1
|
Whelpley MJ, Zhou LH, Rascon J, Payne B, Moehn B, Young KI, Mire CE, Peters DPC, Rodriguez LL, Hanley KA. Community composition of black flies during and after the 2020 vesicular stomatitis virus outbreak in Southern New Mexico, USA. Parasit Vectors 2024; 17:93. [PMID: 38414030 PMCID: PMC10900647 DOI: 10.1186/s13071-024-06127-6] [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: 10/06/2023] [Accepted: 01/08/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Vesicular stomatitis virus (VSV), a vector-borne pathogen of livestock, emerges periodically in the western US. In New Mexico (NM), US, most cases occur close to the Rio Grande River, implicating black flies (Simulium spp.) as a possible vector. In 2020, VS cases were reported in NM from April to May, although total black fly abundance remained high until September. We investigated the hypothesis that transience of local VSV transmission results from transient abundance of key, competent black fly species. Additionally, we investigated whether irrigation canals in southern NM support a different community of black flies than the main river. Lastly, to gain insight into the source of local black flies, in 2023 we collected black fly larvae prior to the release of water into the Rio Grande River channel. METHODS We randomly sub-sampled adult black flies collected along the Rio Grande during and after the 2020 VSV outbreak. We also collected black fly adults along the river in 2021 and 2022 and at southern NM farms and irrigation canals in 2022. Black fly larvae were collected from dams in the area in 2023. All collections were counted, and individual specimens were subjected to molecular barcoding for species identification. RESULTS DNA barcoding of adult black flies detected four species in 2020: Simulium meridionale (N = 158), S. mediovittatum (N = 83), S. robynae (N = 26) and S. griseum/notatum (N = 1). Simulium robynae was only detected during the VSV outbreak period, S. meridionale showed higher relative abundance, but lower absolute abundance, during the outbreak than post-outbreak period, and S. mediovittatum was rare during the outbreak period but predominated later in the summer. In 2022, relative abundance of black fly species did not differ significantly between the Rio Grande sites and farm and irrigation canals. Intriguingly, 63 larval black flies comprised 56% Simulium vittatum, 43% S. argus and 1% S. encisoi species that were either extremely rare or not detected in previous adult collections. CONCLUSIONS Our results suggest that S. robynae and S. meridionale could be shaping patterns of VSV transmission in southern NM. Thus, field studies of the source of these species as well as vector competence studies are warranted.
Collapse
Affiliation(s)
- Madelin J Whelpley
- Department of Biology, College of Arts and Sciences, New Mexico State University, Las Cruces, NM, USA
| | - Lawrence H Zhou
- Department of Biology, College of Arts and Sciences, New Mexico State University, Las Cruces, NM, USA
| | - Jeremy Rascon
- Department of Biology, College of Arts and Sciences, New Mexico State University, Las Cruces, NM, USA
| | - Bailey Payne
- Department of Biology, College of Arts and Sciences, New Mexico State University, Las Cruces, NM, USA
| | - Brett Moehn
- Department of Biology, College of Arts and Sciences, New Mexico State University, Las Cruces, NM, USA
| | - Katherine I Young
- Department of Biological Sciences, University of Texas El Paso, El Paso Texas, USA
| | - Chad E Mire
- United States Department of Agriculture, Agricultural Research Services, National Bio and Agro-Defense Facility, Foreign Arthropod-Borne Animal Diseases Research Unit, Manhattan, KS, USA
| | - Debra P C Peters
- United States Department of Agriculture, Office of National Programs, Beltsville, MD, USA
| | - Luis L Rodriguez
- United States, Department of Agriculture, Agricultural Research Services, Plum Island Animal Disease Center and National Bio- and Agro-Defense Facility, Manhattan, KS, USA
| | - Kathryn A Hanley
- Department of Biology, College of Arts and Sciences, New Mexico State University, Las Cruces, NM, USA.
| |
Collapse
|
2
|
McCleery R, Guralnick R, Beatty M, Belitz M, Campbell CJ, Idec J, Jones M, Kang Y, Potash A, Fletcher RJ. Uniting Experiments and Big Data to advance ecology and conservation. Trends Ecol Evol 2023; 38:970-979. [PMID: 37330409 DOI: 10.1016/j.tree.2023.05.010] [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: 01/16/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 06/19/2023]
Abstract
Many ecologists increasingly advocate for research frameworks centered on the use of 'big data' to address anthropogenic impacts on ecosystems. Yet, experiments are often considered essential for identifying mechanisms and informing conservation interventions. We highlight the complementarity of these research frameworks and expose largely untapped opportunities for combining them to speed advancements in ecology and conservation. With nascent but increasing application of model integration, we argue that there is an urgent need to unite experimental and big data frameworks throughout the scientific process. Such an integrated framework offers potential for capitalizing on the benefits of both frameworks to gain rapid and reliable answers to ecological challenges.
