The importance of accounting for imperfect detection when estimating functional and phylogenetic community structure

Si, Xingfeng; Cadotte, Marc W.; Zhao, Yongqiang; Zhou, Haonan; Zeng, Di; Li, Jiaqi; Jin, Tinghao; Peng, Ren; Wang, Yanping; Ding, Ping; Tingley, Morgan W.

doi:10.1002/ecy.2438

Cited by 45 publications

(35 citation statements)

References 47 publications

(93 reference statements)

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“…Low occupancy probability has been examined broadly in single‐species studies, where precision in parameter estimates from single‐species models declines non‐linearly with decreasing occupancy (MacKenzie & Royle, ). In a multi‐species context, however, low average occupancy has been observed as a phenomenon, particularly when combined with low average detectability (Si et al, ), but it has been otherwise little explored. Guillera‐Arroita et al () explored two scenarios of MSOM performance with low average occupancy (0.27 and 0.13) but did not contrast these scenarios to those others with higher or lower occupancy.…”

Section: Discussionmentioning

confidence: 99%

Multi‐species occupancy models as robust estimators of community richness

2020

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1. Understanding patterns of diversity is central to ecology and conservation, yet estimates of diversity are often biased by imperfect detection. In recent years, multi-species occupancy models (MSOM) have been developed as a statistical tool to account for species-specific heterogeneity in detection while estimating true measures of diversity. Although the power of these models has been tested in various ways, their ability to estimate gamma diversity-or true community size, N is a largely unrecognized feature that needs rigorous evaluation.2. We use both simulations and an empirical dataset to evaluate the bias, precision, accuracy and coverage of estimates of N from MSOM compared to the widely applied iChao2 non-parametric estimator. We simulated 5,600 datasets across seven scenarios of varying average occupancy and detectability covariates, as well as varying numbers of sites, replicates and true community size. Additionally, we use a real dataset of surveys over 9 years (where species accumulation reached an asymptote, indicating true N), to estimate N from each annual survey.3. Simulations showed that both MSOM and iChao2 estimators are generally accurate (i.e. unbiased and precise) except under unideal scenarios where mean species occupancy is low. In such scenarios, MSOM frequently overestimated N. Across all scenarios, MSOM estimates were less certain than iChao2, but this led to over-confident iChao2 estimates that showed poor coverage. Results from the real dataset largely confirmed the simulation findings, with MSOM estimates showing greater accuracy and coverage than iChao2. Community ecologists have a wide choice of analytical methods, and both iChao2and MSOM estimates of N are substantially preferable to raw species counts. The simplicity of non-parametric estimators has obvious advantages, but our results show that in many cases, MSOM may provide superior estimates that also account more accurately for uncertainty. Both methods can show strong bias when average occupancy is very low, and practitioners should show caution when using estimates derived from either method under such conditions. K E Y W O R D SChao estimator, community richness, data augmentation, gamma diversity, imperfect detection, multi-species occupancy models, occupancy modelling S U PP O RTI N G I N FO R M ATI O NAdditional supporting information may be found online in the Supporting Information section.

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Section: Discussionmentioning

confidence: 99%

Multi‐species occupancy models as robust estimators of community richness

2020

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“…This indicates that although historical mechanisms, such as niche conservatism could help explain elevational diversity gradients of Himalayan birds (e.g., Wiens & Graham, ; Price et al, ), ecological processes still play an important role in shaping gradients of richness in this study, given the multiple families in each guild. Some degree of care is required when interpreting our results, because our line‐transect surveys may underestimate rare, or secretive species living in dense forests due to imperfect detection, and thus affect our observed biodiversity patterns (MacKenzie et al, ; Si et al, ). In our study, the problem of imperfect detection may be more likely to occur in areas of low and mid‐elevations as dense forests were often found in such areas (Wu, ), so that future studies may wish to allocate more survey efforts to these areas, or improve the sampling design to target rare species (Specht et al, ).…”

Section: Discussionmentioning

confidence: 99%

“…In this study, we found the hump-shaped patterns of elevational diversity gradients are generally congruence across bird guilds that peaked at different elevation bands and were explained by divergent spatial and environmental factors. In practice, however, the same patterns could also be driven by other processes, such as historical imprints, instead of ecological limits to diversity (Wiens, 2011 Si et al, 2018). In our study, the problem of imperfect detection may be more likely to occur in areas of low and mid-elevations as dense forests were often found in such areas (Wu, 1983(Wu, -1987, so that future studies may wish to allocate more survey efforts to these areas, or improve the sampling design to target rare species (Specht et al, 2017).…”

