Biology subjects

Socolar, J. B.

Publications and source records attributed to Socolar, J. B..

4 recordsLinked to original sources

bioRxiv2023

Introducing flocker: an R package for flexible occupancy modeling via brms and Stan

O_LIOccupancy models are a widespread tool for analyzing biological survey data, but packages for fitting these models offer a limited variety of effects structures. C_LIO_LIWe developed Rpackage flocker to connect occupancy models (single- and multi- species; single- and multi-season) to the uniquely powerful formula syntax of Rpackage brms. C_LIO_LIUsing familiar formula-based syntax, flocker models can readily incorporate a wide array of effects structures, including phylogenetic random effects, splines, Gaussian processes, autoregressive structures, monotonic effects, and nonlinear predictors. These are available for use in formulas for occupancy, detection, colonization, extinction, and autologistic terms (as applicable to the model type). flocker additionally provides functionality for data simulation, posterior prediction, and model comparison, following well-documented statistical decisions that we put forward as best practices. C_LIO_LIWe anticipate that flocker will facilitate the work of practitioners who seek added realism in occupancy models. We further hope that flockers synthesis of these models will help inform best practices around occupancy modeling. C_LI

ecology↗

bioRxiv2021

Biogeographic multi-species occupancy models for large-scale survey data

O_LIEcologists often seek to infer patterns of species occurrence or community structure from survey data. Hierarchical models, including multi-species occupancy models (MSOMs), can improve inference by pooling information across multiple species via random effects. Originally developed for local-scale survey data, MSOMs are increasingly applied to larger spatial scales that transcend major abiotic gradients and dispersal barriers. At biogeographic scales, the benefits of partial pooling in MSOMs trade off against the difficulty of incorporating sufficiently complex spatial effects to account for biogeographic variation in occupancy across multiple species simultaneously. C_LIO_LIWe show how this challenge can be overcome by incorporating pre-existing range information into MSOMs, yielding a biogeographic multi-species occupancy model (bMSOM). We illustrate the bMSOM using two published datasets: Parulid warblers in the United States Breeding Bird Survey, and entire avian communities in forests and pastures of Colombias West Andes. C_LIO_LICompared to traditional MSOMs, the bMSOM provides dramatically better predictive performance at lower computational cost. The bMSOM avoids severe spatial biases in predictions of the traditional MSOM and provides principled species-specific inference even for never-observed species. C_LIO_LIIncorporating pre-existing range data enables principled partial pooling of information across species in large-scale MSOMs. Our biogeographic framework for multi-species modeling should be broadly applicable in hierarchical models that predict species occurrences, whether or not false-absences are modeled in an occupancy framework. C_LI

ecology↗

bioRxiv2017

Diversification, sympatry, and the emergence of mega-diverse tropical assemblages

Geographic gradients in species richness, including latitudinal gradients, can arise from geographic variation in any of three mechanisms: the geologic age of habitats, net rates of evolutionary diversification, or rates of sympatry among diversifying lineages. Here we show that variation in rates of sympatry is a dominant force structuring geographic richness gradients in birds. Species-rich sites contain disproportionately high numbers of recently diverged sympatric species but contain lineages with slower-than-average diversification rates. The positive sympatry-diversity relationship consistently overwhelms the negative diversification-diversity relationship, particularly among high-diversity sites (>250 species). These patterns repeat across biomes and continents with striking regularity, and remain consistent across multiple timescales, including the recent evolutionary past. Biogeographic and evolutionary patterns in birds are consistent with a role for ecological conditions in promoting species coexistence, which allows sister species to co-occur and potentially lowers extinction rates.

ecology↗

bioRxiv2017

Smallholder agriculture and the fate of a hyperdiverse tropical biota

Diversified smallholder agriculture is the main human land-use affecting the western Amazon, home to the worlds richest terrestrial biota, but the scant available data to date have suggested that the biodiversity impacts of this land-use are small. Here, we present comprehensive surveys of birds and trees in primary forest and smallholder agricultural mosaics in northern Peru. These surveys reveal substantial biodiversity losses that have been overlooked by other studies. Avian biodiversity losses arise primarily from biotic homogenization across infrequently surveyed forest habitats (a loss of beta-diversity). Furthermore, tree species richness declines much more steeply than bird richness. Statistical modeling of local habitat features that allow forest-associated species to persist in the smallholder mosaic strongly suggests that our results represent a best-case scenario for Amazonian agricultural biodiversity. We conclude that previous assessments of the biodiversity value of Amazonian smallholder agriculture have been overly optimistic because they are restricted to upland habitat, thereby missing losses in beta diversity; do not evaluate trees; and/or rely on generalizations from less speciose areas of the Neotropics, where habitat specialization amongst species is less prevalent. Smallholder agriculture will likely expand in western Amazonia due to infrastructure development, and it must be seen as a serious threat to the regions biodiversity.

ecology↗