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Nabias J, Barbaro L, Fontaine B, Dupuy J, Couzi L, Vallé C, Lorrilliere R. Reassessment of French breeding bird population sizes using citizen science and accounting for species detectability. PeerJ 2024; 12:e17889. [PMID: 39221279 PMCID: PMC11363910 DOI: 10.7717/peerj.17889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 07/18/2024] [Indexed: 09/04/2024] Open
Abstract
Higher efficiency in large-scale and long-term biodiversity monitoring can be obtained through the use of Essential Biodiversity Variables, among which species population sizes provide key data for conservation programs. Relevant estimations and assessment of actual population sizes are critical for species conservation, especially in the current context of global biodiversity erosion. However, knowledge on population size varies greatly, depending on species conservation status and ranges. While the most threatened or restricted-range species generally benefit from exhaustive counts and surveys, monitoring common and widespread species population size tends to be neglected or is simply more challenging to achieve. In such a context, citizen science (CS) is a powerful tool for the long-term monitoring of common species through the engagement of various volunteers, permitting data acquisition on the long term and over large spatial scales. Despite this substantially increased sampling effort, detectability issues imply that even common species may remain unnoticed at suitable sites. The use of structured CS schemes, including repeated visits, enables to model the detection process, permitting reliable inferences of population size estimates. Here, we relied on a large French structured CS scheme (EPOC-ODF) comprising 27,156 complete checklists over 3,873 sites collected during the 2021-2023 breeding seasons to estimate the population size of 63 common bird species using hierarchical distance sampling (HDS). These population size estimates were compared to the previous expert-based French breeding bird atlas estimations, which did not account for detectability issues. We found that population size estimates from the former French breeding bird atlas were lower than those estimated using HDS for 65% of species. Such a prevalence of lower estimations is likely due to more conservative estimates inferred from semi-quantitative expert-based assessments used for the previous atlas. We also found that species with long-range songs such as the Common Cuckoo (Cuculus canorus), Eurasian Hoopoe (Upupa epops) or the Eurasian Blackbird (Turdus merula) had, in contrast, higher estimated population sizes in the previous atlas than in our HDS models. Our study highlights the need to rely on sound statistical methodology to ensure reliable ecological inferences with adequate uncertainty estimation and advocates for a higher reliance on structured CS in support of long-term biodiversity monitoring.
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Affiliation(s)
- Jean Nabias
- Muséum National d’Histoire Naturelle, Centre d’Ecologie et des Sciences de la Conservation, Paris, France
- Ligue Pour la Protection des Oiseaux, Rochefort, France
| | - Luc Barbaro
- Muséum National d’Histoire Naturelle, Centre d’Ecologie et des Sciences de la Conservation, Paris, France
- Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Auzeville-Tolosane, France
| | - Benoît Fontaine
- Muséum National d’Histoire Naturelle, Centre d’Ecologie et des Sciences de la Conservation, Paris, France
- Patrimoine Naturel, Office Français de la Biodiversité, Paris, France
| | - Jérémy Dupuy
- Ligue Pour la Protection des Oiseaux, Rochefort, France
| | - Laurent Couzi
- Ligue Pour la Protection des Oiseaux, Rochefort, France
| | - Clément Vallé
- Muséum National d’Histoire Naturelle, Centre d’Ecologie et des Sciences de la Conservation, Paris, France
| | - Romain Lorrilliere
- Muséum National d’Histoire Naturelle, Centre d’Ecologie et des Sciences de la Conservation, Paris, France
- Centre de Recherches sur la Biologie des Populations d’Oiseaux, Paris, France
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2
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Ruzi SA, Youngsteadt E, Cherveny AH, Kettenbach J, Levenson HK, Carley DS, Collazo JA, Irwin RE. Bee species richness through time in an urbanizing landscape of the southeastern United States. GLOBAL CHANGE BIOLOGY 2024; 30:e17060. [PMID: 38273538 DOI: 10.1111/gcb.17060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/10/2023] [Accepted: 11/03/2023] [Indexed: 01/27/2024]
Abstract
Compared to non-urban environments, cities host ecological communities with altered taxonomic diversity and functional trait composition. However, we know little about how these urban changes take shape over time. Using historical bee (Apoidea: Anthophila) museum specimens supplemented with online repositories and researcher collections, we investigated whether bee species richness tracked urban and human population growth over the past 118 years. We also determined which species were no longer collected, whether those species shared certain traits, and if collector behavior changed over time. We focused on Wake County, North Carolina, United States where human population size has increased over 16 times over the last century along with the urban area within its largest city, Raleigh, which has increased over four times. We estimated bee species richness with occupancy models, and rarefaction and extrapolation curves to account for imperfect detection and sample coverage. To determine if bee traits correlated with when species were collected, we compiled information on native status, nesting habits, diet breadth, and sociality. We used non-metric multidimensional scaling to determine if individual collectors contributed different bee assemblages over time. In total, there were 328 species collected in Wake County. We found that although bee species richness varied, there was no clear trend in bee species richness over time. However, recent collections (since 2003) were missing 195 species, and there was a shift in trait composition, particularly lost species were below-ground nesters. The top collectors in the dataset differed in how often they collected bee species, but this was not consistent between historic and contemporary time periods; some contemporary collectors grouped closer together than others, potentially due to focusing on urban habitats. Use of historical collections and complimentary analyses can fill knowledge gaps to help understand temporal patterns of species richness in taxonomic groups that may not have planned long-term data.
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Affiliation(s)
- Selina A Ruzi
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Elsa Youngsteadt
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
- Center for Geospatial Analytics, North Carolina State University, Raleigh, North Carolina, USA
| | - April Hamblin Cherveny
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Jessica Kettenbach
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
| | - Hannah K Levenson
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Danesha Seth Carley
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, USA
| | - Jaime A Collazo
- U.S. Geological Survey, North Carolina Cooperative Fish and Wildlife Research Unit, Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
| | - Rebecca E Irwin
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
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3
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Assessing the Influence of Anthropogenic Land-Use Changes on Bird Diversity and Feeding Guilds—A Case Study of Kalametiya Lagoon (Southern Sri Lanka). DIVERSITY 2023. [DOI: 10.3390/d15030383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Kalametiya Lagoon, a highly threatened Sri Lankan wetland, has undergone drastic hydrological changes in recent decades, due to an upstream irrigation project. These changes led to the invasion of the lagoon water by monospecific Sonneratia caseolaris mangrove stands and Typha angustifolia reedbeds. As Kalametiya has been a nationally recognized bird sanctuary since 1984, this invasion is expected to have brought significant changes upon local avifauna. Therefore, this study aimed at determining the lagoon’s current bird diversity and distribution in relation with habitat types and environmental variables. Thirty-seven point-count stations were studied, between January and April 2022. Seventy-nine bird species, including four endemic and ten nationally threatened species, were encountered during the study period. Invertebrate feeders and polyphages were the richest and most diverse guilds. Bird communities were also found richer and more diverse in T. angustifolia reedbeds than in S. caseolaris mangroves. As feeding guild composition was significantly influenced by several environmental variables (i.e., water nitrate content, water TDS, water pH, soil pH), guilds could have great potential as bioindicators of the ecosystem if further studies are done to explore these relationships. Considering the important bird diversity found in the new habitats, this research brings additional proof that a management aiming at restoring the lagoon to its past state would bring significant changes to its avifaunal community. These changes could, in the future, be more precisely defined by a thorough comparison with past inventories of the lagoon’s bird community.
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4
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Biodiversity assessment and ecotypology of the Taanzoult plain running water (Aguelmam Sidi Ali, Morocco). SCIENTIFIC AFRICAN 2023. [DOI: 10.1016/j.sciaf.2023.e01631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023] Open
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5
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Wright AD, Campbell Grant EH, Zipkin EF. A comparison of monitoring designs to assess wildlife community parameters across spatial scales. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2621. [PMID: 35389538 DOI: 10.1002/eap.2621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Dedicated long-term monitoring at appropriate spatial and temporal scales is necessary to understand biodiversity losses and develop effective conservation plans. Wildlife monitoring is often achieved by obtaining data at a combination of spatial scales, ranging from local to broad, to understand the status, trends, and drivers of individual species or whole communities and their dynamics. However, limited resources for monitoring necessitates tradeoffs in the scope and scale of data collection. Careful consideration of the spatial and temporal allocation of finite sampling effort is crucial for monitoring programs that span multiple spatial scales. Here we evaluate the ability of five monitoring designs-stratified random, weighted effort, indicator unit, rotating panel, and split panel-to recover parameter values that describe the status (occupancy), trends (change in occupancy), and drivers (spatially varying covariate and an autologistic term) of wildlife communities at two spatial scales. Using an amphibian monitoring program that spans a network of US national parks as a motivating example, we conducted a simulation study for a regional community occupancy sampling program to compare the monitoring designs across varying levels of sampling effort (ranging from 10% to 50%). We found that the stratified random design outperformed the other designs for most parameters of interest at both scales and was thus generally preferable in balancing the estimation of status, trends, and drivers across scales. However, we found that other designs had improved performance in specific situations. For example, the rotating panel design performed best at estimating spatial drivers at a regional level. Thus, our results highlight the nuanced scenarios in which various design strategies may be preferred and offer guidance as to how managers can balance common tradeoffs in large-scale and long-term monitoring programs in terms of the specific knowledge gained. Monitoring designs that improve accuracy in parameter estimates are needed to guide conservation policy and management decisions in the face of broad-scale environmental challenges, but the preferred design is sensitive to the specific objectives of a monitoring program.
