M (BAM) factors need to be reconsidered to understand and quantify species' distributions in a world with a pervasive signature of human impacts. Here, we present a framework, termed human-influenced BAM (Hi-BAM, for distributional ecology that (i) conceptualizes human impacts in the form of six drivers, and (ii) synthesizes previous studies to show how each driver modifies the natural BAM and species' distributions. Given the importance and prevalence of human impacts on species distributions globally, we also discuss implications of this framework for ENM/SDM methods, and explore strategies by which to incorporate increasing human impacts in the methodology. Human impacts are redefining biogeographic patterns; as such, future studies should incorporate signals of human impacts integrally in modeling and forecasting species' distributions.
Collapse
Affiliation(s)
- Xiao Feng
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | | | | | - Joseph R Burger
- Department of Biology, University of Kentucky, Lexington, KY, 40502, USA
| | - Xin Chen
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, 21532, USA
| | - Monica Papeş
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
| |
Collapse
|
2
|
Mlambo S, Mubayiwa M, Tarusikirwa VL, Machekano H, Mvumi BM, Nyamukondiwa C. The Fall Armyworm and Larger Grain Borer Pest Invasions in Africa: Drivers, Impacts and Implications for Food Systems. BIOLOGY 2024; 13:160. [PMID: 38534430 DOI: 10.3390/biology13030160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 03/28/2024]
Abstract
Invasive alien species (IAS) are a major biosecurity threat affecting globalisation and the international trade of agricultural products and natural ecosystems. In recent decades, for example, field crop and postharvest grain insect pests have independently accounted for a significant decline in food quantity and quality. Nevertheless, how their interaction and cumulative effects along the ever-evolving field production to postharvest continuum contribute towards food insecurity remain scant in the literature. To address this within the context of Africa, we focus on the fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), and the larger grain borer, Prostephanus truncatus (Horn) (Coleoptera: Bostrichidae), two of the most important field and postharvest IAS, respectively, that have invaded Africa. Both insect pests have shown high invasion success, managing to establish themselves in >50% of the African continent within a decade post-introduction. The successive and summative nature of field and postharvest damage by invasive insect pests on the same crop along its value chain results in exacerbated food losses. This systematic review assesses the drivers, impacts and management of the fall armyworm and larger grain borer and their effects on food systems in Africa. Interrogating these issues is important in early warning systems, holistic management of IAS, maintenance of integral food systems in Africa and the development of effective management strategies.
Collapse
Affiliation(s)
- Shaw Mlambo
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye 10071, Botswana
| | - Macdonald Mubayiwa
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye 10071, Botswana
| | - Vimbai L Tarusikirwa
- Department of Biology, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Honest Machekano
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Brighton M Mvumi
- Department of Agricultural and Biosystems Engineering, University of Zimbabwe, Mount Pleasant, Harare P.O. Box MP167, Zimbabwe
| | - Casper Nyamukondiwa
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye 10071, Botswana
- Department of Zoology and Entomology, Rhodes University, Makhanda 6140, South Africa
| |
Collapse
|
3
|
Lu WX, Wang ZZ, Hu XY, Rao GY. Incorporating eco-evolutionary information into species distribution models provides comprehensive predictions of species range shifts under climate change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169501. [PMID: 38145682 DOI: 10.1016/j.scitotenv.2023.169501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 11/29/2023] [Accepted: 12/17/2023] [Indexed: 12/27/2023]
Abstract
As climate changes increasingly influence species distributions, ecosystem functions, and biodiversity, the urgency to understand how species' ranges shift under those changes is great. Species distribution models (SDMs) are vital approaches that can predict species distributions under changing climates. However, SDMs based on the species' current occurrences may underestimate the species' climatic tolerances. Integrating species' realized niches at different periods, also known as multi-temporal calibration, can provide an estimation closer to its fundamental niche. Based on this, we further proposed an integrated framework that combines eco-evolutionary data and SDMs (phylogenetically-informed SDMs) to provide comprehensive predictions of species range shifts under climate change. To evaluate our approach's performance, we applied it to a group of related species, the Chrysanthemum zawadskii species complex (Anthemidae, Asteracee). First, we investigated the niche differentiation between species and intraspecific lineages of the complex and estimated their rates of niche evolution. Next, using both standard SDMs and our phylogenetically-informed SDMs, we generated predictions of suitability areas for all species and lineages and compared the results. Finally, we reconstructed the historical range dynamics for the species of this complex. Our results showed that the species and intraspecific lineages of the complex had varying degrees of niche differentiation and different rates of niche evolution. Lineage-level SDMs can provide more realistic predictions for species with intraspecific differentiation than species-level models can. The phylogenetically-informed SDMs provided more complete environmental envelopes and predicted broader potential distributions for all species than the standard SDMs did. Range dynamics varied among the species that have different rates of niche evolution. Our framework integrating eco-evolutionary data and SDMs contributes to a better understanding of the species' responses to climate change and can help to make more targeted conservation efforts for the target species under climate change, particularly for rare species.