Collapse
Affiliation(s)
- Robert McCleery
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32618, USA.
| | - Robert Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32618, USA
| | - Meghan Beatty
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32618, USA
| | - Michael Belitz
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32618, USA
| | - Caitlin J Campbell
- Department of Biology, University of Florida, Gainesville, FL 32618, USA
| | - Jacob Idec
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32618, USA
| | - Maggie Jones
- School of Natural Resources and the Environment, University of Florida, Gainesville, FL 32618, USA
| | - Yiyang Kang
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL 32618, USA
| | - Alex Potash
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32618, USA
| | - Robert J Fletcher
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32618, USA
| |
Collapse
|
3
|
Barrile GM, Augustine DJ, Porensky LM, Duchardt CJ, Shoemaker KT, Hartway CR, Derner JD, Hunter EA, Davidson AD. A big data-model integration approach for predicting epizootics and population recovery in a keystone species. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2827. [PMID: 36846939 DOI: 10.1002/eap.2827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/21/2022] [Accepted: 01/10/2023] [Indexed: 06/02/2023]
Abstract
Infectious diseases pose a significant threat to global health and biodiversity. Yet, predicting the spatiotemporal dynamics of wildlife epizootics remains challenging. Disease outbreaks result from complex nonlinear interactions among a large collection of variables that rarely adhere to the assumptions of parametric regression modeling. We adopted a nonparametric machine learning approach to model wildlife epizootics and population recovery, using the disease system of colonial black-tailed prairie dogs (BTPD, Cynomys ludovicianus) and sylvatic plague as an example. We synthesized colony data between 2001 and 2020 from eight USDA Forest Service National Grasslands across the range of BTPDs in central North America. We then modeled extinctions due to plague and colony recovery of BTPDs in relation to complex interactions among climate, topoedaphic variables, colony characteristics, and disease history. Extinctions due to plague occurred more frequently when BTPD colonies were spatially clustered, in closer proximity to colonies decimated by plague during the previous year, following cooler than average temperatures the previous summer, and when wetter winter/springs were preceded by drier summers/falls. Rigorous cross-validations and spatial predictions indicated that our final models predicted plague outbreaks and colony recovery in BTPD with high accuracy (e.g., AUC generally >0.80). Thus, these spatially explicit models can reliably predict the spatial and temporal dynamics of wildlife epizootics and subsequent population recovery in a highly complex host-pathogen system. Our models can be used to support strategic management planning (e.g., plague mitigation) to optimize benefits of this keystone species to associated wildlife communities and ecosystem functioning. This optimization can reduce conflicts among different landowners and resource managers, as well as economic losses to the ranching industry. More broadly, our big data-model integration approach provides a general framework for spatially explicit forecasting of disease-induced population fluctuations for use in natural resource management decision-making.
Collapse
Affiliation(s)
- Gabriel M Barrile
- Colorado Natural Heritage Program, Colorado State University, Fort Collins, Colorado, USA
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA
| | | | | | - Courtney J Duchardt
- Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Kevin T Shoemaker
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, Nevada, USA
| | | | | | - Elizabeth A Hunter
- U.S. Geological Survey, Virginia Cooperative Fish and Wildlife Research Unit, Department of Fisheries and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, USA
| | - Ana D Davidson
- Colorado Natural Heritage Program, Colorado State University, Fort Collins, Colorado, USA
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA
| |
Collapse
|
4
|
Duniway MC, Benson C, Nauman TW, Knight A, Bradford JB, Munson SM, Witwicki D, Livensperger C, Van Scoyoc M, Fisk TT, Thoma D, Miller ME. Geologic, geomorphic, and edaphic underpinnings of dryland ecosystems: Colorado Plateau landscapes in a changing world. Ecosphere 2022. [DOI: 10.1002/ecs2.4273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
| | | | - Travis W. Nauman
- US Geological Survey Southwest Biological Science Center Moab Utah USA
| | - Anna Knight
- US Geological Survey Southwest Biological Science Center Moab Utah USA
| | - John B. Bradford
- US Geological Survey Southwest Biological Science Center Flagstaff Arizona USA
| | - Seth M. Munson
- US Geological Survey Southwest Biological Science Center Flagstaff Arizona USA
| | - Dana Witwicki
- National Park Service Northern Colorado Plateau Network Moab Utah USA
- National Park Service Natural Resource Condition Assessment Fort Collins Colorado USA
| | - Carolyn Livensperger
- National Park Service Northern Colorado Plateau Network Moab Utah USA
- National Park Service Capitol Reef National Park Fruita Utah USA
| | | | - Terry T. Fisk
- National Park Service Southeast Utah Group Parks Moab Utah USA
- National Park Service Water Resources Division Fort Collins Colorado USA
| | - David Thoma
- National Park Service Northern Colorado Plateau Network Moab Utah USA
| | - Mark E. Miller
- National Park Service Southeast Utah Group Parks Moab Utah USA
- National Park Service Wrangell‐St. Elias National Park and Preserve Copper Center Alaska USA
| |
Collapse
|
5
|
Elias E, Savoy HM, Swanson DA, Cohnstaedt LW, Peters DPC, Derner JD, Pelzel‐McCluskey A, Drolet B, Rodriguez L. Landscape dynamics of a vector‐borne disease in the western
US
: How vector–habitat relationships inform disease hotspots. Ecosphere 2022. [DOI: 10.1002/ecs2.4267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Emile Elias
- US Department of Agriculture, Agricultural Research Service Jornada Experimental Range Unit Las Cruces New Mexico USA
| | - Heather M. Savoy
- US Department of Agriculture, Agricultural Research Service, Big Data Initiative and the SCINet Program for Scientific Computing Office of National Programs Beltsville Maryland USA
| | - Dustin A. Swanson
- US Department of Agriculture, Agricultural Research Service, Arthropod‐Borne Animal Diseases Research Unit Center for Grain and Animal Health Research Manhattan Kansas USA
| | - Lee W. Cohnstaedt
