BEAST log files for Leave-one-out-cross-validation

Example BEAST log files for Leave-one-out-cross-validation analysis and additional files to plot results using the "PlotLOOCV" function using the R-package TipDatingBeast. See tutorial included in package for commands

Example datafile for BEAST 2

Example datafile for BEAST 2 used to produce the log files deposited here

Example BEAST log files for Date-randomized test

Example BEAST log files for Date-randomized test to plot results using the "PlotDRT" function using the R-package TipDatingBeast. See tutorial included in package for commands

Data from: TipDatingBeast: an R package to assist the implementation of phylogenetic tip-dating tests using BEAST

Molecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. In this context, BEAST, a program for Bayesian analysis of molecular sequences, is the most widely used phylogenetic tool. Here, we introduce TipDatingBeast, an R package built to assist the implementation of various phylogenetic tip-dating tests using BEAST. TipDatingBeast currently contains two main functions. The first one allows preparing date-randomization analyses, which assess the temporal signal of a dataset. The second function allows performing leave-one-out analyses, which test for the consistency between independent calibration sequences and allow pinpointing those leading to potential bias. We apply those functions to an empirical dataset and supply practical guidance for results interpretation

Data from: Population structure of the Chagas disease vector, Triatoma infestans, at the urban-rural interface

The increasing rate of biological invasions resulting from human transport or human-mediated changes to the environment have had devastating ecologic and public health consequences. The kissing bug, Triatoma infestans, has dispersed through the Peruvian city of Arequipa. The biological invasion of this insect has resulted in a public health crisis, putting thousands of residents of this city at risk of infection by Trypanosoma cruzi and subsequent development of Chagas disease. Here we show that populations of Tria. infestans in geographically distinct districts within and around this urban center share a common recent evolutionary history although current gene flow is restricted even between proximal sites. The population structure among the Tria. infestans in different districts is not correlated with the geographic distance between districts. These data suggest that migration among the districts is mediated by factors beyond the short-range migratory capabilities of Tria. Infestans and that human movement has played a significant role in the structuring of the Tria. infestans population in the region. Rapid urbanization across southern South America will continue to create suitable environments for Tria. infestans and knowledge of its urban dispersal patterns may play a fundamental role in mitigating human disease risk

Data from: Population structure of the Chagas disease vector Triatoma infestans in an urban environment

Chagas disease is a vector-borne disease endemic in Latin America. Triatoma infestans, a common vector of this disease, has recently expanded its range into rapidly developing cities of Latin America. We aim to identify the environmental features that affect the colonization and dispersal of T. infestans in an urban environment. We amplified 13 commonly used microsatellites from 180 T. infestans samples collected from a sampled transect in the city of Arequipa, Peru, in 2007 and 2011. We assessed the clustering of subpopulations and the effect of distance, sampling year, and city block location on genetic distance among pairs of insects. Despite evidence of genetic similarity, the majority of city blocks are characterized by one dominant insect genotype, suggesting the existence of barriers to dispersal. Our analyses show that streets represent an important barrier to the colonization and dispersion of T. infestans in Arequipa. The genetic data describe a T. infestans infestation history characterized by persistent local dispersal and occasional long-distance migration events that partially parallels the history of urban development

Microsatellite allele lengths

The data file consists of microsatellite allele lengths for 13 loci described in the paper. The data file has individuals organized in rows, with the abbreviation of the district in the first column. The subsequent 26 columns correspond to microsatellite data (two columns per locus). Missing data are coded as zeros

Data from: Population structure of the Chagas disease vector Triatoma infestans in an urban environment

Chagas disease is a vector-borne disease endemic in Latin America. Triatoma infestans, a common vector of this disease, has recently expanded its range into rapidly developing cities of Latin America. We aim to identify the environmental features that affect the colonization and dispersal of T. infestans in an urban environment. We amplified 13 commonly used microsatellites from 180 T. infestans samples collected from a sampled transect in the city of Arequipa, Peru, in 2007 and 2011. We assessed the clustering of subpopulations and the effect of distance, sampling year, and city block location on genetic distance among pairs of insects. Despite evidence of genetic similarity, the majority of city blocks are characterized by one dominant insect genotype, suggesting the existence of barriers to dispersal. Our analyses show that streets represent an important barrier to the colonization and dispersion of T. infestans in Arequipa. The genetic data describe a T. infestans infestation history characterized by persistent local dispersal and occasional long-distance migration events that partially parallels the history of urban development