Collapse
Affiliation(s)
- Wen-Xun Lu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Zi-Zhao Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Xue-Ying Hu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Guang-Yuan Rao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
| |
Collapse
|
4
|
Lippi CA, Mundis SJ, Sippy R, Flenniken JM, Chaudhary A, Hecht G, Carlson CJ, Ryan SJ. Trends in mosquito species distribution modeling: insights for vector surveillance and disease control. Parasit Vectors 2023; 16:302. [PMID: 37641089 PMCID: PMC10463544 DOI: 10.1186/s13071-023-05912-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/04/2023] [Indexed: 08/31/2023] Open
Abstract
Species distribution modeling (SDM) has become an increasingly common approach to explore questions about ecology, geography, outbreak risk, and global change as they relate to infectious disease vectors. Here, we conducted a systematic review of the scientific literature, screening 563 abstracts and identifying 204 studies that used SDMs to produce distribution estimates for mosquito species. While the number of studies employing SDM methods has increased markedly over the past decade, the overwhelming majority used a single method (maximum entropy modeling; MaxEnt) and focused on human infectious disease vectors or their close relatives. The majority of regional models were developed for areas in Africa and Asia, while more localized modeling efforts were most common for North America and Europe. Findings from this study highlight gaps in taxonomic, geographic, and methodological foci of current SDM literature for mosquitoes that can guide future efforts to study the geography of mosquito-borne disease risk.
Collapse
Affiliation(s)
- Catherine A Lippi
- Quantitative Disease Ecology and Conservation (QDEC) Lab, Department of Geography, University of Florida, Gainesville, FL, 32601, USA.
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32601, USA.
| | - Stephanie J Mundis
- Quantitative Disease Ecology and Conservation (QDEC) Lab, Department of Geography, University of Florida, Gainesville, FL, 32601, USA
| | - Rachel Sippy
- Quantitative Disease Ecology and Conservation (QDEC) Lab, Department of Geography, University of Florida, Gainesville, FL, 32601, USA
- School of Mathematics and Statistics, University of St Andrews, St Andrews, KY16 9SS, UK
| | - J Matthew Flenniken
- Quantitative Disease Ecology and Conservation (QDEC) Lab, Department of Geography, University of Florida, Gainesville, FL, 32601, USA
| | - Anusha Chaudhary
- Quantitative Disease Ecology and Conservation (QDEC) Lab, Department of Geography, University of Florida, Gainesville, FL, 32601, USA
| | - Gavriella Hecht
- Quantitative Disease Ecology and Conservation (QDEC) Lab, Department of Geography, University of Florida, Gainesville, FL, 32601, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32601, USA
| | - Colin J Carlson
- Center for Global Health Science and Security, Georgetown University Medical Center, Georgetown University, Washington, DC, USA
| | - Sadie J Ryan
- Quantitative Disease Ecology and Conservation (QDEC) Lab, Department of Geography, University of Florida, Gainesville, FL, 32601, USA.