- US Department of Agriculture, Agricultural Research Service, Arthropod‐Borne Animal Diseases Research Unit Center for Grain and Animal Health Research Manhattan Kansas USA
| | - Debra P. C. Peters
- US Department of Agriculture, Agricultural Research Service, Big Data Initiative and the SCINet Program for Scientific Computing Office of National Programs Beltsville Maryland USA
| | - Justin D. Derner
- US Department of Agriculture, Agricultural Research Service Rangeland Resources and Systems Research Unit Cheyenne Wyoming USA
| | - Angela Pelzel‐McCluskey
- US Department of Agriculture, Animal and Plant Health Inspection Service Veterinary Services Fort Collins Colorado USA
| | - Barbara Drolet
- US Department of Agriculture, Agricultural Research Service, Arthropod‐Borne Animal Diseases Research Unit Center for Grain and Animal Health Research Manhattan Kansas USA
| | - Luis Rodriguez
- US Department of Agriculture, Agricultural Research Service Foreign Animal Disease Research Unit, Plum Island Animal Disease Center Orient Point New York USA
| |
Collapse
|
6
|
Sports Economic Mining Algorithm Based on Association Analysis and Big Data Model. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:1518202. [PMID: 35655506 PMCID: PMC9152385 DOI: 10.1155/2022/1518202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/01/2022] [Accepted: 04/13/2022] [Indexed: 12/15/2022]
Abstract
With the implementation of national strategies such as sports power and national fitness, the sports economy has become an important element of high-quality national development, and the demand for sports economy and management talents is greatly increased. Particularly in the new area with big data as the typical feature, the teaching content, teaching method, and teaching mode of sports economics and management majors have put forward new requirements. The continuous progress of storage and network technology has prompted the generation of massive multisource spatiotemporal data in various fields. The advantage of association analysis algorithms is that they are easy to code and implement. The relationships found by association analysis can take two forms: frequent itemsets or association rules. We use correlation analysis methods to perform correlation learning between sports economy and related big data and thus improve the development of sports economy. Mining and analyzing the relevant big data can precisely reveal the problems of sports economic development and can realize the fine management of sports, thus contributing to the healthy development of sports. Mastering the skills of acquiring, analyzing, and applying big data is the core content of sports economic analysis. The sports economy has refined and intelligent management means, and its adoption of virtual reality reflects the current situation and development trend of the sports business, which further highlights the status and role of multisource big data in the sports economy. Based on these, this paper proposed a sports economy mining algorithm in view of the correlation analysis and big data model. Then, we verified the effectiveness of the model through experiments, which laid the foundation for the development of the sports economy.
Collapse
|
7
|
Burruss ND, Peters DPC, Huang H, Yao J. Simulated distribution of
Eragrostis lehmanniana
(Lehmann lovegrass): Soil–climate interactions complicate predictions. Ecosphere 2022. [DOI: 10.1002/ecs2.3974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- N. Dylan Burruss
- Jornada Basin Long Term Ecological Research Program New Mexico State University Las Cruces New Mexico USA
| | - Debra P. C. Peters
- Jornada Basin Long Term Ecological Research Program New Mexico State University Las Cruces New Mexico USA
- Jornada Experimental Range Unit US Department of Agriculture, Agricultural Research Service Las Cruces New Mexico USA
- SCINet/Big Data Program US Department of Agriculture, Agricultural Research Service Beltsville Maryland USA
| | - Haitao Huang
- Jornada Basin Long Term Ecological Research Program New Mexico State University Las Cruces New Mexico USA
- SCINet/Big Data Program US Department of Agriculture, Agricultural Research Service Beltsville Maryland USA
| | - Jin Yao
- Jornada Basin Long Term Ecological Research Program New Mexico State University Las Cruces New Mexico USA
- Jornada Experimental Range Unit US Department of Agriculture, Agricultural Research Service Las Cruces New Mexico USA
| |
Collapse
|
8
|
Predicting the Geographic Range of an Invasive Livestock Disease across the Contiguous USA under Current and Future Climate Conditions. CLIMATE 2021. [DOI: 10.3390/cli9110159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Vesicular stomatitis (VS) is the most common vesicular livestock disease in North America. Transmitted by direct contact and by several biting insect species, this disease results in quarantines and animal movement restrictions in horses, cattle and swine. As changes in climate drive shifts in geographic distributions of vectors and the viruses they transmit, there is considerable need to improve understanding of relationships among environmental drivers and patterns of disease occurrence. Multidisciplinary approaches integrating pathology, ecology, climatology, and biogeophysics are increasingly relied upon to disentangle complex relationships governing disease. We used a big data model integration approach combined with machine learning to estimate the potential geographic range of VS across the continental United States (CONUS) under long-term mean climate conditions over the past 30 years. The current extent of VS is confined to the western portion of the US and is related to summer and winter precipitation, winter maximum temperature, elevation, fall vegetation biomass, horse density, and proximity to water. Comparison with a climate-only model illustrates the importance of current processes-based parameters and identifies regions where uncertainty is likely to be greatest if mechanistic processes change. We then forecast shifts in the range of VS using climate change projections selected from CMIP5 climate models that most realistically simulate seasonal temperature and precipitation. Climate change scenarios that altered climatic conditions resulted in greater changes to potential range of VS, generally had non-uniform impacts in core areas of the current potential range of VS and expanded the range north and east. We expect that the heterogeneous impacts of climate change across the CONUS will be exacerbated with additional changes in land use and land cover affecting biodiversity and hydrological cycles that are connected to the ecology of insect vectors involved in VS transmission.
