How Should Ecologists Define Sampling Effort? The Potential of Procrustes Analysis for Studying Variation in Community Composition

Biotropica ◽  
2015 ◽  
Vol 47 (4) ◽  
pp. 399-402 ◽  
Author(s):  
Victor S. Saito ◽  
Alaide A. Fonseca-Gessner ◽  
Tadeu Siqueira
Keyword(s):  
Community Composition ◽  
Procrustes Analysis ◽  
Sampling Effort

scholarly journals Hunter-gatherers in context: Mammal community composition in a northern Tanzania landscape used by Hadza foragers and Datoga pastoralists

2020 ◽  
Author(s):  
Brian Wood ◽  
Riccardo S. Millar ◽  
Nicholas Wright ◽  
Joshua Baumgartner ◽  
Hannah Holmquist ◽  
...  
Keyword(s):  
Community Composition ◽  
Camera Traps ◽  
Sub Saharan Africa ◽  
Sampling Effort ◽  
Mammal Species ◽  
Hunter Gatherers ◽  
Wild Mammals ◽  
Northern Tanzania ◽  
Mammal Community ◽  
Species Specific

In many regions of sub Saharan Africa large mammals occur in human-dominated areas, yet their community composition and species-specific densities have rarely been described in areas occupied by traditional hunter-gatherers and pastoralists. Surveys of mammal populations in such areas provide important measures of biodiversity and provide ecological context for understanding hunting practices. Using a sampling grid centered on a Hadza hunter-gatherer camp and covering 36 km² of semi-arid savannah in northern Tanzania, we assessed mammals using camera traps (n = 19 stations) for c. 5 months (2,182 trap nights). In the study area (Tli’ika in the Hadza language), we recorded 36 wild mammal species, resembling a near complete mammal community. Rarefaction curves suggest that sampling effort was sufficient to capture mammal species richness. Species-specific densities were estimated using a random encounter model and site- and species’ body mass- specific estimates of the area sampled at each camera; confidence intervals were estimated using bootstrapping. Point estimates of densities varied by c. four orders of magnitude, from 0.003 ind./km² (African wild dog) to 27.5 ind./km² (Kirk’s dik dik). Densities of livestock (cattle, donkey, sheep and goat) were high, particularly when estimated using directly observed herd sizes. Cumulative biomass density of herbivorous livestock species exceeded that of all wild mammals by a factor of 3.3-38.7. We compare our study’s data to camera trap rates recorded in a fully protected area of northern Tanzania with similar precipitation (Lake Manyara National Park), revealing that abundance indices of most wildlife species in Tli’ika were much lower. We discuss how these data inform studies of Hadza hunting and models of hunter-gatherer foraging ecology and diet.

scholarly journals A comparative assessment of adult mosquito trapping methods to estimate spatial patterns of abundance and community composition in southern Africa

2019 ◽  
Author(s):  
Erin E. Gorsich ◽  
Brianna R. Beechler ◽  
Peter M. van Bodegom ◽  
Danny Govender ◽  
Milehna M. Guarido ◽  
...  
Keyword(s):  
Community Composition ◽  
Southern Africa ◽  
Light Trap ◽  
Regional Distribution ◽  
Adult Mosquito ◽  
Sampling Effort ◽  
Regional Patterns ◽  
Mosquito Abundance ◽  
Trapping Methods ◽  
Surveillance Programs

AbstractBackgroundAssessing adult mosquito populations is an important component of disease surveillance programs and ecosystem health assessments. Inference from adult trapping datasets involves comparing populations across space and time, but comparisons based on different trapping methods may be biased if traps have different efficiencies or sample different subsets of the mosquito community.MethodsWe compared four widely-used trapping methods for adult mosquito data collection in Kruger National Park (KNP), South Africa: Centers for Disease Control miniature light trap (CDC), Biogents Sentinel trap (BG), Biogents gravid Aedes trap (GAT) and a net trap. We quantified how trap choice and sampling effort influence inferences on the regional distribution of mosquito abundance, richness and community composition.ResultsThe CDC and net traps together collected 96% (47% and 49% individually) of the 955 female mosquitoes sampled and 100% (85% and 78% individually) of the 40 species or species complexes identified. The CDC and net trap also identified similar regional patterns of community composition. However, inference on the regional patterns of abundance differed between these traps because mosquito abundance in the net trap was influenced by variation in weather conditions. The BG and GAT traps collected significantly fewer mosquitoes, limiting regional comparisons of abundance and community composition.ConclusionsThis study represents the first systematic assessment of trapping methods in natural savanna ecosystems in southern Africa. We recommend the CDC trap or the net trap for future monitoring and surveillance programs.