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32601, USA.
| |
Collapse
|
5
|
Strubbe D, Jiménez L, Barbosa AM, Davis AJS, Lens L, Rahbek C. Mechanistic models project bird invasions with accuracy. Nat Commun 2023; 14:2520. [PMID: 37130835 PMCID: PMC10154326 DOI: 10.1038/s41467-023-38329-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/26/2023] [Indexed: 05/04/2023] Open
Abstract
Invasive species pose a major threat to biodiversity and inflict massive economic costs. Effective management of bio-invasions depends on reliable predictions of areas at risk of invasion, as they allow early invader detection and rapid responses. Yet, considerable uncertainty remains as to how to predict best potential invasive distribution ranges. Using a set of mainly (sub)tropical birds introduced to Europe, we show that the true extent of the geographical area at risk of invasion can accurately be determined by using ecophysiological mechanistic models that quantify species' fundamental thermal niches. Potential invasive ranges are primarily constrained by functional traits related to body allometry and body temperature, metabolic rates, and feather insulation. Given their capacity to identify tolerable climates outside of contemporary realized species niches, mechanistic predictions are well suited for informing effective policy and management aimed at preventing the escalating impacts of invasive species.
Collapse
Affiliation(s)
- Diederik Strubbe
- Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Gent, Belgium.
- Center for Macroecology, Evolution, and Climate (CMEC), GLOBE Institute, University of Copenhagen, 2100, Copenhagen Ø, Denmark.
| | - Laura Jiménez
- School of Life Sciences, University of Hawai'i at Mānoa, 2538 McCarthy Mall, Honolulu, HI, 96822, USA
- Centro de Modelamiento Matemático (CNRS IRL2807), Universidad de Chile, Santiago, Chile
| | - A Márcia Barbosa
- CICGE-Centro de Investigação em Ciências Geo-Espaciais, Alameda do Monte da Virgem, 4430-146, Vila Nova de Gaia, Portugal
| | - Amy J S Davis
- Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Gent, Belgium
- Ecology, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Luc Lens
- Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Gent, Belgium
| | - Carsten Rahbek
- Center for Macroecology, Evolution, and Climate (CMEC), GLOBE Institute, University of Copenhagen, 2100, Copenhagen Ø, Denmark
| |
Collapse
|
6
|
López-Reyes K, Osorio-Olvera L, Rojas-Soto O, Chiappa-Carrara X, Patrón-Rivero C, Yáñez-Arenas C. An exhaustive evaluation of modeling ecological niches above species level to predict marine biological invasions. MARINE ENVIRONMENTAL RESEARCH 2023; 186:105926. [PMID: 36898302 DOI: 10.1016/j.marenvres.2023.105926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/02/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Identifying the areas of the world with suitable environmental conditions for the establishment of invasive species represents a fundamental basis for preventing their impacts. One of the most widely used tools for this is ecological niche modeling. Nonetheless, this approach may underestimate the specie's physiological tolerances (it's potential niche) since wildlife populations of species usually do not occupy their entire environmental tolerance. Recently, it has been suggested that incorporating occurrences of phylogenetically related species improves the prediction of biological invasions. However, the reproducibility of this technique remains unclear. Here, we evaluated the generality of this protocol by assessing whether the construction of modeling units above species level improves the capacity of niche models to predict the distribution of 26 target marine invasive species. For each, we constructed supraspecific modeling units based on published phylogenies by grouping the native occurrence records of each invasive species with the records of its phylogenetically closest relative. We also considered units at species level, including only the presence of records in the native areas of the target species. We generated ecological niche models for each unit with three modeling methods (minimum volume ellipsoids - MVE, machine learning algorithms - Maxent and a presence-absence method - GLM). In addition, we grouped the 26 target species based on whether or not the species are in environmental pseudo-equilibrium (i.e., it occupies all habitats where it can disperse) and have any geographical or biological constraints. Our results suggest that the construction of supraspecific units improves the predictive capacity of correlative models to estimate the invasion area of our target species. This modeling approach consistently generated models with a higher predictive ability for species in non-environmental pseudo-equilibrium and with geographical constraints.