Collapse
|
9
|
McCord SE, Webb NP, Van Zee JW, Burnett SH, Christensen EM, Courtright EM, Laney CM, Lunch C, Maxwell C, Karl JW, Slaughter A, Stauffer NG, Tweedie C. Provoking a Cultural Shift in Data Quality. Bioscience 2021; 71:647-657. [PMID: 34084097 PMCID: PMC8169311 DOI: 10.1093/biosci/biab020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ecological studies require quality data to describe the nature of ecological processes and to advance understanding of ecosystem change. Increasing access to big data has magnified both the burden and the complexity of ensuring quality data. The costs of errors in ecology include low use of data, increased time spent cleaning data, and poor reproducibility that can result in a misunderstanding of ecosystem processes and dynamics, all of which can erode the efficacy of and trust in ecological research. Although conceptual and technological advances have improved ecological data access and management, a cultural shift is needed to embed data quality as a cultural practice. We present a comprehensive data quality framework to evoke this cultural shift. The data quality framework flexibly supports different collaboration models, supports all types of ecological data, and can be used to describe data quality within both short- and long-term ecological studies.
Collapse
Affiliation(s)
- Sarah E McCord
- US Department of Agriculture ARS Jornada Experimental Range, Las Cruces, New Mexico, United States
| | - Nicholas P Webb
- US Department of Agriculture ARS Jornada Experimental Range, Las Cruces, New Mexico, United States
| | - Justin W Van Zee
- US Department of Agriculture ARS Jornada Experimental Range, Las Cruces, New Mexico, United States
| | - Sarah H Burnett
- Bureau of Land Management, National Operations Center, Denver, Colorado, United States
| | - Erica M Christensen
- US Department of Agriculture ARS Jornada Experimental Range, Las Cruces, New Mexico, United States
| | - Ericha M Courtright
- US Department of Agriculture ARS Jornada Experimental Range, Las Cruces, New Mexico, United States
| | - Christine M Laney
- Battelle-National Ecological Observatory Network, Boulder, Colorado, United States
| | - Claire Lunch
- US Department of Agriculture ARS Jornada Experimental Range, Las Cruces, New Mexico, United States
| | - Connie Maxwell
- New Mexico State University, in Las Cruces, New Mexico,United States
| | - Jason W Karl
- Department of Forest, Rangeland, and Fire Sciences, University of Idaho, Moscow, Idaho, United States
| | - Amalia Slaughter
- US Department of Agriculture ARS Jornada Experimental Range, Las Cruces, New Mexico, United States
| | - Nelson G Stauffer
- US Department of Agriculture ARS Jornada Experimental Range, Las Cruces, New Mexico, United States
| | - Craig Tweedie
- University of Texas-El Paso, El Paso, Texas, United States
| |
Collapse
|
10
|
Graham EB, Averill C, Bond-Lamberty B, Knelman JE, Krause S, Peralta AL, Shade A, Smith AP, Cheng SJ, Fanin N, Freund C, Garcia PE, Gibbons SM, Van Goethem MW, Guebila MB, Kemppinen J, Nowicki RJ, Pausas JG, Reed SP, Rocca J, Sengupta A, Sihi D, Simonin M, Słowiński M, Spawn SA, Sutherland I, Tonkin JD, Wisnoski NI, Zipper SC. Toward a Generalizable Framework of Disturbance Ecology Through Crowdsourced Science. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.588940] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Disturbances fundamentally alter ecosystem functions, yet predicting their impacts remains a key scientific challenge. While the study of disturbances is ubiquitous across many ecological disciplines, there is no agreed-upon, cross-disciplinary foundation for discussing or quantifying the complexity of disturbances, and no consistent terminology or methodologies exist. This inconsistency presents an increasingly urgent challenge due to accelerating global change and the threat of interacting disturbances that can destabilize ecosystem responses. By harvesting the expertise of an interdisciplinary cohort of contributors spanning 42 institutions across 15 countries, we identified an essential limitation in disturbance ecology: the word ‘disturbance’ is used interchangeably to refer to both the events that cause, and the consequences of, ecological change, despite fundamental distinctions between the two meanings. In response, we developed a generalizable framework of ecosystem disturbances, providing a well-defined lexicon for understanding disturbances across perspectives and scales. The framework results from ideas that resonate across multiple scientific disciplines and provides a baseline standard to compare disturbances across fields. This framework can be supplemented by discipline-specific variables to provide maximum benefit to both inter- and intra-disciplinary research. To support future syntheses and meta-analyses of disturbance research, we also encourage researchers to be explicit in how they define disturbance drivers and impacts, and we recommend minimum reporting standards that are applicable regardless of scale. Finally, we discuss the primary factors we considered when developing a baseline framework and propose four future directions to advance our interdisciplinary understanding of disturbances and their social-ecological impacts: integrating across ecological scales, understanding disturbance interactions, establishing baselines and trajectories, and developing process-based models and ecological forecasting initiatives. Our experience through this process motivates us to encourage the wider scientific community to continue to explore new approaches for leveraging Open Science principles in generating creative and multidisciplinary ideas.