Ant Species Diversity, Distribution, and Community Composition in Different Forest Types in Papua New Guinea

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Jacob Yombai ◽  
Petr Klimes ◽  
Paul Dargusch ◽  
Aloysius Posman ◽  
Ondrej Mottl ◽  
...  
Keyword(s):  
Species Richness ◽  
Species Diversity ◽  
Sea Level ◽  
Papua New Guinea ◽  
Community Composition ◽  
Scientific Information ◽  
New Guinea ◽  
Sampling Effort ◽  
Forest Types ◽  
The Impact

Previous studies have provided important scientific information on ant species richness and composition relating to the effects of elevation, sampling approaches, stratification, and forest succession. Yet, they have primarily focused on single sites or regions. Knowledge of ant ecology should also include the impact of disturbance in various forest types. Tuna baiting and hand collection methods were used to investigate diversity and community composition of ants in 16 sites sampled across Papua New Guinea, in both disturbed and pristine forest, at heights ranging from 28 to 2,728 m above sea level. We found 176 species as a result of exposing 320 tuna baits and traversing 72 hand-searched plots. Baiting samples were strongly dominated by a few common species, while the hand-collecting captured more species per plot. The Chao 2 richness estimator for both methods predicted undersampling of the local community. As expected, ant species diversity and richness significantly decrease with increasing elevation. We observed, on average, greater species diversity of ground-dwelling ant communities in disturbed compared to undisturbed forests. The effect was not significant using multivariate randomisations, since the same species dominated both forest classes. The unexpected pattern of ant species richness being locally higher in the disturbed sites is driven by our sampling of undisturbed communities at all elevations, but sampling of the disturbed communities only up to 1,600 m above sea level. Hence, future studies should consider more locations, aiming ideally for an equal sampling effort to capture disturbance stage and elevation.

scholarly journals Optimizing Large-Scale Biodiversity Sampling Effort: Toward an Unbalanced Survey Design

Oceanography ◽  
2021 ◽  
Vol 34 (2) ◽  
Author(s):  
Enrique Montes ◽  
◽  
Jonathan Lefcheck ◽  
Edlin Guerra Castro ◽  
Eduardo Klein ◽  
...  
Keyword(s):  
Species Richness ◽  
Community Composition ◽  
Statistical Power ◽  
Large Scale ◽  
Survey Design ◽  
Quality Data ◽  
Taxonomic Resolution ◽  
Marine Biodiversity ◽  
Sampling Effort ◽  
Biodiversity Survey

Acquiring marine biodiversity data is difficult, costly, and time-consuming, making it challenging to understand the distribution and abundance of life in the ocean. Historically, approaches to biodiversity sampling over large geographic scales have advocated for equivalent effort across multiple sites to minimize comparative bias. When effort cannot be equalized, techniques such as rarefaction have been applied to minimize biases by reverting diversity estimates to equivalent numbers of samples or individuals. This often results in oversampling and wasted resources or inaccurately characterized communities due to undersampling. How, then, can we better determine an optimal survey design for characterizing species richness and community composition across a range of conditions and capacities without compromising taxonomic resolution and statistical power? Researchers in the Marine Biodiversity Observation Network Pole to Pole of the Americas (MBON Pole to Pole) are surveying rocky shore macroinvertebrates and algal communities spanning ~107° of latitude and 10 biogeographic ecoregions to address this question. Here, we apply existing techniques in the form of fixed-coverage subsampling and a complementary multivariate analysis to determine the optimal effort necessary for characterizing species richness and community composition across the network sampling sites. We show that oversampling for species richness varied between ~20% and 400% at over half of studied areas, while some locations were undersampled by up to 50%. Multivariate error analysis also revealed that most of the localities were oversampled by several-fold for benthic community composition. From this analysis, we advocate for an unbalanced sampling approach to support field programs in the collection of high-quality data, where preliminary information is used to set the minimum required effort to generate robust values of diversity and composition on a site-to-site basis. As part of this recommendation, we provide statistical tools in the open-source R statistical software to aid researchers in implementing optimization strategies and expanding the geographic footprint or sampling frequency of regional biodiversity survey programs.

scholarly journals A comparative assessment of adult mosquito trapping methods to estimate spatial patterns of abundance and community composition in southern Africa

