A probabilistic model for analysing species co‐occurrence

Abstract

Aim To develop a new probabilistic model that can be used to test for statistically significant pair-wise patterns of species co-occurrence. The model gives the probability that two species would co-occur at a frequency less than (or greater than) the observed frequency if the two species were distributed independently of one another among a set of sites. The model can be used to classify species associations as negative, positive or random.Innovation Historically, the analysis of species co-occurrence has involved the use of data randomization. An observed species presence-absence matrix is compared with randomized matrices to determine if the observed matrix has structure, either an excess or deficit of species positively or negatively associated with each other. The computer algorithms used to randomize matrices can sometimes produce Type I and Type II errors (when the randomization algorithm produces a biased set of all possible matrices) due to the randomization process itself. The probabilistic model does not rely on any data randomization, hence it has a very low Type I error rate and is powerful having a low Type II error rate.Main conclusions When applied to 10 different data sets the probabilistic model revealed significant positive and negative species associations in most of the data sets. Compared with previous analyses the model tended to find fewer significant associations; this may indicate a generally low rate of Type I error in the model. The model is easy to implement and requires no special software. The model could potentially transform the way that ecologists test for species co-occurrence in a wide range of ecological studies.

Sydowia polyspora Dominates Fungal Communities Carried by Two Tomicus Species in Pine Plantations Threatened by Fusarium circinatum

“…This statistical software was also used to perform a co-occurrence analysis using the package "cooccur" [45]. The function "co-occur" provides the observed and expected frequencies of co-occurrence by pairs of taxa (F obs and F exp respectively) and two associated probabilities (P gt and P lt ) that could be interpreted as p-values [46]. These probabilities identify each pairwise association between fungi as follows: (a) positive association between taxa if F obs > F exp and P gt < 0.05; (b) negative association if F obs < F exp and P lt < 0.05 or (c) random association in the remaining cases.…”

Fine-scale spatial patterns of the Tertiary relict Zelkova abelicea (Ulmaceae) indicate possible processes contributing to its persistence to climate changes

“…Pairwise tests of species associations have been carried out using the method of Veech (2013). The probabilistic model of species co-occurrence allows to analytically (i.e., without randomization or simulation) obtain the probability that two selected species co-occur at a frequency either smaller or greater than the observed frequency of cooccurrence.…”

“…This probabilistic model does not rely on any data randomization; hence, it has a very low Type I error rate and is powerful since it also has a low Type II error rate. Nevertheless, taking into consideration the weakness of the probabilistic model in small data sets (Veech 2013), the classical chi-square method for species association has also been implemented.…”

“…However, a divergence from this pattern is observed at the patch level, where the two species seem to Table 6 Results of the pairwise association tests using chi-squared tests and the probabilistic method of Veech (2013) chi squared Probabilistic In columns, pairs of the three species Z. abelicea, A. sempervirens and Q. coccifera are denoted by pairs of the letters Z, A and Q, respectively. Matrix codes are the same as in Table 3 0 No statistically significant association detected ?…”

Comparison of aquatic macrophyte community structure between natural wetlands and rice fields with different cultivation ages

“…The species co-occurrence pattern (positive, negative and random association) was tested by probabilistic model of pair-wise species co-occurrence (Veech, 2013). The probabilistic model or species co-occurrence was based on observed and expected frequencies of pair-wise species co-occurrence; and the expected frequency is based on each species distribution being random and independent of other species (Griffith et al, 2014).…”