Collapse
|
11
|
Soranno PA, Cheruvelil KS, Liu B, Wang Q, Tan PN, Zhou J, King KBS, McCullough IM, Stachelek J, Bartley M, Filstrup CT, Hanks EM, Lapierre JF, Lottig NR, Schliep EM, Wagner T, Webster KE. Ecological prediction at macroscales using big data: Does sampling design matter? ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e02123. [PMID: 32160362 DOI: 10.1002/eap.2123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 12/13/2019] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Although ecosystems respond to global change at regional to continental scales (i.e., macroscales), model predictions of ecosystem responses often rely on data from targeted monitoring of a small proportion of sampled ecosystems within a particular geographic area. In this study, we examined how the sampling strategy used to collect data for such models influences predictive performance. We subsampled a large and spatially extensive data set to investigate how macroscale sampling strategy affects prediction of ecosystem characteristics in 6,784 lakes across a 1.8-million-km2 area. We estimated model predictive performance for different subsets of the data set to mimic three common sampling strategies for collecting observations of ecosystem characteristics: random sampling design, stratified random sampling design, and targeted sampling. We found that sampling strategy influenced model predictive performance such that (1) stratified random sampling designs did not improve predictive performance compared to simple random sampling designs and (2) although one of the scenarios that mimicked targeted (non-random) sampling had the poorest performing predictive models, the other targeted sampling scenarios resulted in models with similar predictive performance to that of the random sampling scenarios. Our results suggest that although potential biases in data sets from some forms of targeted sampling may limit predictive performance, compiling existing spatially extensive data sets can result in models with good predictive performance that may inform a wide range of science questions and policy goals related to global change.
Collapse
Affiliation(s)
- Patricia A Soranno
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Road, East Lansing, Michigan, 48824, USA
| | - Kendra Spence Cheruvelil
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Road, East Lansing, Michigan, 48824, USA
- Lyman Briggs College, Michigan State University, 919 East Shaw Lane, East Lansing, Michigan, 48825, USA
| | - Boyang Liu
- Department of Computer Science and Engineering, Michigan State University, 428 South Shaw Lane, East Lansing, Michigan, 48824, USA
| | - Qi Wang
- Department of Computer Science and Engineering, Michigan State University, 428 South Shaw Lane, East Lansing, Michigan, 48824, USA
| | - Pang-Ning Tan
- Department of Computer Science and Engineering, Michigan State University, 428 South Shaw Lane, East Lansing, Michigan, 48824, USA
| | - Jiayu Zhou
- Department of Computer Science and Engineering, Michigan State University, 428 South Shaw Lane, East Lansing, Michigan, 48824, USA
| | - Katelyn B S King
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Road, East Lansing, Michigan, 48824, USA
| | - Ian M McCullough
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Road, East Lansing, Michigan, 48824, USA
| | - Joseph Stachelek
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Road, East Lansing, Michigan, 48824, USA
| | - Meridith Bartley
- Department of Statistics, The Pennsylvania State University, 324 Thomas Building, University Park, Pennsylvania, 16802, USA
| | - Christopher T Filstrup
- Natural Resources Research Institute, University of Minnesota Duluth, 5013 Miller Trunk Highway, Duluth, Minnesota, 55811, USA
| | - Ephraim M Hanks
- Department of Statistics, The Pennsylvania State University, 324 Thomas Building, University Park, Pennsylvania, 16802, USA
| | - Jean-François Lapierre
- Sciences Biologiques, Universite de Montreal, Pavillon Marie-Victorin, CP 6128, succursale Centre-Ville, Montreal, Quebec, H3C 3J7, Canada
| | - Noah R Lottig
- Center for Limnology Trout Lake Station, University of Wisconsin Madison, Boulder Junction, Wisconsin, 54512, USA
| | - Erin M Schliep
- Department of Statistics, University of Missouri, 146 Middlebush Hall, Columbia, Missouri, 65211, USA
| | - Tyler Wagner
- U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research Unit, Pennsylvania State University, Forest Resources Building, University Park, Pennsylvania, 16802, USA
| | - Katherine E Webster
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Road, East Lansing, Michigan, 48824, USA
| |
Collapse
|
12
|
Alberti M, Palkovacs E, Roches S, Meester L, Brans K, Govaert L, Grimm NB, Harris NC, Hendry AP, Schell CJ, Szulkin M, Munshi-South J, Urban MC, Verrelli BC. The Complexity of Urban Eco-evolutionary Dynamics. Bioscience 2020. [DOI: 10.1093/biosci/biaa079] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Abstract
Urbanization is changing Earth's ecosystems by altering the interactions and feedbacks between the fundamental ecological and evolutionary processes that maintain life. Humans in cities alter the eco-evolutionary play by simultaneously changing both the actors and the stage on which the eco-evolutionary play takes place. Urbanization modifies land surfaces, microclimates, habitat connectivity, ecological networks, food webs, species diversity, and species composition. These environmental changes can lead to changes in phenotypic, genetic, and cultural makeup of wild populations that have important consequences for ecosystem function and the essential services that nature provides to human society, such as nutrient cycling, pollination, seed dispersal, food production, and water and air purification. Understanding and monitoring urbanization-induced evolutionary changes is important to inform strategies to achieve sustainability. In the present article, we propose that understanding these dynamics requires rigorous characterization of urbanizing regions as rapidly evolving, tightly coupled human–natural systems. We explore how the emergent properties of urbanization affect eco-evolutionary dynamics across space and time. We identify five key urban drivers of change—habitat modification, connectivity, heterogeneity, novel disturbances, and biotic interactions—and highlight the direct consequences of urbanization-driven eco-evolutionary change for nature's contributions to people. Then, we explore five emerging complexities—landscape complexity, urban discontinuities, socio-ecological heterogeneity, cross-scale interactions, legacies and time lags—that need to be tackled in future research. We propose that the evolving metacommunity concept provides a powerful framework to study urban eco-evolutionary dynamics.