Collapse
Affiliation(s)
- Kevin López-Reyes
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mérida, Yucatán, Mexico
| | - Luis Osorio-Olvera
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Octavio Rojas-Soto
- Red de Biología Evolutiva, Instituto de Ecología, A.C., Xalapa, Veracruz, Mexico
| | - Xavier Chiappa-Carrara
- Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de México, Mérida, Yucatán, Mexico
| | - Carlos Patrón-Rivero
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mérida, Yucatán, Mexico
| | - Carlos Yáñez-Arenas
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mérida, Yucatán, Mexico.
| |
Collapse
|
7
|
Nizamani MM, Papeş M, Wang H, Harris AJ. How does spatial extent and environmental limits affect the accuracy of species richness estimates from ecological niche models? A case study with North American Pinaceae and Cactaceae. Ecol Evol 2023; 13:e10007. [PMID: 37091570 PMCID: PMC10121319 DOI: 10.1002/ece3.10007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 03/13/2023] [Accepted: 03/31/2023] [Indexed: 04/25/2023] Open
Abstract
Measuring species richness at varying spatial extents can be challenging, especially at large extents where exhaustive species surveys are difficult or impossible. Our work aimed at determining the reliability of species richness estimates from stacked ecological niche models at different spatial extents for taxonomic groups with vastly different environmental dependencies and interactions. To accomplish this, we generated ecological niche models for the species of Cactaceae and Pinaceae that occur within 180 published floras from North America north of Mexico. We overlaid or stacked the resulting species' potential distribution estimates over the bounding boxes representing each of the 180 floras to generate predictions of species richness. In general, our stacked models of Cactaceae and Pinaceae were poor predictors of species richness. The relationships between observed and predicted values improved noticeably with the size of spatial extents. However, the stacked models tended to overpredict the richness of Cactaceae and over- and underpredict the richness of Pinaceae. Cactaceae stacked models showed higher sensitivity and lower specificity than those for Pinaceae. We conclude that stacked ecological niche models may be somewhat poor predictors of species richness at smaller spatial extents and should be used with caution for this purpose. Perhaps more importantly, abilities to compensate for their limitations or apply corrections to their reliability may vary with taxonomic groups.
Collapse
Affiliation(s)
- Mir Muhammad Nizamani
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical CropsHainan UniversityHaikouChina
| | - Monica Papeş
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Hua‐Feng Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical CropsHainan UniversityHaikouChina
| | - AJ Harris
- South China Botanical Garden, Chinese Academy of ScienceGuangzhouChina
| |
Collapse
|
8
|
Cuervo PF, Artigas P, Lorenzo-Morales J, Bargues MD, Mas-Coma S. Ecological Niche Modelling Approaches: Challenges and Applications in Vector-Borne Diseases. Trop Med Infect Dis 2023; 8:tropicalmed8040187. [PMID: 37104313 PMCID: PMC10141209 DOI: 10.3390/tropicalmed8040187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Vector-borne diseases (VBDs) pose a major threat to human and animal health, with more than 80% of the global population being at risk of acquiring at least one major VBD. Being profoundly affected by the ongoing climate change and anthropogenic disturbances, modelling approaches become an essential tool to assess and compare multiple scenarios (past, present and future), and further the geographic risk of transmission of VBDs. Ecological niche modelling (ENM) is rapidly becoming the gold-standard method for this task. The purpose of this overview is to provide an insight of the use of ENM to assess the geographic risk of transmission of VBDs. We have summarised some fundamental concepts and common approaches to ENM of VBDS, and then focused with a critical view on a number of crucial issues which are often disregarded when modelling the niches of VBDs. Furthermore, we have briefly presented what we consider the most relevant uses of ENM when dealing with VBDs. Niche modelling of VBDs is far from being simple, and there is still a long way to improve. Therefore, this overview is expected to be a useful benchmark for niche modelling of VBDs in future research.
