Biodiversity of man-made open habitats in an underused country: a class of multispecies abundance models for count data

Abstract

Since the 1960s, Japan has become highly dependent on foreign countries for natural resources, and the amount of managed lands (e.g. coppice, grassland, and agricultural field) has declined. Due to infrequent natural and human disturbance, early-successional species are now declining in Japan. Here we surveyed bees, birds, and plants in four human-disturbed open habitats (pasture, meadow, young planted forest, and abandoned clear-cut) and two forest habitats (mature planted forest and natural old-growth). We extended a recently developed multispecies abundance model to accommodate count data, and used the resulting models to estimate species-, functional group-, and community-level state variables (abundance and species richness) at each site, and compared them among the six habitats. Estimated individual-level detection probability was quite low for bee Electronic supplementary material The online version of this article (species (mean across species = 0.003; 0.16 for birds). Thirty-two (95% credible interval: 13-64) and one (0-4) bee and bird species, respectively, were suggested to be undetected by the field survey. Although habitats in which community-level abundance and species richness was highest differed among taxa, species richness and abundance of early-successional species were similar in the four disturbed open habitats across taxa except for plants in the pasture habitat which was a good habitat only for several exotic species. Our results suggest that human disturbance, especially the revival of plantation forestry, may contribute to the restoration of early-successional species in Japan.

Detecting diversity: emerging methods to estimate species diversity

“…Only two studies have extended the N-mixture model to a multispecies framework to evaluate communities. Yamaura et al [66] modeled community responses of birds and bees to land-use change, using guild-level hyperparameters and data augmentation to differentiate estimated abundances and species richness between early successional and mature forest species. Chandler et al [67] …”

Study of biological communities subject to imperfect detection: bias and precision of communityN‐mixture abundance models in small‐sample situations

“…Under this model the community-level hyper-parameters, i.e., the mean and the standard deviation of these normal distributions, are shared by all species in the community; they describe the average of the community and the among-species heterogeneity, respectively. We can also use separate normal distributions for individual species (functional) groups, and examine group-specific responses to covariates (Yamaura et al 2012;Chen et al 2013;Barnagaud et al 2014). Thanks to this sharing of hyperparameters among species, we can obtain better estimates of the parameters of rare species and even those of unobserved species by ''borrowing strength'' (i.e., sharing information) among similar but more common species (Zipkin et al 2009;Ovaskainen and Soininen 2011).…”

“…Following previous studies with community abundance models (Yamaura et al 2011(Yamaura et al , 2012, we formulate this zero-inflation in y ijk by modifying Eq. 3 (but see also the ''Discussion''):…”

“…Hence, community occupancy models produce a species richness estimator that accounts (1) for species that occurred in at least one sampling site but were missed in any of the other sites (i.e., were detected at least once), (2) for species that occurred in at least one sampling site but were missed in all other sampling sites (i.e., were never detected), and (3) for species that did occur in the meta-community (i.e., in the wider region that is sampled near the studied sites), but did not occur (and therefore were not detected) at any of the sampling sites (Ke´ry and Royle 2009;Ke´ry 2011;Iknayan et al 2014). This modeling framework has recently been extended for abundance as a state variable based on count data (Yamaura et al 2012;Chandler et al 2013;Barnagaud et al 2014;Dorazio and Connor 2014). In these models which estimate abundance of species (herein, community abundance or community N-mixture models), the occurrence (or occupancy) of a species is naturally a function of its local abundance (i.e., a species occurs if its local abundance is greater than zero), and community-level species richness and total abundance is obtained as a derived parameter.…”

“…In these models which estimate abundance of species (herein, community abundance or community N-mixture models), the occurrence (or occupancy) of a species is naturally a function of its local abundance (i.e., a species occurs if its local abundance is greater than zero), and community-level species richness and total abundance is obtained as a derived parameter. We can assume that a studied community is composed of multiple (functional) groups in which species may have similar parameters, which are summarized by group-level hyper-parameters (Sauer and Link 2002;Ruiz-Gutie´rrez et al 2010;Yamaura et al 2012;Chen et al 2013;Barnagaud et al 2014;Pacifici et al 2014).…”