Collapse
Affiliation(s)
- Marina Alberti
- Department of Urban Design and Planning, University of Washington, Seattle, Washington
| | - Eric P Palkovacs
- Department of Ecology and Evolutionary Biology,University of California, Santa Cruz, California
| | | | - Luc De Meester
- Laboratory of Aquatic Ecology Evolution, and Conservation, Katholieke Universiteit Leuven, Leuven, Belgium
- Leibniz Institut für Gewässerökologie und Binnenfischerei, Berlin, Germany, and with the Institute of Biology at Freie Universität Berlin, also in Berlin, Germany
| | - Kristien I Brans
- Laboratory of Aquatic Ecology Evolution, and Conservation, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Lynn Govaert
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland; with the Department of Aquatic Ecology, in the Swiss Federal Institute of Aquatic Science and Technology, in Dübendorf, Switzerland; and with the University Research Priority Programme on Global Change and Biodiversity at the University of Zurich, in Zurich, Switzerland
| | | | - Nyeema C Harris
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Andrew P Hendry
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Christopher J Schell
- Department of Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, Washington
| | | | - Jason Munshi-South
- Louis Calder Center Biological Field Station, Fordham University, Armonk, New York
| | - Mark C Urban
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut
| | - Brian C Verrelli
- Center for Life Sciences Education, Virginia Commonwealth University, Richmond, Virginia
| |
Collapse
|
13
|
Peters DPC, McVey DS, Elias EH, Pelzel‐McCluskey AM, Derner JD, Burruss ND, Schrader TS, Yao J, Pauszek SJ, Lombard J, Rodriguez LL. Big data–model integration and AI for vector‐borne disease prediction. Ecosphere 2020. [DOI: 10.1002/ecs2.3157] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Debra P. C. Peters
- US Department of Agriculture Agricultural Research Service Jornada Experimental Range Unit, and Jornada Basin Long Term Ecological Research Program New Mexico State University Las Cruces New Mexico 88003 USA
| | - D. Scott McVey
- US Department of Agriculture Agricultural Research Service Center for Grain and Animal Health Research Arthropod‐Borne Animal Diseases Research Unit Manhattan Kansas 66506 USA
| | - Emile H. Elias
- US Department of Agriculture Agricultural Research Service Jornada Experimental Range Unit, and Jornada Basin Long Term Ecological Research Program New Mexico State University Las Cruces New Mexico 88003 USA
| | - Angela M. Pelzel‐McCluskey
- US Department of Agriculture, Animal and Plant Health Inspection Service Veterinary Services Fort Collins Colorado 80526 USA
| | - Justin D. Derner
- US Department of Agriculture Agricultural Research Service Rangeland Resources and Systems Research Unit Cheyenne Wyoming 82009 USA
| | - N. Dylan Burruss
- Jornada Experimental Range New Mexico State University Las Cruces New Mexico 88003 USA
| | - T. Scott Schrader
- US Department of Agriculture Agricultural Research Service Jornada Experimental Range Unit, and Jornada Basin Long Term Ecological Research Program New Mexico State University Las Cruces New Mexico 88003 USA
| | - Jin Yao
- US Department of Agriculture Agricultural Research Service Jornada Experimental Range Unit, and Jornada Basin Long Term Ecological Research Program New Mexico State University Las Cruces New Mexico 88003 USA
| | - Steven J. Pauszek
- US Department of Agriculture, Agricultural Research Service Plum Island Animal Disease Center Orient Point New York 11957 USA
| | - Jason Lombard
- US Department of Agriculture, Animal and Plant Health Inspection Service Veterinary Services Fort Collins Colorado 80526 USA
| | - Luis L. Rodriguez
- US Department of Agriculture, Agricultural Research Service Plum Island Animal Disease Center Orient Point New York 11957 USA
| |
Collapse
|
14
|
Peck DE, Reeves WK, Pelzel-McCluskey AM, Derner JD, Drolet B, Cohnstaedt LW, Swanson D, McVey DS, Rodriguez LL, Peters DPC. Management Strategies for Reducing the Risk of Equines Contracting Vesicular Stomatitis Virus (VSV) in the Western United States. J Equine Vet Sci 2020; 90:103026. [PMID: 32534788 DOI: 10.1016/j.jevs.2020.103026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 04/12/2020] [Accepted: 04/12/2020] [Indexed: 11/24/2022]
Abstract
Vesicular stomatitis viruses (VSVs) cause a condition known as vesicular stomatitis (VS), which results in painful lesions in equines, cattle, swine, and camelids, and when transmitted to humans, can cause flu-like symptoms. When animal premises are affected by VS, they are subject to a quarantine. The equine industry more broadly may incur economic losses due to interruptions of animal trade and transportation to shows, competitions, and other events. Equine owners, barn managers, and veterinarians can take proactive measures to reduce the risk of equines contracting VS. To identify appropriate risk management strategies, it helps to understand which biting insects are capable of transmitting the virus to animals, and to identify these insect vectors' preferred habitats and behaviors. We make this area of science more accessible to equine owners, barn managers, and veterinarians, by (1) translating the most relevant scientific information about biting insect vectors of VSV and (2) identifying practical management strategies that might reduce the risk of equines contracting VSV from infectious biting insects or from other equines already infected with VSV. We address transmission risk at four different spatial scales-the animal, the barn/shelter, the barnyard/premises, and the surrounding environment/neighborhood-noting that a multiscale and spatially collaborative strategy may be needed to reduce the risk of VS.