Collapse
Affiliation(s)
- Pablo Fernando Cuervo
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Av. Vicent Andres Estelles s/n, 46100 Burjassot, Valencia, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos IIII, C/Monforte de Lemos 3-5. Pabellón 11, Planta 0, 28029 Madrid, Madrid, Spain
- Correspondence:
| | - Patricio Artigas
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Av. Vicent Andres Estelles s/n, 46100 Burjassot, Valencia, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos IIII, C/Monforte de Lemos 3-5. Pabellón 11, Planta 0, 28029 Madrid, Madrid, Spain
| | - Jacob Lorenzo-Morales
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos IIII, C/Monforte de Lemos 3-5. Pabellón 11, Planta 0, 28029 Madrid, Madrid, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Av. Astrofísico Fco. Sánchez s/n, 38203 La Laguna, Canary Islands, Spain
| | - María Dolores Bargues
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Av. Vicent Andres Estelles s/n, 46100 Burjassot, Valencia, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos IIII, C/Monforte de Lemos 3-5. Pabellón 11, Planta 0, 28029 Madrid, Madrid, Spain
| | - Santiago Mas-Coma
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Av. Vicent Andres Estelles s/n, 46100 Burjassot, Valencia, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos IIII, C/Monforte de Lemos 3-5. Pabellón 11, Planta 0, 28029 Madrid, Madrid, Spain
| |
Collapse
|
9
|
Discrepancies between point process models and environmental envelopes identify the niche centroid – geography configuration. Ecol Modell 2022. [DOI: 10.1016/j.ecolmodel.2022.109974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
10
|
Paganeli B, Toussaint A, Bueno CG, Fujinuma J, Reier Ü, Pärtel M. Dark diversity at home describes the success of cross‐continent tree invasions. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Bruno Paganeli
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Aurèle Toussaint
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Carlos Guillermo Bueno
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Junichi Fujinuma
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Ülle Reier
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Meelis Pärtel
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| |
Collapse
|
11
|
Contreras-Díaz RG, Falconi M, Osorio-Olvera L, Cobos ME, Soberón J, Townsend Peterson A, Lira-Noriega A, Álvarez-Loayza P, Luis Gonçalves A, Hurtado-Astaiza J, Gonzáles RDPR, Zubileta IS, Spironello WR, Vásquez-Martínez R. On the relationship between environmental suitability and habitat use for three neotropical mammals. J Mammal 2022. [DOI: 10.1093/jmammal/gyab152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Recent studies have used occupancy models (OM) and ecological niche models (ENM) to provide a better understanding of species’ distributions at different scales. One of the main ideas underlying the theoretical foundations of both OM and ENM is that they are positively related to abundance: higher occupancy implies higher density and more suitable areas are likely to have more abundant populations. Here, we analyze the relationship between habitat use measured in terms of occupancy probabilities from OM and environmental suitability derived from ENM in three different Neotropical mammal species: Leopardus wiedii, Cuniculus paca, and Dasypus novemcinctus. For ENM, we used climatic and vegetation cover variables and implemented a model calibration and selection protocol to select the most competitive models. For OM, we used a single-species, single-season model with site covariates for camera-trap data from six different sites throughout the Neotropical realm. Covariates included vegetation percentage, normalized difference vegetation index, normalized difference water index, and elevation. For each site, we fit OM using all possible combinations of variables and selected the most competitive (ΔAICc < 2) to build an average OM. We explored relationships between estimated suitability and occupancy values using Spearman correlation analysis. Relationships between ENM and OM tended to be positive for the three Neotropical mammals, but the strength varied among sites, which could be explained by local factors such as site characteristics and conservation status of areas. We conjecture that ENM are suitable to understand spatial patterns at coarser geographic scales because the concept of the niche is about the species as a whole, whereas OM are more relevant to explain the distribution locally, likely reflecting transient dynamics of populations resulting from many local factors such as community composition and biotic processes.
