Data from: Fragmentation of Atlantic Forest has not affected gene flow of a widespread seed-dispersing batEve S. McCulloch, J. Sebastian Tello, Andrew Whitehead, Claudia M. J. Rolón-Mendoza, Mario C. D. Maldonado-Rodríguez & Richard D. Stevens
Habitat loss and resultant fragmentation are major threats to biodiversity, particularly in tropical and subtropical ecosystems. It is increasingly urgent to understand fragmentation effects, which are often complex and vary across taxa, time and space. We determined whether recent fragmentation of Atlantic forest is causing population subdivision in a widespread and important Neotropical seed-disperser: Artibeus lituratus (Chiroptera: Phyllostomidae). Genetic structure within highly fragmented forest in Paraguay was compared to that in mostly contiguous forest in...
Data from: Multilocus phylogeny and biogeography of the New World Pheucticus grosbeaks (Aves: Cardinalidae)Paulo C. Pulgarín-R, Brian Tilston Smith, , Garth M. Spellman, John Klicka & Robert W. Bryson
Using a multilocus approach, we investigated the tempo and pattern of diversification in a widely distributed New World songbird, the cardinalid genus Pheucticus. Each of the three geographic groups recovered (North American, Middle American, and South American) was comprised of a pair of currently recognized species, and four, three, and three geographically and genetically distinct phylogeographic lineages respectively. Diversification within Pheucticus appears to have occurred at a relatively constant pace throughout the Pleistocene and evenly...
Data from: Stochastic faunal exchanges drive diversification in widespread Wallacean and Pacific island lizards (Squamata: Scincidae: Lamprolepis smaragdina)Charles W. Linkem, Rafe M. Brown, Cameron D. Siler, Ben J. Evans, Christopher C. Austin, Djoko T. Iskandar, Arvin C. Diesmos, Jatna Supriatna, Noviar Andayani, Jimmy A. McGuire & Malte Ebach
Aim: Widespread species found in disturbed habitats are often expected to be human commensals. In island systems, this association predicts that dispersal will be mediated by humans. We investigated the biogeographical relationships among populations of a widespread tree skink that inhabits coastal forest and human-cultivated plantations in Southeast Asia. We sought to determine whether populations of the emerald tree skink, Lamprolepis smaragdina, dis- persed via mechanisms that were not human-mediated (‘natural’ dispersal) or whether dispersal...
Aim: To examine the history of diversification of ‘blue’ cardinalids (Cardinalidae) across North and South America. Location: North America (including Middle America) and South America. Methods: We collected 163 individuals of the 14 species of blue cardinalids and generated multilocus sequence data (3193 base pairs from one mitochondrial and three nuclear genes) to infer phylogeographical structure and reconstruct time-calibrated species trees. We then estimated the ancestral range at each divergence event and tested for temporal...
Data from: Temporal patterns of diversification across global cichlid biodiversity (Acanthomorpha: Cichlidae)Caleb D. McMahan, Prosanta Chakrabarty, John S. Sparks, Wm. Leo Smith & Matthew P. Davis
The contrasting distribution of species diversity across the major lineages of cichlids makes them an ideal group for investigating macroevolutionary processes. In this study, we investigate whether different rates of diversification may explain the disparity in species richness across cichlid lineages globally. We present the most taxonomically robust time-calibrated hypothesis of cichlid evolutionary relationships to date. We then utilize this temporal framework to investigate whether both species-rich and depauperate lineages are associated with rapid shifts...
Data from: Evaluating summary statistics used to test for incomplete lineage sorting: mito-nuclear discordance in the reef sponge Callyspongia vaginalisMelissa B. DeBiasse, Bradley J. Nelson & Michael E. Hellberg
Conflicting patterns of population differentiation between the mitochondrial and nuclear genomes (mito-nuclear discordance) have become increasingly evident as multilocus datasets have become easier to generate. Incomplete lineage sorting (ILS) of nucDNA is often implicated as the cause of such discordance, stemming from the large effective population size of nucDNA relative to mtDNA. However, selection, sex-biased dispersal, and historical demography can also lead to mito-nuclear discordance. Here we compare patterns of genetic diversity and subdivision for...
Porites corals are foundation species on Pacific reefs but a confused taxonomy hinders understanding of their ecosystem function and responses to climate change. Here, we show that what has been considered a single species in the eastern tropical Pacific, Porites lobata, includes a morphologically similar yet ecologically distinct species, Porites evermanni. While P. lobata reproduces mainly sexually, P. evermanni dominates in areas where triggerfish prey on bioeroding mussels living within the coral skeleton, thereby generating...
Data from: Model selection as a tool for phylogeographic inference: an example from the willow Salix melanopsisBryan C. Carstens, Reid S. Brennan, Vivien Chua, Caroline V. Duffie, Michael G. Harvey, Rachel A. Koch, Caleb D. McMahan, Bradley J. Nelson, Catherine E. Newman, Jordan D. Satler, Glenn Seeholzer, Karine Posbic, David C. Tank & Jack Sullivan
Phylogeographic inference has typically relied on analyses of data from one or a few genes to provide estimates of demography and population histories. While much has been learned from these studies, all phylogeographic analysis is conditioned on the data, and thus, inferences derived from data that represent a small sample of the genome are unavoidably tenuous. Here, we demonstrate one approach for moving beyond classic phylogeographic research. We use sequence capture probes and Illumina sequencing...
Louisiana State University of Alexandria8
University of Washington2
University of Kansas1
Institut Teknologi Bandung1
Field Museum of Natural History1
The Ohio State University1
University of Indonesia1
Burke Museum of Natural History and Culture1
University of California, Berkeley1