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Affiliation(s)
- Alexander D Wright
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
| | - Evan H Campbell Grant
- SO Conte Anadromous Fish Research Laboratory, USGS Patuxent Wildlife Research Center, Turners Falls, Massachusetts, USA
| | - Elise F Zipkin
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
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6
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Bruneel S, Ho L, Van Echelpoel W, Schoeters A, Raat H, Moens T, Bermudez R, Luca S, Goethals P. Sampling errors and variability in video transects for assessment of reef fish assemblage structure and diversity. PLoS One 2022; 17:e0271043. [PMID: 35877762 PMCID: PMC9312474 DOI: 10.1371/journal.pone.0271043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/23/2022] [Indexed: 11/17/2022] Open
Abstract
Video monitoring is a rapidly evolving tool in aquatic ecological research because of its non-destructive ability to assess fish assemblages. Nevertheless, methodological considerations of video monitoring techniques are often overlooked, especially in more complex sampling designs, causing inefficient data collection, processing, and interpretation. In this study, we discuss how video transect sampling designs could be assessed and how the inter-observer variability, design errors and sampling variability should be quantified and accounted for. The study took place in the coastal areas of the Galapagos archipelago and consisted of a hierarchical repeated-observations sampling design with multiple observers. Although observer bias was negligible for the assessment of fish assemblage structure, diversity and counts of individual species, sampling variability caused by simple counting/detection errors, observer effects and instantaneous fish displacement was often important. Especially for the counts of individual species, sampling variability most often exceeded the variability of the transects and sites. An extensive part of the variability in the fish assemblage structure was explained by the different transects (13%), suggesting that a sufficiently high number of transects is required to account for the within-location variability. Longer transect lengths allowed a better representation of the fish assemblages as sampling variability decreased by 33% if transect length was increased from 10 to 50 meters. However, to increase precision, including more repeats was typically more efficient than using longer transect lengths. The results confirm the suitability of the technique to study reef fish assemblages, but also highlight the importance of a sound methodological assessment since different biological responses and sampling designs are associated with different levels of sampling variability, precision and ecological relevance. Therefore, besides the direct usefulness of the results, the procedures to establish them may be just as valuable for researchers aiming to optimize their own sampling technique and design.
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Affiliation(s)
- Stijn Bruneel
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Ghent, Belgium
- Marine Biology Research Group, Ghent University, Ghent, Belgium
- * E-mail:
| | - Long Ho
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Wout Van Echelpoel
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Amber Schoeters
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Heleen Raat
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Tom Moens
- Marine Biology Research Group, Ghent University, Ghent, Belgium
| | - Rafael Bermudez
- Galapagos Marine Research and Exploration, GMaRE, Joint ESPOL-CDF Program, Charles Darwin Research Station, Galapagos Islands, Ecuador
- Facultad de Ingeniería Marítima y Ciencias del Mar, Escuela Superior Politécnica del Litoral (ESPOL), Campus Gustavo Galindo, Guayaquil, Ecuador
| | - Stijn Luca
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Peter Goethals
- Department of Animal Sciences and Aquatic Ecology, Ghent University, Ghent, Belgium
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7
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van Noort S, Shaw SR, Copeland RS. Revision of the endemic African genus Dinapsis (Dinapsini, Megalyridae, Hymenoptera) with description of seven new species. Zookeys 2022; 1112:27-122. [PMID: 36760621 PMCID: PMC9848780 DOI: 10.3897/zookeys.1112.82307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/16/2022] [Indexed: 11/12/2022] Open
Abstract
The endemic Afrotropical genus Dinapsis is revised, and seven new species are described and illustrated: D.bicolor van Noort & Shaw, sp. nov., D.gamka van Noort & Shaw, sp. nov., D.igneus van Noort & Shaw, sp. nov., D.spinitibia van Noort & Shaw, sp. nov., D.taita van Noort & Shaw, sp. nov., D.tricolor Shaw & van Noort, sp. nov., D.zulu Shaw & van Noort, sp. nov. The distribution of the Central African Republican species D.centralis Shaw & van Noort, 2009 is extended to include Cameroon, Kenya and Uganda. Dinapsisturneri Waterston, 1922, previously only known from the poorly preserved holotype female, is redescribed based on newly collected specimens. The distribution of this Western Cape species is extended to include the Eastern and Northern Cape provinces of South Africa. Four distinct species groups within the genus are proposed and diagnosed. An illustrated identification key to all described species of Dinapsis is provided. Online interactive Lucid keys to Afrotropical megalyrid genera and Dinapsis species are available at http://www.waspweb.org.
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Affiliation(s)
- Simon van Noort
- Research and Exhibitions Department, South African Museum, Iziko Museums of South Africa, PO Box 61, Cape Town 8000 South AfricaSouth African Museum, Iziko Museums of South AfricaCape TownSouth Africa,Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch, 7701, South AfricaUniversity of Cape TownCape TownSouth Africa
| | - Scott Richard Shaw
- U.W. Insect Museum, Department of Ecosystem Science and Management (3354), University of Wyoming, 1000 East University Avenue, Laramie, Wyoming 82071-3354, USAUniversity of WyomingLaramieUnited States of America
| | - Robert S. Copeland
- International Centre of Insect Physiology and Ecology (ICIPE), P.O. Box 30772 Nairobi, KenyaInternational Centre of Insect Physiology and Ecology (ICIPE)NairobiKenya,Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington DC, USANational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
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8
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Hackworth ZJ, Felch JM, Murphy SM, Cox JJ. Detectability of common ravens (
Corvus corax
) in the eastern
USA
: Rapid assessment of a recolonizing species. Ecosphere 2022. [DOI: 10.1002/ecs2.4148] [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)
- Zachary J. Hackworth
- Department of Forestry and Natural Resources University of Kentucky Lexington Kentucky USA
| | - Joshua M. Felch
- Department of Forestry and Natural Resources University of Kentucky Lexington Kentucky USA
| | - Sean M. Murphy
- Department of Forestry and Natural Resources University of Kentucky Lexington Kentucky USA
| | - John J. Cox
- Department of Forestry and Natural Resources University of Kentucky Lexington Kentucky USA
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9
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Ankori‐Karlinsky R, Kalyuzhny M, Barnes KF, Wilson AM, Flather C, Renfrew R, Walsh J, Guk E, Kadmon R. North American Breeding Bird Survey underestimates regional bird richness compared to Breeding Bird Atlases. Ecosphere 2022. [DOI: 10.1002/ecs2.3925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Roi Ankori‐Karlinsky
- Department of Ecology, Evolution, and Environmental Biology Columbia University New York New York USA
| | - Michael Kalyuzhny
- Department of Ecology, Evolution & Behavior Institute of Life Sciences, The Hebrew University of Jerusalem, Campus Edmond J. Safra, Givat Ram Jerusalem Israel
| | | | - Andrew M. Wilson
- Environmental Studies, Science Center Gettysburg College Gettysburg Pennsylvania USA
| | - Curtis Flather
- USDA Forest Service, Rocky Mountain Research Station Fort Collins Colorado USA
| | - Rosalind Renfrew
- Rubenstein School of Environment and Natural Resources, The University of Vermont Burlington Vermont USA
| | - Joan Walsh
- Massachusetts Audubon Headquarters Lincoln Massachusetts USA
| | - Edna Guk
- Department of Geography, Faculty of Social Sciences The Hebrew University of Jerusalem, Mt. Scopus Jerusalem Israel
| | - Ronen Kadmon
- Department of Ecology, Evolution & Behavior Institute of Life Sciences, The Hebrew University of Jerusalem, Campus Edmond J. Safra, Givat Ram Jerusalem Israel
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10
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Tinoco BA, Latta SC, Astudillo PX, Nieto A, Graham CH. Temporal stability in species richness but reordering in species abundances within avian assemblages of a tropical Andes conservation hot spot. Biotropica 2021; 53:1673-1684. [PMID: 35874905 PMCID: PMC9293307 DOI: 10.1111/btp.13016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 07/13/2021] [Accepted: 08/30/2021] [Indexed: 11/28/2022]
Affiliation(s)
| | - Steven C. Latta
- National Aviary Allegheny Commons West Pittsburgh Pennsylvania USA
| | | | - Andrea Nieto
- Escuela de Biología Universidad del Azuay Cuenca Ecuador
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11
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Baumgardt JA, Morrison ML, Brennan LA, Thornley M, Campbell TA. Variation in herpetofauna detection probabilities: implications for study design. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:658. [PMID: 34533627 PMCID: PMC8448696 DOI: 10.1007/s10661-021-09424-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Population monitoring is fundamental for informing management decisions aimed at reducing the rapid rate of global biodiversity decline. Herpetofauna are experiencing declines worldwide and include species that are challenging to monitor. Raw counts and associated metrics such as richness indices are common for monitoring populations of herpetofauna; however, these methods are susceptible to bias as they fail to account for varying detection probabilities. Our goal was to develop a program for efficiently monitoring herpetofauna in southern Texas. Our objectives were to (1) estimate detection probabilities in an occupancy modeling framework using trap arrays for a diverse group of herpetofauna and (2) to evaluate the relative effectiveness of funnel traps, pitfall traps, and cover boards. We collected data with 36 arrays at 2 study sites in 2015 and 2016, for 2105 array-days resulting in 4839 detections of 51 species. We modeled occupancy for 21 species and found support for the hypothesis that detection probability varied over our sampling duration for 10 species and with rainfall for 10 species. For herpetofauna in our study, we found 14 and 12 species were most efficiently captured with funnel traps and pitfall traps, respectively, and no species were most efficiently captured with cover boards. Our results show that using methods that do not account for variations in detection probability are highly subject to bias unless the likelihood of false absences is minimized with exceptionally long capture durations. For monitoring herpetofauna in southern Texas, we recommend using arrays with funnel and pitfall traps and an analytical method such as occupancy modeling that accounts for variation in detection.