Section: Caveats and Limitationsmentioning

confidence: 99%

Different responses of avian feeding guilds to spatial and environmental factors across an elevation gradient in the central Himalaya

Ding¹,

Liang²,

et al. 2019

Ecology and Evolution

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Although elevational patterns of species richness have been well documented, how the drivers of richness gradients vary across ecological guilds has rarely been reported. Here, we examined the effects of spatial factors (area and mid‐domain effect; MDE) and environmental factors, including metrics of climate, productivity, and plant species richness on the richness of breeding birds across different ecological guilds defined by diet and foraging strategy. We surveyed 12 elevation bands at intervals of 300 m between 1,800 and 5,400 m a.s.l using line‐transect methods throughout the wet season in the central Himalaya, China. Multiple regression models and hierarchical partitioning were used to assess the relative importance of spatial and environmental factors on overall bird richness and guild richness (i.e., the richness of species within each guild). Our results showed that richness for all birds and most guilds displayed hump‐shaped elevational trends, which peaked at an elevation of 3,300–3,600 m, although richness of ground‐feeding birds peaked at a higher elevation band (4,200–4,500 m). The Normalized Difference Vegetation Index (NDVI)—an index of primary productivity—and habitat heterogeneity were important factors in explaining overall bird richness as well as that of insectivores and omnivores, with geometric constraints (i.e., the MDE) of secondary importance. Granivore richness was not related to primary production but rather to open habitats (granivores were negatively influenced by habitat heterogeneity), where seeds might be abundant. Our findings provide direct evidence that the richness–environment relationship is often guild‐specific. Taken together, our study highlights the importance of considering how the effects of environmental and spatial factors on patterns of species richness may differ across ecological guilds, potentially leading to a deeper understanding of elevational diversity gradients and their implications for biodiversity conservation.

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“…We defined the areas within a radius of 1 km at each counting point as observation areas, and these areas were not overlapping to avoid double counting. The relatively small areas and clear boundaries of the wetlands guaranteed good detection of waterbirds, which is important when quantifying assemblage structures (Si et al, ).…”

Section: Methodsmentioning

confidence: 99%

Assembly processes of waterbird communities across subsidence wetlands in China: A functional and phylogenetic approach

Yong

Zha

et al. 2019

Diversity and Distributions

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Aim Although assembly processes have been studied in a wide range of taxa, determining assembly rules remains controversial, particularly in assemblages consisted of species with strong dispersal capacities. Moreover, few studies focused on communities in recently human‐created habitats. We tested two prevailing but opposing hypotheses, environmental filtering and limiting similarity, in waterbird communities across subsidence wetlands created by underground coal mining in China, with an aim to better understand assembly processes in communities composed of highly mobile species in human‐dominated landscape. Location The North China Plain. Methods We quantified taxonomic, functional and phylogenetic diversity of the waterbird assemblages in different seasons and compared the mean pairwise distances (MPD) and the mean nearest taxon distances (MNTD) with null models to examine whether co‐occurring species were clustered or overdispersed on the functional dendrogram or phylogenetic tree. Independent contributions of multi‐scale habitat variables therein were determined using a hierarchical partitioning method. Results We showed asynchronous patterns of seasonal dynamics among the multiple diversity metrics, with highest species diversity during autumn migration. Generally, the co‐occurring species were functionally and phylogenetically clustered. Habitat variables had stronger effects on the functional structure than on the phylogenetic structure of the communities. The degree of functional clustering increased in older and larger wetlands, while the assemblages shifted from functional clustering to overdispersion with increasing habitat diversity, landscape connectivity and human disturbance. Main conclusions The waterbird assemblages were mainly structured by environmental filtering, and the assembly processes were significantly affected by habitat variables, with stronger effects on functional diversity. Our study highlights the importance of environmental filtering and habitat variables in structuring assemblages dominated by species with high dispersal capacities and suggests that increasing habitat diversity and reducing disturbances will contribute to waterbird conservation in this human‐dominated landscape.

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The importance of accounting for imperfect detection when estimating functional and phylogenetic community structure

Cited by 45 publications

References 47 publications

Multi‐species occupancy models as robust estimators of community richness

Multi‐species occupancy models as robust estimators of community richness

Different responses of avian feeding guilds to spatial and environmental factors across an elevation gradient in the central Himalaya

Assembly processes of waterbird communities across subsidence wetlands in China: A functional and phylogenetic approach

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