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Erin E. Gorsich ◽  
Brianna R. Beechler ◽  
Peter M. van Bodegom ◽  
Danny Govender ◽  
Milehna M. Guarido ◽  
...  
Keyword(s):  
Community Composition ◽  
Southern Africa ◽  
Light Trap ◽  
Regional Distribution ◽  
Adult Mosquito ◽  
Sampling Effort ◽  
Regional Patterns ◽  
Mosquito Abundance ◽  
Trapping Methods ◽  
Surveillance Programs

Abstract Background Assessing adult mosquito populations is an important component of disease surveillance programs and ecosystem health assessments. Inference from adult trapping datasets involves comparing populations across space and time, but comparisons based on different trapping methods may be biased if traps have different efficiencies or sample different subsets of the mosquito community. Methods We compared four widely-used trapping methods for adult mosquito data collection in Kruger National Park (KNP), South Africa: Centers for Disease Control miniature light trap (CDC), Biogents Sentinel trap (BG), Biogents gravid Aedes trap (GAT) and a net trap. We quantified how trap choice and sampling effort influence inferences on the regional distribution of mosquito abundance, richness and community composition. Results The CDC and net traps together collected 96% (47% and 49% individually) of the 955 female mosquitoes sampled and 100% (85% and 78% individually) of the 40 species or species complexes identified. The CDC and net trap also identified similar regional patterns of community composition. However, inference on the regional patterns of abundance differed between these traps because mosquito abundance in the net trap was influenced by variation in weather conditions. The BG and GAT traps collected significantly fewer mosquitoes, limiting regional comparisons of abundance and community composition. Conclusions This study represents the first systematic assessment of trapping methods in natural savanna ecosystems in southern Africa. We recommend the CDC trap or the net trap for future monitoring and surveillance programs.

scholarly journals Mosquito Communities Vary across Landscape and Vertical Strata in Indian River County, Florida

Pathogens ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1575
Author(s):  
Bryan V. Giordano ◽  
Anthony Cruz ◽  
Daniel W. Pérez-Ramos ◽  
Martina M. Ramos ◽  
Yasmin Tavares ◽  
...  
Keyword(s):  
Community Composition ◽  
Ground Level ◽  
Sampling Effort ◽  
Site Location ◽  
Conservation Area ◽  
Coastal Conservation ◽  
Culex Nigripalpus ◽  
Nuisance Species ◽  
Landscape Types ◽  
Species Specific

Mosquito and arbovirus surveillance is essential to the protection of public health. A majority of surveys are undertaken at ground level. However, mosquitoes shelter, breed, and quest for hosts across vertical strata, thus limiting our ability to fully describe mosquito and arboviral communities. To elucidate patterns of mosquito vertical stratification, canopy traps were constructed to sample mosquitoes at heights of 1.5, 5.0, and 8.7 m across three different landscape types in a Florida coastal conservation area. We assessed trapping efforts using individual-based rarefaction and extrapolation. The effects of height, landscape, site location, and sampling date on mosquito community composition were parsed out using permutational ANOVA on a Hellinger-transformed Bray–Curtis dissimilarity abundance matrix. Lastly, a generalized linear mixed effects model (GLMM) was used to explore species-specific vertical patterns. We observed differences in sampling effort and community composition structure across various heights and landscapes. Our GLMM revealed significant effects of trap height for Aedes taeniorhynchus, Anopheles crucians, Anopheles quadrimaculatus, and Culex coronator, but not for Culex nigripalpus, the ultra-dominant species present in this area. Together these data provide evidence that height and landscape significantly affect mosquito community structures and highlight a need to develop sampling regimes to target specific vector and nuisance species at their preferred height and across different landscape types.

Changes in littoral benthic macroinvertebrate communities in relation to water chemistry in 17 Precambrian Shield lakes

2008 ◽  
Vol 65 (5) ◽  
pp. 906-918 ◽  
Author(s):  
Jennifer Lento ◽  
Peter J Dillon ◽  
Keith M Somers ◽  
Ron A Reid
Keyword(s):  
Water Chemistry ◽  
Community Composition ◽  
Correspondence Analysis ◽  
Benthic Community ◽  
Sampling Period ◽  
Procrustes Analysis ◽  
Benthic Macroinvertebrate ◽  
Macroinvertebrate Communities ◽  
Biological Interactions ◽  
Recovery From Acidification

