Data from: Investigating the effects of Pleistocene events on genetic divergence within Richardsonius balteatus, a widely distributed western North American minnowDerek D. Houston, Dennis K. Shiozawa, Brian Tilston Smith & Brett R. Riddle
Background: Biogeographers seek to understand the influences of global climate shifts and geologic changes to the landscape on the ecology and evolution of organisms. Across both longer and shorter timeframes, the western North American landscape has experienced dynamic transformations related to various geologic processes and climatic oscillations, including events as recently as the Last Glacial Maximum (LGM; ~20 Ka) that have impacted the evolution of the North American biota. Redside shiner is a cyprinid species...
Increasing data have supported the importance of divergence with gene flow (DGF) in the generation of biological diversity. In such cases, lineage divergence occurs on a shorter timescale than does the completion of reproductive isolation. Although it is critical to explore the mechanisms driving divergence and preventing homogenization by hybridization, it is equally important to document cases of DGF in nature. Here we synthesize data that have accumulated over the last dozen or so years...
Data from: Speciation in Western Scrub-Jays, Haldane’s rule, and genetic clines in secondary contactFiona C. Gowen, James M. Maley, Carla Cicero, A. Townsend Peterson, Brant C. Faircloth, T. Caleb Warr & John E. McCormack
Background: Haldane’s Rule, the tendency for the heterogametic sex to show reduced fertility in hybrid crosses, can obscure the signal of gene flow in mtDNA between species where females are heterogametic. Therefore, it is important when studying speciation and species limits in female-heterogametic species like birds to assess the signature of gene flow in the nuclear genome as well. We studied introgression of microsatellites and mtDNA across a secondary contact zone between coastal and interior...
Shallow water anthozoans, the major builders of modern coral reefs, enhance their metabolic and calcification rates with algal symbionts. Controversy exists over whether these anthozoan-algae associations are flexible over the lifetimes of individual hosts, promoting acclimative plasticity, or are closely linked, such that hosts and symbionts coevolve across generations. Given the diversity of algal symbionts and the morphological plasticity of many host species, cryptic variation within either partner could potentially confound studies of anthozoan-algal associations....
Data from: Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae)Gustavo A. Bravo, , Robb Thomas Brumfield & J. V. Remsen
Phylogenetic niche conservatism and convergence are contrasting evolutionary patterns that describe phenotypic similarity across independent lineages. Assessing whether and how adaptive processes give origin to these patterns represent a fundamental step toward understanding phenotypic evolution. Phylogenetic model-based approaches offer the opportunity not only to distinguish between phylogenetic niche conservatism and convergence, but also to determine the extent that adaptive processes explain phenotypic similarity. The Myrmotherula complex in the Neotropical family Thamnophilidae is a polyphyletic group...
Collective phenomena, whereby agent-agent interactions determine spatial patterns, are ubiquitous in the animal kingdom. On the other hand, movement and space use are also greatly influenced by the interactions between animals and their environment. Despite both types of interaction fundamentally influencing animal behaviour, there has hitherto been no unifying framework for the models proposed in both areas. Here, we construct a general method for inferring population-level spatial patterns from underlying individual movement and interaction processes,...
Data from: Nonrandom, diversifying processes are disproportionately strong in the smallest size classes of a tropical forestPeter T. Green, Kyle E. Harms & Joseph H. Connell
A variety of ecological processes influence diversity and species composition in natural communities. Most of these processes, whether abiotic or biotic, differentially filter individuals from birth to death, thereby altering species’ relative abundances. Nonrandom outcomes could accrue throughout ontogeny, or the processes that generate them could be particularly influential at certain stages. One long-standing paradigm in tropical forest ecology holds that patterns of relative abundance among mature trees are largely set by processes operating at...
Data from: Investigating sensitivity of phylogenetic community structure metrics using North American desert batsLorelei E. Patrick & Richard D. Stevens
A relatively recent approach to characterizing structure of natural communities is to use phylogenies of species pools to compare patterns of relatedness between real and simulated communities. Such an approach can provide mechanistic insights into structure. Despite popularity of phylogenetic approaches, we do not yet fully understand how phylogenetic community structure (PCS) metrics might be impacted by changes to the phylogeny or community membership data from which they are calculated. We investigate metric sensitivity and...
Data from: Detection of implausible phylogenetic inferences using posterior predictive assessment of model fitJeremy M. Brown
Systematic phylogenetic error caused by the simplifying assumptions made in models of molecular evolution may be impossible to avoid entirely when attempting to model evolution across massive, diverse datasets. However, not all deficiencies of inference models result in unreliable phylogenetic estimates. The field of phylogenetics lacks a direct method to identify cases where model specification adversely affects inferences. Posterior predictive simulation is a flexible and intuitive approach for assessing goodness-of-fit of the assumed model and...
Data from: Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among HymenopteraBrant C. Faircloth, Michael G. Branstetter, Noor D. White & Séan G. Brady
Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome...
Data from: A generalized residual technique for analyzing complex movement models using earth mover's distanceJonathan R. Potts, Marie Auger-Méthé, Karl Mokross & Mark A. Lewis
1. Complex systems of moving and interacting objects are ubiquitous in the natural and social sciences. Predicting their behavior often requires models that mimic these systems with sufficient accuracy, while accounting for their inherent stochasticity. Though tools exist to determine which of a set of candidate models is best relative to the others, there is currently no generic goodness-of-fit framework for testing how close the best model is to the real complex stochastic system. 2....
Data from: Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scalesBrian Tilston Smith, Michael G. Harvey, Brant C. Faircloth, Travis C. Glenn & Robb T. Brumfield
Comparative genetic studies of non-model organisms are transforming rapidly due to major advances in sequencing technology. A limiting factor in these studies has been the identification and screening of orthologous loci across an evolutionarily distant set of taxa. Here, we evaluate the efficacy of genomic markers targeting ultraconserved DNA elements (UCEs) for analyses at shallow evolutionary timescales. Using sequence capture and massively parallel sequencing to generate UCE data for five co-distributed Neotropical rainforest bird species,...
Louisiana State University12
University of Alberta2
Louisiana State University of Alexandria2
University of Kansas1
Denver Museum of Nature and Science1
University of Montana1
University of California System1
Louisiana State University Agricultural Center1