Collapse
Affiliation(s)
| | - Will K Reeves
- USDA Animal and Plant Health Inspection Service, Fort Collins, CO
| | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Kulmatiski A, Yu K, Mackay DS, Holdrege MC, Staver AC, Parolari AJ, Liu Y, Majumder S, Trugman AT. Forecasting semi-arid biome shifts in the Anthropocene. THE NEW PHYTOLOGIST 2020; 226:351-361. [PMID: 31853979 DOI: 10.1111/nph.16381] [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: 09/19/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Shrub encroachment, forest decline and wildfires have caused large-scale changes in semi-arid vegetation over the past 50 years. Climate is a primary determinant of plant growth in semi-arid ecosystems, yet it remains difficult to forecast large-scale vegetation shifts (i.e. biome shifts) in response to climate change. We highlight recent advances from four conceptual perspectives that are improving forecasts of semi-arid biome shifts. Moving from small to large scales, first, tree-level models that simulate the carbon costs of drought-induced plant hydraulic failure are improving predictions of delayed-mortality responses to drought. Second, tracer-informed water flow models are improving predictions of species coexistence as a function of climate. Third, new applications of ecohydrological models are beginning to simulate small-scale water movement processes at large scales. Fourth, remotely-sensed measurements of plant traits such as relative canopy moisture are providing early-warning signals that predict forest mortality more than a year in advance. We suggest that a community of researchers using modeling approaches (e.g. machine learning) that can integrate these perspectives will rapidly improve forecasts of semi-arid biome shifts. Better forecasts can be expected to help prevent catastrophic changes in vegetation states by identifying improved monitoring approaches and by prioritizing high-risk areas for management.
Collapse
Affiliation(s)
- Andrew Kulmatiski
- Department of Wildland Resources and the Ecology Center, Utah State University, Logan, UT, 84322-5230, USA
| | - Kailiang Yu
- Department of Environmental Systems Science, ETH Zurich, Universitatstrasse 16, 8092, Zurich, Switzerland
- Laboratoire des Sciences du Climat et de l'Environnement, IPSL-LSCE CEA/CNRS/UVSQ, F-91191, Gif-sur-Yvette, France
| | - D Scott Mackay
- Department of Geography and Department of Environment and Sustainability, University at Buffalo, Buffalo, NY, 14261, USA
| | - Martin C Holdrege
- Department of Wildland Resources and the Ecology Center, Utah State University, Logan, UT, 84322-5230, USA
| | - Ann Carla Staver
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
| | - Anthony J Parolari
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI, 53233, USA
| | - Yanlan Liu
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Sabiha Majumder
- Department of Physics, Indian Institute of Science, Bengaluru, 560012, India
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, 560012, India
| | - Anna T Trugman
- Department of Geography, University of California Santa Barbara, Santa Barbara, CA, 93117, USA
| |
Collapse
|
16
|
Gaiser EE, Bell DM, Castorani MCN, Childers DL, Groffman PM, Jackson CR, Kominoski JS, Peters DPC, Pickett STA, Ripplinger J, Zinnert JC. Long-Term Ecological Research and Evolving Frameworks of Disturbance Ecology. Bioscience 2020. [DOI: 10.1093/biosci/biz162] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
AbstractDetecting and understanding disturbance is a challenge in ecology that has grown more critical with global environmental change and the emergence of research on social–ecological systems. We identify three areas of research need: developing a flexible framework that incorporates feedback loops between social and ecological systems, anticipating whether a disturbance will change vulnerability to other environmental drivers, and incorporating changes in system sensitivity to disturbance in the face of global changes in environmental drivers. In the present article, we review how discoveries from the US Long Term Ecological Research (LTER) Network have influenced theoretical paradigms in disturbance ecology, and we refine a framework for describing social–ecological disturbance that addresses these three challenges. By operationalizing this framework for seven LTER sites spanning distinct biomes, we show how disturbance can maintain or alter ecosystem state, drive spatial patterns at landscape scales, influence social–ecological interactions, and cause divergent outcomes depending on other environmental changes.