Few studies of biological recovery from acidification have dealt with community responses to changes in water chemistry, despite the importance of environmental tolerance and biological interactions that may only be visible by examining the community as a whole. In this study, we examined the ability of pH and several water chemistry covariables to explain temporal changes in the littoral benthic macroinvertebrate communities of lakes recovering from acidification. Data from 17 lakes sampled from 1988 to 2002 were summarized using correspondence analysis and compared using Procrustes analysis. Canonical correspondence analysis was used to examine the relationship between chemical variables and community structure. Benthic community composition changed over the sampling period, with significant year-to-year changes from 1993 to 1998. Community composition and water chemistry were highly correlated throughout the study period, although the strongest correlations were found from 1993 to 1997, coinciding with the period of greatest change in the benthic community. These results suggest that benthic macroinvertebrate communities in these lakes have changed in response to changes in water chemistry that are consistent with recovery from acidification.

scholarly journals A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1599 ◽  
Author(s):  
Nagaraju Indugu ◽  
Kyle Bittinger ◽  
Sanjay Kumar ◽  
Bonnie Vecchiarelli ◽  
Dipti Pitta
Keyword(s):  
Microbial Community ◽  
Dairy Cows ◽  
Community Composition ◽  
Transition Period ◽  
Microbial Community Composition ◽  
Procrustes Analysis ◽  
Ion Torrent ◽  
Sequencing Data ◽  
Bacterial Phyla ◽  
Ion Torrent Pgm

Next generation sequencing (NGS) technology is a widely accepted tool used by microbial ecologists to explore complex microbial communities in different ecosystems. As new NGS platforms continue to become available, it becomes imperative to compare data obtained from different platforms and analyze their effect on microbial community structure. In the present study, we compared sequencing data from both the 454 and Ion Torrent (PGM) platforms on the same DNA samples obtained from the rumen of dairy cows during their transition period. Despite the substantial difference in the number of reads, error rate and length of reads among both platforms, we identified similar community composition between the two data sets. Procrustes analysis revealed similar correlations (M2= 0.319;P= 0.001) in the microbial community composition between the two platforms. Both platforms revealed the abundance of the same bacterial phyla which were Bacteroidetes and Firmicutes; however, PGM recovered an additional four phyla. Comparisons made at the genus level by each platforms revealed differences in only a few genera such asPrevotella,Ruminococcus,SucciniclasticumandTreponema(p< 0.05; chi square test). Collectively, we conclude that the output generated from PGM and 454 yielded concurrent results, provided stringent bioinformatics pipelines are employed.

Temporal dynamics of mycorrhizal fungal communities and co-associations with grassland plant communities following experimental manipulation of rainfall

2019 ◽  
Author(s):  
Coline Deveautour ◽  
Sally Power ◽  
Kirk Barnett ◽  
Raul Ochoa-Hueso ◽  
Suzanne Donn ◽  
...  
Keyword(s):  
Community Composition ◽  
Plant Community ◽  
Plant Communities ◽  
Fungal Community ◽  
Mycorrhizal Fungi ◽  
Temporal Dynamics ◽  
Arbuscular Mycorrhizal ◽  
Fungal Communities ◽  
Plant Responses ◽  
Rainfall Regimes

Climate models project overall a reduction in rainfall amounts and shifts in the timing of rainfall events in mid-latitudes and sub-tropical dry regions, which threatens the productivity and diversity of grasslands. Arbuscular mycorrhizal fungi may help plants to cope with expected changes but may also be impacted by changing rainfall, either via the direct effects of low soil moisture on survival and function or indirectly via changes in the plant community. In an Australian mesic grassland (former pasture) system, we characterised plant and arbuscular mycorrhizal (AM) fungal communities every six months for nearly four years to two altered rainfall regimes: i) ambient, ii) rainfall reduced by 50% relative to ambient over the entire year and iii) total summer rainfall exclusion. Using Illumina sequencing, we assessed the response of AM fungal communities sampled from contrasting rainfall treatments and evaluated whether variation in AM fungal communities was associated with variation in plant community richness and composition. We found that rainfall reduction influenced the fungal communities, with the nature of the response depending on the type of manipulation, but that consistent results were only observed after more than two years of rainfall manipulation. We observed significant co-associations between plant and AM fungal communities on multiple dates. Predictive co-correspondence analyses indicated more support for the hypothesis that fungal community composition influenced plant community composition than vice versa. However, we found no evidence that altered rainfall regimes were leading to distinct co-associations between plants and AM fungi. Overall, our results provide evidence that grassland plant communities are intricately tied to variation in AM fungal communities. However, in this system, plant responses to climate change may not be directly related to impacts of altered rainfall regimes on AM fungal communities. Our study shows that AM fungal communities respond to changes in rainfall but that this effect was not immediate. The AM fungal community may influence the composition of the plant community. However, our results suggest that plant responses to altered rainfall regimes at our site may not be resulting via changes in the AM fungal communities.

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