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Affiliation(s)
- Jeremy A Baumgardt
- Texas A&M Natural Resources Institute, 578 John Kimbrough Boulevard, College Station, TX, 77843, USA.
- Caesar Kleberg Wildlife Research Institute, Texas A&M University-Kingsville, MSC 218, 700 University Boulevard, Kingsville, TX, 78363, USA.
| | - Michael L Morrison
- Department of Rangeland, Wildlife and Fisheries Management, Texas A&M University, College Station, TX, 2258 TAMU77843, USA
| | - Leonard A Brennan
- Caesar Kleberg Wildlife Research Institute, Texas A&M University-Kingsville, MSC 218, 700 University Boulevard, Kingsville, TX, 78363, USA
| | - Madeleine Thornley
- Department of Rangeland, Wildlife and Fisheries Management, Texas A&M University, College Station, TX, 77843, USA
| | - Tyler A Campbell
- East Foundation, 200 Concord Plaza Drive, Suite 410, San Antonio, TX, 78216, USA
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12
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Sard NM, Hunter RD, Roseman EF, Hayes DB, DeBruyne RL, Scribner KT. Pedigree accumulation analysis: Combining methods from community ecology and population genetics for breeding adult estimation. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Nicholas M. Sard
- Department of Biological Sciences State University of New York‐Oswego Oswego NY USA
| | - Robert D. Hunter
- Department of Fisheries and Wildlife Michigan State University East Lansing MI USA
- Department of Environmental Sciences University of Toledo Lake Erie Center Oregon OH USA
| | | | - Daniel B. Hayes
- Department of Fisheries and Wildlife Michigan State University East Lansing MI USA
| | - Robin L. DeBruyne
- Department of Environmental Sciences University of Toledo Lake Erie Center Oregon OH USA
| | - Kim T. Scribner
- Department of Fisheries and Wildlife Michigan State University East Lansing MI USA
- Department of Integrative Biology Michigan State University East Lansing MI USA
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13
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Richter A, Nakamura G, Agra Iserhard C, da Silva Duarte L. The hidden side of diversity: Effects of imperfect detection on multiple dimensions of biodiversity. Ecol Evol 2021; 11:12508-12519. [PMID: 34594516 PMCID: PMC8462181 DOI: 10.1002/ece3.7995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 07/15/2021] [Indexed: 11/08/2022] Open
Abstract
Studies on ecological communities often address patterns of species distribution and abundance, but few consider uncertainty in counts of both species and individuals when computing diversity measures.We evaluated the extent to which imperfect detection may influence patterns of taxonomic, functional, and phylogenetic diversity in ecological communities.We estimated the true abundance of fruit-feeding butterflies sampled in canopy and understory strata in a subtropical forest. We compared the diversity values calculated by observed and estimated abundance data through the hidden diversity framework. This framework evaluates the deviation of observed diversity when compared with diversities derived from estimated true abundances and whether such deviation represents a bias or a noise in the observed diversity pattern.The hidden diversity values differed between strata for all diversity measures, except for functional richness. The taxonomic measure was the only one where we observed an inversion of the most diverse stratum when imperfect detection was included. Regarding phylogenetic and functional measures, the strata showed distinct responses to imperfect detection, despite the tendency to overestimate observed diversity. While the understory showed noise for the phylogenetic measure, since the observed pattern was maintained, the canopy had biased diversity for the functional metric. This bias occurred since no significant differences were found between strata for observed diversity, but rather for estimated diversity, with the canopy being more clustered.We demonstrate that ignore imperfect detection may lead to unrealistic estimates of diversity and hence to erroneous interpretations of patterns and processes that structure biological communities. For fruit-feeding butterflies, according to their phylogenetic position or functional traits, the undetected individuals triggered different responses in the relationship of the diversity measures to the environmental factor. This highlights the importance to evaluate and include the uncertainty in species detectability before calculating biodiversity measures to describe communities.
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Affiliation(s)
- Aline Richter
- Departamento de EcologiaUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
| | - Gabriel Nakamura
- Departamento de BiologiaUniversidade Federal do CearáFortalezaBrazil
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14
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Snell Taylor S, Di Cecco G, Hurlbert AH. Using temporal occupancy to predict avian species distributions. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Sara Snell Taylor
- Department of Biology University of North Carolina Chapel Hill North Carolina USA
| | - Grace Di Cecco
- Department of Biology University of North Carolina Chapel Hill North Carolina USA
| | - Allen H. Hurlbert
- Department of Biology University of North Carolina Chapel Hill North Carolina USA
- Environment, Ecology, and Energy Program University of North Carolina Chapel Hill North Carolina USA
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15
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Duckworth GD, Altwegg R. Why a landscape view is important: nearby urban and agricultural land affects bird abundances in protected areas. PeerJ 2021; 9:e10719. [PMID: 34395062 PMCID: PMC8325429 DOI: 10.7717/peerj.10719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 12/15/2020] [Indexed: 11/20/2022] Open
Abstract
Protected areas are one of the primary conservation tools used worldwide. However, they are often embedded in a landscape that is intensely used by people, such as for agriculture or urban development. The proximity of these land-use types to protected areas can potentially affect the ecological effectiveness (or conservation effectiveness) of protected areas. In this article, we examine to what degree adjacent agricultural and urban land uses affect the ecological effectiveness of protected areas over the greater Gauteng region of South Africa. We selected 198 common, resident bird species, and analysed detection/non-detection data for these species collected over regular grid cells (approximately 61 km2 in area). For each species, we estimated abundance per grid cell with the Royle-Nichols model in relation to the proportion of protected area as a covariate. Our study focused on how this relationship between proportion of protected area and abundance (which we term the ‘protection–abundance relationship’) changed as a function of other land-use types in the grid cell. Specifically, we examined the interaction effects between protected area and both urban and agricultural land-use type per grid cell on bird abundance. We assigned each species to one of seven guilds, namely: frugivores, gleaners, granivores, ground-feeders, hawkers, predators and vegivores, and examined how the protection–abundance relationship varied across guilds in relation to agriculture and urban area. As urban area within a grid cell increased, the protection–abundance relationship became more positive for 58% of all species. At the level of guilds, the protection–abundance relationship became more positive for two guilds (granivores and ground-feeders), more negative for frugivores, and remained unchanged for the other four guilds (gleaners, hawkers, predators and vegivores). As agricultural area within a grid cell increased, the protection–abundance relationship became more positive for 49% of all species. At the guild level, the protection–abundance relationship became more positive for six guilds (frugivores, gleaners, ground-feeders, hawkers, predators and vegivores) and remained unchanged for the granivores. Our results show land-use type near protected areas modified the effect protected areas had on bird abundances, and hence the ecological effectiveness of protected areas. Our results suggest that protected areas should be viewed as constituents within the landscape, rather than islands of protection.