Collapse
Affiliation(s)
- Rusby G Contreras-Díaz
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio A, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, 04510 Mexico City, Mexico
- Departamento de Matemáticas, Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito exterior s/n, Ciudad Universitaria, 04510 Mexico City, Mexico
| | - Manuel Falconi
- Departamento de Matemáticas, Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito exterior s/n, Ciudad Universitaria, 04510 Mexico City, Mexico
| | - Luis Osorio-Olvera
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito exterior s/n anexo al Jardín Botánico, 04500 Mexico City, Mexico
| | - Marlon E Cobos
- Biodiversity Institute, University of Kansas, Dyche Hall, 1345 Jayhawk Boulevard, Lawrence, KS 66045, USA
| | - Jorge Soberón
- Biodiversity Institute, University of Kansas, Dyche Hall, 1345 Jayhawk Boulevard, Lawrence, KS 66045, USA
| | - A Townsend Peterson
- Biodiversity Institute, University of Kansas, Dyche Hall, 1345 Jayhawk Boulevard, Lawrence, KS 66045, USA
| | - Andrés Lira-Noriega
- CONACyT Research Fellow, Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, El Haya, 91073, Xalapa, Veracruz, Mexico
| | - Patricia Álvarez-Loayza
- Center for Tropical Conservation, Nicholas School of the Environment, Duke University, Durham, NC 27705, USA
- Tropical Ecology Assessment and Monitoring Network, Science and Knowledge Division, Conservation International, 2011 Crystal Drive, Suite 500, VA 22202, USA
| | - André Luis Gonçalves
- Tropical Ecology Assessment and Monitoring Network, Science and Knowledge Division, Conservation International, 2011 Crystal Drive, Suite 500, VA 22202, USA
- Grupo de Pesquisa de Mamíferos Amazônicos, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo 2936, Petrópolis, CEP 69067-375, Manaus, Brazil
| | - Johanna Hurtado-Astaiza
- Tropical Ecology Assessment and Monitoring Network, Science and Knowledge Division, Conservation International, 2011 Crystal Drive, Suite 500, VA 22202, USA
| | - Rocío del Pilar Rojas Gonzáles
- Tropical Ecology Assessment and Monitoring Network, Science and Knowledge Division, Conservation International, 2011 Crystal Drive, Suite 500, VA 22202, USA
- Estación Biológica del Jardín Botánico de Missouri c/o Herbario HOXA, Prolongación Bolognesi Mz. E-6, Oxapampa 19230, Pasco, Peru
| | - Ingrid Serrano Zubileta
- Tropical Ecology Assessment and Monitoring Network, Science and Knowledge Division, Conservation International, 2011 Crystal Drive, Suite 500, VA 22202, USA
| | - Wilson Roberto Spironello
- Tropical Ecology Assessment and Monitoring Network, Science and Knowledge Division, Conservation International, 2011 Crystal Drive, Suite 500, VA 22202, USA
- Grupo de Pesquisa de Mamíferos Amazônicos, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo 2936, Petrópolis, CEP 69067-375, Manaus, Brazil
| | - Rodolfo Vásquez-Martínez
- Tropical Ecology Assessment and Monitoring Network, Science and Knowledge Division, Conservation International, 2011 Crystal Drive, Suite 500, VA 22202, USA
- Estación Biológica del Jardín Botánico de Missouri c/o Herbario HOXA, Prolongación Bolognesi Mz. E-6, Oxapampa 19230, Pasco, Peru
| |
Collapse
|
12
|
Chaves A, Dolz G, Ibarra-Cerdeña CN, Núñez G, Ortiz-Malavasi E E, Bernal-Valle S, Gutiérrez-Espeleta GA. Presence and potential distribution of malaria-infected New World primates of Costa Rica. Malar J 2022; 21:17. [PMID: 34998402 PMCID: PMC8742953 DOI: 10.1186/s12936-021-04036-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/21/2021] [Indexed: 11/11/2022] Open
Abstract
Background In South and Central America, Plasmodium malariae/Plasmodium brasilianum, Plasmodium vivax, Plasmodium simium, and Plasmodium falciparum has been reported in New World primates (NWP). Specifically in Costa Rica, the presence of monkeys positive to P. malariae/P brasilianum has been identified in both captivity and in the wild. The aim of the present study was to determine the presence of P. brasilianum, P. falciparum, and P. vivax, and the potential distribution of these parasites-infecting NWP from Costa Rica. Methods The locations with PCR (Polymerase Chain Reaction) positive results and bioclimatic predictors were used to construct ecological niche models based on a modelling environment that uses the Maxent algorithm, named kuenm, capable to manage diverse settings to better estimate the potential distributions and uncertainty indices of the potential distribution. Results PCR analysis for the Plasmodium presence was conducted in 384 samples of four primates (Howler monkey [n = 130], White-face monkey [n = 132], Squirrel monkey [n = 50], and red spider monkey [n = 72]), from across Costa Rica. Three Plasmodium species were detected in all primate species (P. falciparum, P. malariae/P. brasilianum, and P. vivax). Overall, the infection prevalence was 8.9%, but each Plasmodium species ranged 2.1–3.4%. The niche model approach showed that the Pacific and the Atlantic coastal regions of Costa Rica presented suitable climatic conditions for parasite infections. However, the central pacific coast has a more trustable prediction for malaria in primates. Conclusions The results indicate that the regions with higher suitability for Plasmodium transmission in NWP coincide with regions where most human cases have been reported. These regions were also previously identified as areas with high suitability for vector species, suggesting that enzootic and epizootic cycles occur. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-04036-y.
