Computational protocol: Seasonal cycles, phylogenetic assembly, and functional diversity of orchid bee communities

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Protocol publication

[…] To reconstruct a species-level phylogeny of the euglossine bee lineages present in our three communities, we used DNA sequence data generated in our previous study (Ramírez et al. ). Briefly, we used a total of ∼4.0 kb of DNA sequences from three nuclear and one mitochondrial loci; including 1200 base pairs of the mitochondrial cytochrome oxidase, CO1; 1200 base pairs of the nuclear elongation factor 1-alpha (EF1-α); 700 base pairs of the arginine kinase, ArgK; and 800 base pairs of the RNA polymerase II (Pol-II). We performed a new set of phylogenetic tree searches with the software package MRBAYES v3.2.2, where we assigned each locus a different model of sequence evolution. Tree searches were performed assuming multiple models of sequence evolution for each locus, and Markov Chain Monte Carlo (MCMC) searches were made for 10 million generations, sampling every 1000 generations, for a total of 10,000 trees. We estimated model parameters during runs and Bayesian posterior probabilities as the proportion of trees sampled; the trees obtained in the first 1 million generations were discarded. We determined models of sequence evolution with the software package Modeltest. [...] We calculated two different metrics of phylogenetic community structure: phylogenetic diversity (PD) and mean pairwise phylogenetic distance (MPD). The phylogenetic diversity (PD) index is one of the earliest metrics developed to investigate relatedness within a community, and it measures the sum of the total branch lengths accumulated among the lineages present in a community (Faith ). The MPD index calculates the mean pairwise phylogenetic distance among all species in a community. Both indices can be corrected for communities of different sizes using the standardized effect size (SES) correction. This correction is calculated as the difference between the phylogenetic distances in the observed community and a set of null communities generated by random processes, divided by the standard deviation of the phylogenetic distances in the null communities (Kembel et al. ). We estimated SES-PD and SES-MPD to allow comparison among communities of different richness values. SES-PD and SES-MPD indices were estimated for each month in each community. SES-MPD is related to the previously used net relatedness index (NRI). This metric is a standardized measure of the mean pairwise phylogenetic distance of taxa in a sample, relative the phylogeny of the species pool. In fact, SES-MPD equals −1*NRI.The species pool for the three communities combined consisted of a total of 50 taxa. Measures of phylogenetic and functional diversity are calculated relative to this source pool. Because the three communities we studied are located in the same biogeographic region, we assumed that the source pool is the same for all three locations. In fact, previous studies have documented the presence of these species in the region (Bonilla-Gómez and Nates-Parra ; Ramírez et al. ). In addition, we assume that the source pool does not change over time due to large-scale movement or migration events, as female euglossine bees are central place foragers (Roubik ). All the phylogenetic diversity analyses were performed using the software package Picante v1.6-1 (Kembel et al. ). To test whether abrupt changes in phylogenetic community structure coincide with shifts in rainfall patterns, we calculated a rainfall differential (D) as abs (Rt − Rt + 1), where Rt is the average rainfall at time interval t. We used linear regression models to determine the relationship between D and SES-PD. Thus, a positive correlation between D and SES-PD would indicate that seasonality patterns of community assembly are correlated with changes in rainfall regimes. […]

Pipeline specifications

Software tools MrBayes, ModelTest-NG, Picante
Application Phylogenetics
Organisms Apis mellifera