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Affiliation(s)
- Gregory Duncan Duckworth
- Statistics in Ecology, Environment and Conservation, Department of Statistical Sciences, University of Cape Town, Cape Town, South Africa
| | - Res Altwegg
- Statistics in Ecology, Environment and Conservation, Department of Statistical Sciences, University of Cape Town, Cape Town, South Africa.,African Climate and Development Initiative, University of Cape Town, Cape Town, South Africa
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16
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Influence of invasive Prosopis juliflora on the distribution and ecology of native blackbuck in protected areas of Tamil Nadu, India. EUR J WILDLIFE RES 2021. [DOI: 10.1007/s10344-021-01485-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Vásquez‐Ávila B, Knowlton JL, Espinosa CI, Tinoco BA. Habitat alteration modifies the structure and function of mixed‐species flocks in an Andean landscape. Biotropica 2021. [DOI: 10.1111/btp.12957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | - Carlos I. Espinosa
- Laboratorio de Ecología Tropical y Servicios Ecosistémicos Universidad Técnica Particular de Loja Loja Ecuador
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18
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Coutant O, Richard-Hansen C, de Thoisy B, Decotte JB, Valentini A, Dejean T, Vigouroux R, Murienne J, Brosse S. Amazonian mammal monitoring using aquatic environmental DNA. Mol Ecol Resour 2021; 21:1875-1888. [PMID: 33787010 DOI: 10.1111/1755-0998.13393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/14/2021] [Accepted: 03/22/2021] [Indexed: 11/26/2022]
Abstract
Environmental DNA (eDNA) metabarcoding has emerged as one of the most efficient methods to assess aquatic species presence. While the method can in theory be used to investigate nonaquatic fauna, its development for inventorying semi-aquatic and terrestrial fauna is still at an early stage. Here we investigated the potential of aquatic eDNA metabarcoding for inventorying mammals in Neotropical environments, be they aquatic, semi-aquatic or terrestrial. We collected aquatic eDNA in 96 sites distributed along three Guianese watersheds and compared our inventories to expected species distributions and field observations derived from line transects located throughout French Guiana. Species occurrences and emblematic mammalian fauna richness patterns were consistent with the expected distribution of fauna and our results revealed that aquatic eDNA metabarcoding brings additional data to line transect samples for diurnal nonaquatic (terrestrial and arboreal) species. Aquatic eDNA also provided data on species not detectable in line transect surveys such as semi-aquatic, aquatic and nocturnal terrestrial and arboreal species. Although the application of eDNA to inventory mammals still needs some developments to optimize sampling efficiency, it can now be used as a complement to traditional surveys.
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Affiliation(s)
- Opale Coutant
- Laboratoire Evolution et Diversité Biologique, CNRS, IRD, UPS, (UMR5174) - Université de Toulouse, Toulouse, France
| | | | | | | | | | - Tony Dejean
- VIGILIFE, Le Bourget-du-Lac, France.,SPYGEN, Le Bourget-du-Lac, France
| | - Régis Vigouroux
- Laboratoire Environnement de Petit Saut, HYDRECO, Kourou Cedex, French Guiana
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique, CNRS, IRD, UPS, (UMR5174) - Université de Toulouse, Toulouse, France
| | - Sébastien Brosse
- Laboratoire Evolution et Diversité Biologique, CNRS, IRD, UPS, (UMR5174) - Université de Toulouse, Toulouse, France
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19
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Pease BS, Pacifici K, Collazo JA. Survey design optimization for monitoring wildlife communities in areas managed for federally endangered species. Anim Conserv 2021. [DOI: 10.1111/acv.12681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- B. S. Pease
- Fisheries, Wildlife, and Conservation Biology Program Department of Forestry and Environmental Resources North Carolina State University Raleigh NC USA
| | - K. Pacifici
- Fisheries, Wildlife, and Conservation Biology Program Department of Forestry and Environmental Resources North Carolina State University Raleigh NC USA
| | - J. A. Collazo
- U.S. Geological Survey North Carolina Cooperative Fish and Wildlife Research Unit North Carolina State University Raleigh NC USA
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20
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Runghen R, Poulin R, Monlleó-Borrull C, Llopis-Belenguer C. Network Analysis: Ten Years Shining Light on Host-Parasite Interactions. Trends Parasitol 2021; 37:445-455. [PMID: 33558197 DOI: 10.1016/j.pt.2021.01.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 12/24/2022]
Abstract
Biological interactions are key drivers of ecological and evolutionary processes. The complexity of such interactions hinders our understanding of ecological systems and our ability to make effective predictions in changing environments. However, network analysis allows us to better tackle the complexity of ecosystems because it extracts the properties of an ecological system according to the number and distribution of links among interacting entities. The number of studies using network analysis to solve ecological and evolutionary questions in parasitology has increased over the past decade. Here, we synthesise the contribution of network analysis toward disentangling host-parasite processes. Furthermore, we identify current trends in mainstream ecology and novel applications of network analysis that present opportunities for research on host-parasite interactions.
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Affiliation(s)
- Rogini Runghen
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Private Bag 4800, 8140 Christchurch, New Zealand
| | - Robert Poulin
- Department of Zoology, University of Otago, 340 Great King Street, 9054 Dunedin, New Zealand
| | - Clara Monlleó-Borrull
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, PO Box 22085, ES-46071, Valencia, Spain
| | - Cristina Llopis-Belenguer
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, PO Box 22085, ES-46071, Valencia, Spain.
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21
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Zamora-Marín JM, Zamora-López A, Calvo JF, Oliva-Paterna FJ. Comparing detectability patterns of bird species using multi-method occupancy modelling. Sci Rep 2021; 11:2558. [PMID: 33510205 PMCID: PMC7844255 DOI: 10.1038/s41598-021-81605-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023] Open
Abstract
A robust knowledge of biodiversity distribution is essential for designing and developing effective conservation actions. The choice of a suitable sampling method is key to obtaining sufficiently accurate information of species distribution and consequently to improve biodiversity conservation. This study applies multi-method occupancy models to 36 common bird species associated with small ponds in the province of Murcia (south-eastern Spain), one of the most arid regions of Europe, in order to compare their effectiveness for detecting different bird species: direct observation, combined observation and video monitoring and mist netting captures. The results showed that the combined method and direct observation were similar and most effective than mist netting for detecting species occupancy, although detection rates ranged widely among bird groups, while some large species were poorly detected by all the methods used. Average detectability did not increase during the breeding period. The chosen approach is particularly applicable to both single- and multi-species bird monitoring programmes. However, we recommend evaluating the cost-effectiveness of all the available methods in order to reduce costs and improve the success of sampling designs.
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Affiliation(s)
- José M Zamora-Marín
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad de Murcia, Murcia, Spain.
| | - Antonio Zamora-López
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - José F Calvo
- Departamento de Ecología e Hidrología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Francisco J Oliva-Paterna
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad de Murcia, Murcia, Spain
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22
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Kral‐O'Brien KC, Karasch BM, Hovick TJ, Moranz RA, Harmon JP. Morphological traits determine detectability bias in North American grassland butterflies. Ecosphere 2020. [DOI: 10.1002/ecs2.3304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Brooke M. Karasch
- Range Science North Dakota State University Fargo North Dakota58108USA
| | - Torre J. Hovick
- Range Science North Dakota State University Fargo North Dakota58108USA
| | - Raymond A. Moranz
- Department of Integrative Biology Oklahoma State University Stillwater Oklahoma74078USA
| | - Jason P. Harmon
- Department of Entomology North Dakota State University Fargo North Dakota58102USA
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23
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Snell Taylor S, Coyle JR, White EP, Hurlbert AH. A simulation study of the use of temporal occupancy for identifying core and transient species. PLoS One 2020; 15:e0241198. [PMID: 33095844 PMCID: PMC7584212 DOI: 10.1371/journal.pone.0241198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/09/2020] [Indexed: 11/18/2022] Open
Abstract
Transient species, which do not maintain self-sustaining populations in a system where they are observed, are ubiquitous in nature and their presence often impacts the interpretation of ecological patterns and processes. Identifying transient species from temporal occupancy, the proportion of time a species is observed at a given site over a time series, is subject to classification errors as a result of imperfect detection and source-sink dynamics. We use a simulation-based approach to assess how often errors in detection or classification occur in order to validate the use of temporal occupancy as a metric for inferring whether a species is a core or transient member of a community. We found that low detection increases error in the classification of core species, while high habitat heterogeneity and high detection increase error in classification of transient species. These findings confirm that temporal occupancy is a valid metric for inferring whether a species can maintain a self-sustaining population, but imperfect detection, low abundance, and highly heterogeneous landscapes may yield high misclassification rates.