Collapse
Affiliation(s)
- Andrea Chaves
- Laboratorio de Entomología, Programa de Investigación en Medicina Poblacional, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica. .,Escuela de Biología, Universidad de Costa Rica, San Jose, Costa Rica.
| | - Gaby Dolz
- Laboratorio de Entomología, Programa de Investigación en Medicina Poblacional, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Carlos N Ibarra-Cerdeña
- Departamento de Ecología Humana, Centro de Investigación Y Estudios Avanzados (Cinvestav), Unidad Mérida, Mérida, Yucatan, Mexico
| | - Genuar Núñez
- Escuela de Biología, Universidad de Costa Rica, San Jose, Costa Rica
| | | | - Sofia Bernal-Valle
- Laboratorio de Entomología, Programa de Investigación en Medicina Poblacional, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | | |
Collapse
|
13
|
Etherington TR. Mahalanobis distances for ecological niche modelling and outlier detection: implications of sample size, error, and bias for selecting and parameterising a multivariate location and scatter method. PeerJ 2021; 9:e11436. [PMID: 34026369 PMCID: PMC8121071 DOI: 10.7717/peerj.11436] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/20/2021] [Indexed: 11/24/2022] Open
Abstract
The Mahalanobis distance is a statistical technique that has been used in statistics and data science for data classification and outlier detection, and in ecology to quantify species-environment relationships in habitat and ecological niche models. Mahalanobis distances are based on the location and scatter of a multivariate normal distribution, and can measure how distant any point in space is from the centre of this kind of distribution. Three different methods for calculating the multivariate location and scatter are commonly used: the sample mean and variance-covariance, the minimum covariance determinant, and the minimum volume ellipsoid. The minimum covariance determinant and minimum volume ellipsoid were developed to be robust to outliers by minimising the multivariate location and scatter for a subset of the full sample, with the proportion of the full sample forming the subset being controlled by a user-defined parameter. This outlier robustness means the minimum covariance determinant and the minimum volume ellipsoid are highly relevant for ecological niche analyses, which are usually based on natural history observations that are likely to contain errors. However, natural history observations will also contain extreme bias, to which the minimum covariance determinant and the minimum volume ellipsoid will also be sensitive. To provide guidance for selecting and parameterising a multivariate location and scatter method, a series of virtual ecological niche modelling experiments were conducted to demonstrate the performance of each multivariate location and scatter method under different levels of sample size, errors, and bias. The results show that there is no optimal modelling approach, and that choices need to be made based on the individual data and question. The sample mean and variance-covariance method will perform best on very small sample sizes if the data are free of error and bias. At larger sample sizes the minimum covariance determinant and minimum volume ellipsoid methods perform as well or better, but only if they are appropriately parameterised. Modellers who are more concerned about the prevalence of errors should retain a smaller proportion of the full data set, while modellers more concerned about the prevalence of bias should retain a larger proportion of the full data set. I conclude that Mahalanobis distances are a useful niche modelling technique, but only for questions relating to the fundamental niche of a species where the assumption of multivariate normality is reasonable. Users of the minimum covariance determinant and minimum volume ellipsoid methods must also clearly report their parameterisations so that the results can be interpreted correctly.
Collapse
|