Collapse
Affiliation(s)
- Evelyn E Gaiser
- Department of Biological Sciences, Institute of Environment, Florida International University, Miami, Florida
| | - David M Bell
- Pacific Northwest Research Station, under the US Department of Agriculture Forest Service, Corvallis, Oregon
| | - Max C N Castorani
- Department of Environmental Sciences, University of Virginia, Charlottesville, Virginia
| | | | - Peter M Groffman
- City University of New York's Advanced Science Research Center, Graduate Center, New York, New York, and with the Cary Institute of Ecosystem Studies, Millbrook, New York
| | - C Rhett Jackson
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia
| | - John S Kominoski
- Department of Biological Sciences, Institute of Environment, Florida International University, Miami, Florida
| | - Debra P C Peters
- US Department of Agriculture Agricultural Research Service's Jornada Experimental Range and Jornada Basin LTER Program, New Mexico State University, Las Cruces, New Mexico
| | | | - Julie Ripplinger
- Department of Botany and Plant Sciences, University of California—Riverside, Riverside, California
| | - Julie C Zinnert
- Department of Biology at Virginia Commonwealth University, Richmond, Virginia
| |
Collapse
|
17
|
Williams HJ, Taylor LA, Benhamou S, Bijleveld AI, Clay TA, de Grissac S, Demšar U, English HM, Franconi N, Gómez-Laich A, Griffiths RC, Kay WP, Morales JM, Potts JR, Rogerson KF, Rutz C, Spelt A, Trevail AM, Wilson RP, Börger L. Optimizing the use of biologgers for movement ecology research. J Anim Ecol 2019; 89:186-206. [PMID: 31424571 DOI: 10.1111/1365-2656.13094] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 08/08/2019] [Indexed: 10/26/2022]
Abstract
The paradigm-changing opportunities of biologging sensors for ecological research, especially movement ecology, are vast, but the crucial questions of how best to match the most appropriate sensors and sensor combinations to specific biological questions and how to analyse complex biologging data, are mostly ignored. Here, we fill this gap by reviewing how to optimize the use of biologging techniques to answer questions in movement ecology and synthesize this into an Integrated Biologging Framework (IBF). We highlight that multisensor approaches are a new frontier in biologging, while identifying current limitations and avenues for future development in sensor technology. We focus on the importance of efficient data exploration, and more advanced multidimensional visualization methods, combined with appropriate archiving and sharing approaches, to tackle the big data issues presented by biologging. We also discuss the challenges and opportunities in matching the peculiarities of specific sensor data to the statistical models used, highlighting at the same time the large advances which will be required in the latter to properly analyse biologging data. Taking advantage of the biologging revolution will require a large improvement in the theoretical and mathematical foundations of movement ecology, to include the rich set of high-frequency multivariate data, which greatly expand the fundamentally limited and coarse data that could be collected using location-only technology such as GPS. Equally important will be the establishment of multidisciplinary collaborations to catalyse the opportunities offered by current and future biologging technology. If this is achieved, clear potential exists for developing a vastly improved mechanistic understanding of animal movements and their roles in ecological processes and for building realistic predictive models.
Collapse
Affiliation(s)
- Hannah J Williams
- Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - Lucy A Taylor
- Save the Elephants, Nairobi, Kenya.,Department of Zoology, University of Oxford, Oxford, UK
| | - Simon Benhamou
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS Montpellier, Montpellier, France
| | - Allert I Bijleveld
- NIOZ Royal Netherlands Institute for Sea Research, Department of Coastal Systems, Utrecht University, Den Burg, The Netherlands
| | - Thomas A Clay
- School of Environmental Sciences, University of Liverpool, Liverpool, UK
| | - Sophie de Grissac
- Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - Urška Demšar
- School of Geography & Sustainable Development, University of St Andrews, St Andrews, UK
| | - Holly M English
- Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - Novella Franconi
- Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - Agustina Gómez-Laich
- Instituto de Biología de Organismos Marinos (IBIOMAR), CONICET, Puerto Madryn, Chubut, Argentina
| | - Rachael C Griffiths
- Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - William P Kay
- Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - Juan Manuel Morales
- Grupo de Ecología Cuantitativa, INIBIOMA-Universidad Nacional del Comahue, CONICET, Bariloche, Argentina
| | - Jonathan R Potts
- School of Mathematics and Statistics, University of Sheffield, Sheffield, UK
| | | | - Christian Rutz
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
| | - Anouk Spelt
- Department of Aerospace Engineering, University of Bristol, University Walk, UK
| | - Alice M Trevail
- School of Environmental Sciences, University of Liverpool, Liverpool, UK
| | - Rory P Wilson
- Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - Luca Börger
- Department of Biosciences, College of Science, Swansea University, Swansea, UK
| |
Collapse
|
18
|
|