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Affiliation(s)
- Sara Snell Taylor
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
| | - Jessica R. Coyle
- Department of Biology, Saint Mary’s College of California, Moraga, California, United States of America
| | - Ethan P. White
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, United States of America
- Informatics Institute, University of Florida, Gainesville, Florida, United States of America
| | - Allen H. Hurlbert
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Curriculum for the Environment and Ecology, University of North Carolina, Chapel Hill, North Carolina, United States of America
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24
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Mooney TA, Di Iorio L, Lammers M, Lin TH, Nedelec SL, Parsons M, Radford C, Urban E, Stanley J. Listening forward: approaching marine biodiversity assessments using acoustic methods. ROYAL SOCIETY OPEN SCIENCE 2020; 7:201287. [PMID: 32968541 PMCID: PMC7481698 DOI: 10.1098/rsos.201287] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 08/05/2020] [Indexed: 05/08/2023]
Abstract
Ecosystems and the communities they support are changing at alarmingly rapid rates. Tracking species diversity is vital to managing these stressed habitats. Yet, quantifying and monitoring biodiversity is often challenging, especially in ocean habitats. Given that many animals make sounds, these cues travel efficiently under water, and emerging technologies are increasingly cost-effective, passive acoustics (a long-standing ocean observation method) is now a potential means of quantifying and monitoring marine biodiversity. Properly applying acoustics for biodiversity assessments is vital. Our goal here is to provide a timely consideration of emerging methods using passive acoustics to measure marine biodiversity. We provide a summary of the brief history of using passive acoustics to assess marine biodiversity and community structure, a critical assessment of the challenges faced, and outline recommended practices and considerations for acoustic biodiversity measurements. We focused on temperate and tropical seas, where much of the acoustic biodiversity work has been conducted. Overall, we suggest a cautious approach to applying current acoustic indices to assess marine biodiversity. Key needs are preliminary data and sampling sufficiently to capture the patterns and variability of a habitat. Yet with new analytical tools including source separation and supervised machine learning, there is substantial promise in marine acoustic diversity assessment methods.
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Affiliation(s)
- T. Aran Mooney
- Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA 02543, USA
- Author for correspondence: T. Aran Mooney e-mail:
| | - Lucia Di Iorio
- CHORUS Institute, Phelma Minatec, 3 parvis Louis Néel, 38000 Grenoble, France
| | - Marc Lammers
- Hawaiian Islands Humpback Whale National Marine Sanctuary, 726 South Kihei Road, Kihei, HI 96753, USA
| | - Tzu-Hao Lin
- Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Sophie L. Nedelec
- Biosciences, College of Life and Environmental Sciences, Hatherly Laboratories, University of Exeter, Prince of Wales Road, Exeter EX4 4PS, UK
| | - Miles Parsons
- Australian Institute of Marine Science, Perth, Western Australia 6009, Australia
| | - Craig Radford
- Institute of Marine Science, Leigh Marine Laboratory, University of Auckland, PO Box 349, Warkworth 0941, New Zealand
| | - Ed Urban
- Scientific Committee on Oceanic Research, University of Delaware, Newark, DE 19716, USA
| | - Jenni Stanley
- Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA 02543, USA
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25
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Dimensions of Phyllostomid Bat Diversity and Assemblage Composition in a Tropical Forest-Agricultural Landscape. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12060238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tropical rainforests are suffering rapid habitat loss with large extensions of land transformed into agriculture. We wanted to know whether the type of agricultural activity in forest-agricultural landscapes affects how species composition as well as taxonomic and functional dimensions of diversity respond. We worked in the Amazon forests of southeast Peru and used bats as model organisms. We sampled mosaics characterized by forest adjacent to papaya plantations or cattle pastures. At each sampling site we established a transect in each of the three different vegetation types: forest interior, forest edge and agricultural land. We found that vegetation type was a better predictor of species composition than the type of agricultural land present. Vegetation structure characteristics explained differences in bat species composition between forest interior and edge. Agricultural land type chosen was not irrelevant as we found higher estimated species richness in papaya than in pasture sites. Agricultural land type present in a site and vegetation type affected functional diversity, with both agricultural land types showing a lower number of functionally distinct species than forests. We found papaya plantation sites showed species more evenly dispersed in trait space, suggesting they do better at conserving functional diversity when compared to cattle pasture sites. We demonstrate that sites that harbor agricultural activities can maintain a considerable proportion of the expected bat diversity. We note that this region still has large tracts of intact forest adjacent to agricultural lands, which may explain their ability to maintain relatively high levels bat diversity.
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26
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Rodriguez-Palacios A, Khoretonenko MV, Ilic S. Institutional protocols for the oral administration (gavage) of chemicals and microscopic microbial communities to mice: Analytical consensus. Exp Biol Med (Maywood) 2020; 244:459-470. [PMID: 31038368 DOI: 10.1177/1535370219838203] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
IMPACT STATEMENT Institutional protocols designed for the oral administration of live microbial communities, either complex or microscopic (microcosmic), to mice do not exist. However, this approach is increasingly employed by investigators focusing on the gut microbiome in experimental research. Herein, we propose two analytically Kappa-based consensus protocols to promote reproducibility and standardization in research practices and describe biologically relevant factors in achieving optimal microbial engraftment of communities in germ-free mice.
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Affiliation(s)
- Alexander Rodriguez-Palacios
- 1 Division of Gastroenterology and Liver Diseases, Department of Medicine, and Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,2 Digestive Diseases Mouse Models, Cleveland Digestive Diseases Reserch Core Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | - Sanja Ilic
- 4 Department of Human Sciences and Nutrition, The Ohio State University, Columbus, OH 43210, USA
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27
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Van Dooren TJM. Assessing species richness trends: Declines of bees and bumblebees in the Netherlands since 1945. Ecol Evol 2019; 9:13056-13068. [PMID: 31871629 PMCID: PMC6912890 DOI: 10.1002/ece3.5717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 09/15/2019] [Indexed: 11/24/2022] Open
Abstract
Estimating and predicting temporal trends in species richness is of general importance, but notably difficult because detection probabilities of species are imperfect and many datasets were collected in an opportunistic manner. We need to improve our capabilities to assess richness trends using datasets collected in unstandardized procedures with potential collection bias. Two methods are proposed and applied to estimate richness change, which both incorporate models for sampling effects and detection probability: (a) nonlinear species accumulation curves with an error variance model and (b) Pradel capture-recapture models. The methods are used to assess nationwide temporal trends (1945-2018) in the species richness of wild bees in the Netherlands. Previously, a decelerating decline in wild bee species richness was inferred for part of this dataset. Among the species accumulation curves, those with nonconstant changes in species richness are preferred. However, when analyzing data subsets, constant changes became selected for non-Bombus bees (for samples in collections) and bumblebees (for spatial grid cells sampled in three periods). Smaller richness declines are predicted for non-Bombus bees than bumblebees. However, when relative losses are calculated from confidence intervals limits, they overlap and touch zero loss. Capture-recapture analysis applied to species encounter histories infers a constant colonization rate per year and constant local species survival for bumblebees and other bees. This approach predicts a 6% reduction in non-Bombus species richness from 1945 to 2018 and a significant 19% reduction for bumblebees. Statistical modeling to detect species richness time trends should be systematically complemented with model checking and simulations to interpret the results. Data inspection, assessing model selection bias, and comparisons of trends in data subsets were essential model checking strategies in this analysis. Opportunistic data will not satisfy the assumptions of most models and this should be kept in mind throughout.
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Affiliation(s)
- Tom J. M. Van Dooren
- CNRS ‐ UMR 7618 Institute of Ecology and Environmental Sciences (iEES) ParisSorbonne UniversityParisFrance
- Naturalis Biodiversity CenterLeidenThe Netherlands
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28
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Fritz L, Brost B, Laman E, Luxa K, Sweeney K, Thomason J, Tollit D, Walker W, Zeppelin T. A re-examination of the relationship between Steller sea lion (Eumetopias jubatus) diet and population trend using data from the Aleutian Islands. CAN J ZOOL 2019. [DOI: 10.1139/cjz-2018-0329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Prey diversity and energy density have been linked to each other and to population trends in many studies of bird and mammal diets. We re-examined these relationships in Steller sea lions (Eumetopias jubatus (Schreber, 1776)) using data collected from the Aleutian Islands, where there has been a strong longitudinal gradient in population trend. Diet diversity and energy density metrics were similar in the western Aleutians, where sea lion counts declined consistently, and in the easternmost Aleutian area, where population trends improved significantly. We compared traditional deterministic diet diversity metrics with diversity scores based on an occupancy model that accounts for differences in sample size and uncertainty in prey group detection. This analysis indicated that there was no significant change in diet diversity over the 23-year study period or any significant differences across the Aleutian Islands. These results are consistent with prey abundance data from nine groundfish bottom trawl surveys conducted over the same period. While diet studies detail what Steller sea lions eat and provide an estimate of their energy intake, they provide only limited information on the energy expended to obtain their food or the consequences of their diet and foraging ecology on individual or population fitness.
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Affiliation(s)
- L. Fritz
- NOAA Fisheries, Alaska Fisheries Science Center, 7600 Sand Point Way NE, Seattle, WA 98115, USA
| | - B. Brost
- NOAA Fisheries, Alaska Fisheries Science Center, 7600 Sand Point Way NE, Seattle, WA 98115, USA
| | - E. Laman
- NOAA Fisheries, Alaska Fisheries Science Center, 7600 Sand Point Way NE, Seattle, WA 98115, USA
| | - K. Luxa
- NOAA Fisheries, Alaska Fisheries Science Center, 7600 Sand Point Way NE, Seattle, WA 98115, USA
| | - K. Sweeney
- NOAA Fisheries, Alaska Fisheries Science Center, 7600 Sand Point Way NE, Seattle, WA 98115, USA
| | - J. Thomason
- NOAA Fisheries, Alaska Fisheries Science Center, 7600 Sand Point Way NE, Seattle, WA 98115, USA
| | - D. Tollit
- SMRU Consulting North America, 55 Water Street, Suite 604, Vancouver, BC V6V 1A1, Canada
| | - W. Walker
- NOAA Fisheries, Alaska Fisheries Science Center, 7600 Sand Point Way NE, Seattle, WA 98115, USA
| | - T. Zeppelin
- NOAA Fisheries, Alaska Fisheries Science Center, 7600 Sand Point Way NE, Seattle, WA 98115, USA
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29
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Andersen EM, Steidl RJ. Power to detect trends in abundance within a distance sampling framework. J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13529] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Erik M. Andersen
- School of Natural Resources and the Environment University of Arizona Tucson AZ USA
| | - Robert J. Steidl
- School of Natural Resources and the Environment University of Arizona Tucson AZ USA
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30
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Zúñiga-Vega JJ, Solano-Zavaleta I, Sáenz-Escobar MF, Ramírez-Cruz GA. Habitat traits that increase the probability of occupancy of migratory birds in an urban ecological reserve. ACTA OECOLOGICA 2019. [DOI: 10.1016/j.actao.2019.103480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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31
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Dopheide A, Tooman LK, Grosser S, Agabiti B, Rhode B, Xie D, Stevens MI, Nelson N, Buckley TR, Drummond AJ, Newcomb RD. Estimating the biodiversity of terrestrial invertebrates on a forested island using DNA barcodes and metabarcoding data. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2019; 29:e01877. [PMID: 30811075 DOI: 10.1002/eap.1877] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/13/2019] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
Invertebrates are a major component of terrestrial ecosystems, however, estimating their biodiversity is challenging. We compiled an inventory of invertebrate biodiversity along an elevation gradient on the temperate forested island of Hauturu, New Zealand, by DNA barcoding of specimens obtained from leaf litter samples and pitfall traps. We compared the barcodes and biodiversity estimates from this data set with those from a parallel DNA metabarcoding analysis of soil from the same locations, and with pre-existing sequences in reference databases, before exploring the use of combined data sets as a basis for estimating total invertebrate biodiversity. We obtained 1,282 28S and 1,610 COI barcodes from a total of 1,947 invertebrate specimens, which were clustered into 247 (28S) and 366 (COI) OTUs, of which ≤ 10% were represented in GenBank. Coleoptera were most abundant (730 sequenced specimens), followed by Hymenoptera, Diptera, Lepidoptera, and Amphipoda. The most abundant OTU from both the 28S (153 sequences) and COI (140 sequences) data sets was an undescribed beetle from the family Salpingidae. Based on the occurrences of COI OTUs along the elevation gradient, we estimated there are ~1,000 arthropod species (excluding mites) on Hauturu, including 770 insects, of which 344 are beetles. A DNA metabarcoding analysis of soil DNA from the same sites resulted in the identification of similar numbers of OTUs in most invertebrate groups compared with the DNA barcoding, but less than 10% of the DNA barcoding COI OTUs were also detected by the metabarcoding analysis of soil DNA. A mark-recapture analysis based on the overlap between these data sets estimated the presence of approximately 6,800 arthropod species (excluding mites) on the island, including ~3,900 insects. Estimates of New Zealand-wide biodiversity for selected arthropod groups based on matching of the COI DNA barcodes with pre-existing reference sequences suggested over 13,200 insect species are present, including 4,000 Coleoptera, 2,200 Diptera, and 2,700 Hymenoptera species, and 1,000 arachnid species (excluding mites). These results confirm that metabarcoding analyses of soil DNA tends to recover different components of terrestrial invertebrate biodiversity compared to traditional invertebrate sampling, but the combined methods provide a novel basis for estimating invertebrate biodiversity.
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Affiliation(s)
- Andrew Dopheide
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- The New Zealand Institute for Plant and Food Research, Private Bag 92169, Auckland, 1142, New Zealand
- Manaaki Whenua-Landcare Research, Private Bag 92170, Auckland, 1142, New Zealand
| | - Leah K Tooman
- The New Zealand Institute for Plant and Food Research, Private Bag 92169, Auckland, 1142, New Zealand
| | - Stefanie Grosser
- Manaaki Whenua-Landcare Research, Private Bag 92170, Auckland, 1142, New Zealand
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Geschwister-Scholl-Platz 1, 80539, 80539, Munich, Germany
| | - Barbara Agabiti
- Centre for Computational Evolution, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Birgit Rhode
- Manaaki Whenua-Landcare Research, Private Bag 92170, Auckland, 1142, New Zealand
| | - Dong Xie
- Centre for Computational Evolution, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Mark I Stevens
- South Australian Museum, North Terrace, GPO Box 234, Adelaide, South Australia, 5001, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, GPO Box 2471, Adelaide, South Australia, 5001, Australia
| | - Nicola Nelson
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Thomas R Buckley
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- Manaaki Whenua-Landcare Research, Private Bag 92170, Auckland, 1142, New Zealand
| | - Alexei J Drummond
- Centre for Computational Evolution, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Richard D Newcomb
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- The New Zealand Institute for Plant and Food Research, Private Bag 92169, Auckland, 1142, New Zealand
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32
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Moore JF, Hines JE, Mulindahabi F, Masozera MK. Factors affecting species richness and distribution spatially and temporally within a protected area using multi‐season occupancy models. Anim Conserv 2019. [DOI: 10.1111/acv.12491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- J. F. Moore
- Department of Wildlife Conservation and Ecology University of Florida Gainesville FL USA
| | - J. E. Hines
- U. S. Geological Survey Patuxent Wildlife Research Center Laurel MD USA
| | - F. Mulindahabi
- Rwanda Program Wildlife Conservation Society Kigali Rwanda
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33
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Guillera‐Arroita G, Kéry M, Lahoz‐Monfort JJ. Inferring species richness using multispecies occupancy modeling: Estimation performance and interpretation. Ecol Evol 2019; 9:780-792. [PMID: 30766668 PMCID: PMC6362448 DOI: 10.1002/ece3.4821] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 08/17/2018] [Indexed: 11/16/2022] Open
Abstract
Multispecies occupancy models can estimate species richness from spatially replicated multispecies detection/non-detection survey data, while accounting for imperfect detection. A model extension using data augmentation allows inferring the total number of species in the community, including those completely missed by sampling (i.e., not detected in any survey, at any site). Here we investigate the robustness of these estimates. We review key model assumptions and test performance via simulations, under a range of scenarios of species characteristics and sampling regimes, exploring sensitivity to the Bayesian priors used for model fitting. We run tests when assumptions are perfectly met and when violated. We apply the model to a real dataset and contrast estimates obtained with and without predictors, and for different subsets of data. We find that, even with model assumptions perfectly met, estimation of the total number of species can be poor in scenarios where many species are missed (>15%-20%) and that commonly used priors can accentuate overestimation. Our tests show that estimation can often be robust to violations of assumptions about the statistical distributions describing variation of occupancy and detectability among species, but lower-tail deviations can result in large biases. We obtain substantially different estimates from alternative analyses of our real dataset, with results suggesting that missing relevant predictors in the model can result in richness underestimation. In summary, estimates of total richness are sensitive to model structure and often uncertain. Appropriate selection of priors, testing of assumptions, and model refinement are all important to enhance estimator performance. Yet, these do not guarantee accurate estimation, particularly when many species remain undetected. While statistical models can provide useful insights, expectations about accuracy in this challenging prediction task should be realistic. Where knowledge about species numbers is considered truly critical for management or policy, survey effort should ideally be such that the chances of missing species altogether are low.
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Affiliation(s)
| | - Marc Kéry
- Swiss Ornithological InstituteSempachSwitzerland
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34
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Robinson WD, Lees AC, Blake JG. Surveying tropical birds is much harder than you think: a primer of best practices. Biotropica 2018. [DOI: 10.1111/btp.12608] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- W. Douglas Robinson
- Oak Creek Lab of Biology; Department of Fisheries and Wildlife; Oregon State University; Corvallis OR 97331 USA
| | - Alexander C. Lees
- School of Science and the Environment; Manchester Metropolitan University; Manchester UK
- Laboratory of Ornithology; Cornell University; Ithaca NY 14853 USA
| | - John G. Blake
- Department of Wildlife Ecology and Conservation; University of Florida; Gainesville FL 36211 USA
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35
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Staudhammer CL, Escobedo FJ, Blood A. Assessing methods for comparing species diversity from disparate data sources: the case of urban and peri‐urban forests. Ecosphere 2018. [DOI: 10.1002/ecs2.2450] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Christina L. Staudhammer
- Department of Biological Sciences University of Alabama PO Box 870344 Tuscaloosa Alabama 35406 USA
| | - Francisco J. Escobedo
- Biology Program Faculty of Natural Sciences and Mathematics Universidad del Rosario Kr 26 No 63B‐48 Bogotá Colombia
| | - Amy Blood
- Department of Forest Resources and Environmental Conservation Virginia Tech 310 West Campus Drive Blacksburg Virginia 24061 USA
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36
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Valente JJ, Betts MG. Response to fragmentation by avian communities is mediated by species traits. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12837] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Jonathon J. Valente
- Department of Forest Ecosystems and Society Forest Biodiversity Research Network Oregon State University Corvallis Oregon
| | - Matthew G. Betts
- Department of Forest Ecosystems and Society Forest Biodiversity Research Network Oregon State University Corvallis Oregon
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37
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Ongole S, Sankaran M, Karanth KK. Responses of aerial insectivorous bats to local and landscape-level features of coffee agroforestry systems in Western Ghats, India. PLoS One 2018; 13:e0201648. [PMID: 30114276 PMCID: PMC6095497 DOI: 10.1371/journal.pone.0201648] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 07/19/2018] [Indexed: 11/23/2022] Open
Abstract
Shade coffee has shown great promise in providing crucial habitats for biodiversity outside formal protected areas. Insectivorous bats have been understudied in coffee, although they may provide pest control services. We investigated the influence of local and landscape-level features of coffee farms on aerial insectivorous bats in Chikmagalur district in the Western Ghats biodiversity hotspot, India. Bats were monitored in 20 farm sites using ultrasound detectors, and the response of bat species richness and activity to changes in tree density, proportion of built-up area in the neighborhood, and distance of farm from forest areas quantified. We examined if models built to explain the species richness and activity could also predict them in nine additional sites. We detected nine phonic types/species in the study area. The quantified predictors had no effect on assemblage-level species richness and activity of bats. Responses of edge-space and cluttered-space forager guilds mirrored those of the overall assemblage, but some species vulnerable to forest conversion like Rhinolophus beddomei were detected rarely. Best models explained up to 20% and 15% variation in assemblage-level species richness and activity respectively, and were poor predictors of both response variables. We conclude that coffee farms in our study area offer an important commuting space for insectivorous bats across a gradient of shade management. Further research should include species-specific responses to management decisions for at-risk species and quantification of ecosystem services like natural pest control to inform biodiversity conservation initiatives in the Western Ghats coffee landscapes.
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Affiliation(s)
- Shasank Ongole
- Post-graduate Program in Wildlife Biology & Conservation, Wildlife Conservation Society – India Program & National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India
| | - Mahesh Sankaran
- School of Biology, University of Leeds, Leeds, United Kingdom
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India
| | - Krithi K. Karanth
- Wildlife Conservation Society, New York, New York, United States of America
- Centre for Wildlife Studies, Bangalore, Karnataka, India
- Environmental Science and Policy, Nicholas School of the Environment, Duke University, Durham, North Carolina, United States of America
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38
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Benoit D, Jackson DA, Ridgway MS. Assessing the impacts of imperfect detection on estimates of diversity and community structure through multispecies occupancy modeling. Ecol Evol 2018; 8:4676-4684. [PMID: 29760907 PMCID: PMC5938444 DOI: 10.1002/ece3.4023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 02/15/2018] [Accepted: 02/25/2018] [Indexed: 12/01/2022] Open
Abstract
Detecting all species in a given survey is challenging, regardless of sampling effort. This issue, more commonly known as imperfect detection, can have negative impacts on data quality and interpretation, most notably leading to false absences for rare or difficult‐to‐detect species. It is important that this issue be addressed, as estimates of species richness are critical to many areas of ecological research and management. In this study, we set out to determine the impacts of imperfect detection, and decisions about thresholds for inclusion in occupancy, on estimates of species richness and community structure. We collected data from a stream fish assemblage in Algonquin Provincial Park to be used as a representation of ecological communities. We then used multispecies occupancy modeling to estimate species‐specific occurrence probabilities while accounting for imperfect detection, thus creating a more informed dataset. This dataset was then compared to the original to see where differences occurred. In our analyses, we demonstrated that imperfect detection can lead to large changes in estimates of species richness at the site level and summarized differences in the community structure and sampling locations, represented through correspondence analyses.
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Affiliation(s)
- David Benoit
- Department of Ecology & Evolutionary Biology University of Toronto Toronto ON Canada
| | - Donald A Jackson
- Department of Ecology & Evolutionary Biology University of Toronto Toronto ON Canada
| | - Mark S Ridgway
- Department of Ecology & Evolutionary Biology University of Toronto Toronto ON Canada.,Ontario Ministry of Natural Resources and Forestry Peterborough ON Canada
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39
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Harris DJ, Taylor SD, White EP. Forecasting biodiversity in breeding birds using best practices. PeerJ 2018; 6:e4278. [PMID: 29441230 PMCID: PMC5808145 DOI: 10.7717/peerj.4278] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/29/2017] [Indexed: 11/20/2022] Open
Abstract
Biodiversity forecasts are important for conservation, management, and evaluating how well current models characterize natural systems. While the number of forecasts for biodiversity is increasing, there is little information available on how well these forecasts work. Most biodiversity forecasts are not evaluated to determine how well they predict future diversity, fail to account for uncertainty, and do not use time-series data that captures the actual dynamics being studied. We addressed these limitations by using best practices to explore our ability to forecast the species richness of breeding birds in North America. We used hindcasting to evaluate six different modeling approaches for predicting richness. Hindcasts for each method were evaluated annually for a decade at 1,237 sites distributed throughout the continental United States. All models explained more than 50% of the variance in richness, but none of them consistently outperformed a baseline model that predicted constant richness at each site. The best practices implemented in this study directly influenced the forecasts and evaluations. Stacked species distribution models and "naive" forecasts produced poor estimates of uncertainty and accounting for this resulted in these models dropping in the relative performance compared to other models. Accounting for observer effects improved model performance overall, but also changed the rank ordering of models because it did not improve the accuracy of the "naive" model. Considering the forecast horizon revealed that the prediction accuracy decreased across all models as the time horizon of the forecast increased. To facilitate the rapid improvement of biodiversity forecasts, we emphasize the value of specific best practices in making forecasts and evaluating forecasting methods.
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Affiliation(s)
- David J. Harris
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, United States of America
| | - Shawn D. Taylor
- School of Natural Resources and Environment, University of Florida, Gainesville, FL, United States of America
| | - Ethan P. White
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, United States of America
- Informatics Institute, University of Florida, Gainesville, FL, United States of America
- Biodiversity Institute, University of Florida, Gainesville, FL, United States of America
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40
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Khatchikian CE, Nadelman RB, Nowakowski J, Schwartz I, Wormser GP, Brisson D. The impact of strain-specific immunity on Lyme disease incidence is spatially heterogeneous. Diagn Microbiol Infect Dis 2017; 89:288-293. [PMID: 29021088 DOI: 10.1016/j.diagmicrobio.2017.08.015] [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: 02/04/2017] [Revised: 08/16/2017] [Accepted: 08/20/2017] [Indexed: 10/19/2022]
Abstract
Lyme disease, caused by the bacterium Borrelia burgdorferi, is the most common tick-borne infection in the US. Recent studies have demonstrated that the incidence of human Lyme disease would have been even greater were it not for the presence of strain-specific immunity, which protects previously infected patients against subsequent infections by the same B. burgdorferi strain. Here, spatial heterogeneity is incorporated into epidemiological models to accurately estimate the impact of strain-specific immunity on human Lyme disease incidence. The estimated reduction in the number of Lyme disease cases is greater in epidemiologic models that explicitly include the spatial distribution of Lyme disease cases reported at the county level than those that utilize nationwide data. strain-specific immunity has the greatest epidemiologic impact in geographic areas with the highest Lyme disease incidence due to the greater proportion of people that have been previously infected and have developed strain-specific immunity.
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Affiliation(s)
- Camilo E Khatchikian
- Department of Biology, University of Pennsylvania, PA; Department of Biological Sciences, University of Texas at El Paso, TX.
| | - Robert B Nadelman
- Division of Infectious Diseases, Department of Medicine, New York Medical College, Valhalla, NY
| | - John Nowakowski
- Division of Infectious Diseases, Department of Medicine, New York Medical College, Valhalla, NY
| | - Ira Schwartz
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY
| | - Gary P Wormser
- Division of Infectious Diseases, Department of Medicine, New York Medical College, Valhalla, NY
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41
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Klibansky N, Shertzer KW, Kellison GT, Bacheler NM. Can subsets of species indicate overall patterns in biodiversity? Ecosphere 2017. [DOI: 10.1002/ecs2.1842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Nikolai Klibansky
- Southeast Fisheries Science Center; National Marine Fisheries Service; NOAA; 101 Pivers Island Road Beaufort North Carolina 28516 USA
| | - Kyle W. Shertzer
- Southeast Fisheries Science Center; National Marine Fisheries Service; NOAA; 101 Pivers Island Road Beaufort North Carolina 28516 USA
| | - G. Todd Kellison
- Southeast Fisheries Science Center; National Marine Fisheries Service; NOAA; 101 Pivers Island Road Beaufort North Carolina 28516 USA
| | - Nathan M. Bacheler
- Southeast Fisheries Science Center; National Marine Fisheries Service; NOAA; 101 Pivers Island Road Beaufort North Carolina 28516 USA
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42
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Dallas T, Park AW, Drake JM. Predicting cryptic links in host-parasite networks. PLoS Comput Biol 2017; 13:e1005557. [PMID: 28542200 PMCID: PMC5466334 DOI: 10.1371/journal.pcbi.1005557] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 06/09/2017] [Accepted: 05/09/2017] [Indexed: 12/27/2022] Open
Abstract
Networks are a way to represent interactions among one (e.g., social networks) or more (e.g., plant-pollinator networks) classes of nodes. The ability to predict likely, but unobserved, interactions has generated a great deal of interest, and is sometimes referred to as the link prediction problem. However, most studies of link prediction have focused on social networks, and have assumed a completely censused network. In biological networks, it is unlikely that all interactions are censused, and ignoring incomplete detection of interactions may lead to biased or incorrect conclusions. Previous attempts to predict network interactions have relied on known properties of network structure, making the approach sensitive to observation errors. This is an obvious shortcoming, as networks are dynamic, and sometimes not well sampled, leading to incomplete detection of links. Here, we develop an algorithm to predict missing links based on conditional probability estimation and associated, node-level features. We validate this algorithm on simulated data, and then apply it to a desert small mammal host-parasite network. Our approach achieves high accuracy on simulated and observed data, providing a simple method to accurately predict missing links in networks without relying on prior knowledge about network structure.
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Affiliation(s)
- Tad Dallas
- University of Georgia, Odum School of Ecology, Athens, Georgia, United States of America
- University of California, Department of Environmental Science and Policy, Davis, California, United States of America
| | - Andrew W Park
- University of Georgia, Odum School of Ecology, Athens, Georgia, United States of America
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
| | - John M Drake
- University of Georgia, Odum School of Ecology, Athens, Georgia, United States of America
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
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43
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Multiple methods increase detection of large and medium-sized mammals: working with volunteers in south-eastern Oman. ORYX 2017. [DOI: 10.1017/s0030605315001003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
AbstractWe compared the effectiveness of various methods for surveying medium and large wild mammals in southern Oman. Working with volunteers recruited by Biosphere Expeditions, wildlife professionals and local rangers, we used direct observation, camera traps, sign surveys (tracks and/or dung) and molecular scatology to study 66 sampling units of 2 × 2 km (grid cells) in an area of 32 × 36 km during a 4-week period in February–March 2011. Sixteen mammal species were recorded, and the largest numbers of species were recorded by sign surveys and camera traps (both n = 9); sign surveys, direct sightings and DNA scatology recorded species across the largest number of grid cells. For species with a sample size large enough for comparison (i.e. detected in ≥ 8 grid cells), DNA scatology proved most effective for detecting caracal Caracal caracal, signs for hyaena Hyaena hyaena, ibex Capra nubiana, porcupine Hystrix indica and hyrax Procavia capensis, and signs and direct sightings for mountain gazelle Gazella gazella. Clustering, in which records from multiple methods are either adjacent or overlapping, was highest (≥ 76%) for the wolf Canis lupus, porcupine, ibex and gazelle. Our results indicate the best methods to detect and record the distributions of individual species in the study area, and demonstrate the advantage of using multiple methods to reduce the risk of false absences or partial detections. Our findings also highlight the potential of clustering as a means of cross-checking results of observations that are skill-dependent, which is particularly useful when employing a large workforce.
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44
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Influence of sampling frequency on detectability of fish community and fish species in a fishery-independent survey. AQUACULTURE AND FISHERIES 2017. [DOI: 10.1016/j.aaf.2017.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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45
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Silva VXD, Sacramento M, Hasui É, Cunha RGTD, Ramos FN. Taxonomic groups with lower movement capacity may present higher beta diversity. IHERINGIA. SERIE ZOOLOGIA 2017. [DOI: 10.1590/1678-4766e2017005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT Diversity analysis by partition is an approach employed in order to understand how communities spatially structure themselves and the factors that operate in the generation and maintenance of distribution patterns. We examined the spatial structure of species diversity of four taxonomic groups, with different dispersal abilities, in 16 forest fragments in the southern region of the state of Minas Gerais, Brazil. Specifically, we tested: i) if the similarity in species composition would be negatively related to geographical distance between the 16 fragments; and ii) if the beta diversity of the different groups could be negatively related to their dispersal abilities. Alpha diversity and the compositional similarity between localities were both low. Beta diversity was not correlated with distance for any of the groups. Primates, followed by birds, showed a higher tendency of forming similarity groupings, although in a manner that was independent from distance between fragments, as well as showed the lowest beta diversity relative values. Spermatophytes and amphibians did not define groupings and presented the highest values of beta diversity. We interpreted such results as indications that the groups with higher dispersal ability (primates and birds) tend to reach, on average, farther localities and, therefore, to define more similar groupings (low beta diversity). The groups with lower dispersal ability (spermatophytes and amphibians) showed the opposite tendency. Although most of the species were restricted to few localities, contributing to the low similarity, beta and gamma diversity values showed the extent which the localities are, respectively, different and complementary to each other in terms of species composition. Such features reinforce and justify future conservation initiatives, both in local and regional levels.
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46
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León-Tapia MÁ, Hortelano-Moncada Y. Richness of insectivorous bats in a chaparral area in the municipality of Tecate, Baja California, Mexico. REV MEX BIODIVERS 2016. [DOI: 10.1016/j.rmb.2016.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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47
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Husté A, Selmi S, Boulinier T. Bird communities in suburban patches near Paris: Determinants of local richness in a highly fragmented landscape. ECOSCIENCE 2016. [DOI: 10.2980/i1195-6860-13-2-249.1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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48
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La VT, Nudds TD. Estimation of avian species richness: biases in morning surveys and efficient sampling from acoustic recordings. Ecosphere 2016. [DOI: 10.1002/ecs2.1294] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Van T. La
- Department of Integrative BiologyUniversity of Guelph 50 Stone Road East Guelph Ontario N1G 2W1 Canada
| | - Thomas D. Nudds
- Department of Integrative BiologyUniversity of Guelph 50 Stone Road East Guelph Ontario N1G 2W1 Canada
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49
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Cao Y, Larsen DP, White D. Estimating regional species richness using a limited number of survey units. ECOSCIENCE 2016. [DOI: 10.1080/11956860.2004.11682806] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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50
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Hausner V, Yoccoz N, Strann KB, Strann KB, Ims R. Changes in bird communities by planting non-native spruce in coastal birch forests of northern Norway. ECOSCIENCE 2016. [DOI: 10.1080/11956860.2002.11682735] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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