Data from: Estimating synchronous demographic changes across populations using hABC and its application for a herpetological community from northeastern BrazilMarcelo Gehara, Adrian Antoinio Garda, Fernanda P. Werneck, Eliana F. Oliveira, Emanuel M. Da Fonseca, Felipe Camurugi, Felipe De M. Magalhães, Flavia Mol Lanna, Jack W. Sites, Ricardo Marques, Ricardo Silveira-Filho, Vinícius A. São-Pedro, Guarino R. Colli, Gabriel C. Costa & Frank T. Burbrink
Many studies propose that Quaternary climatic cycles contracted and /or expanded the ranges of species and biomes. Strong expansion-contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Quaternary climate on diversification processes. Hierarchical approximate Bayesian computation (hABC) is a powerful and flexible approach that models genetic data from multiple species, and can be used to estimate the...
In the age of genome-scale DNA sequencing, choice of molecular marker arguably remains an important decision in planning a phylogenetic study. Using published genomes from 23 primate species, we make a standardized comparison of four of the most frequently used protocols in phylogenomics, viz., targeted sequence-enrichment using ultraconserved element and exon-capture probes, and restriction-site-associated DNA sequencing (RADseq and ddRADseq). Here we present a procedure to perform in silico extractions from genomes and create directly comparable...
Data from: Decoupled responses of soil bacteria and their invertebrate consumer to warming, but not freeze-thaw cycles, in the Antarctic Dry ValleysMatthew A. Knox, Walter S. Andriuzzi, Heather N. Buelow, Cristina Takacs-Vesbach, Byron J. Adams & Diana H. Wall
Altered temperature profiles resulting in increased warming and freeze–thaw cycle (FTC) frequency pose great ecological challenges to organisms in alpine and polar ecosystems. We performed a laboratory microcosm experiment to investigate how temperature variability affects soil bacterial cell numbers, and abundance and traits of soil microfauna (the microbivorous nematode Scottnema lindsayae) from McMurdo Dry Valleys, Antarctica. FTCs and constant freezing shifted nematode body size distribution towards large individuals, driven by higher mortality among smaller individuals....
Data from: Sympatry predicts spot pigmentation patterns and female association behavior in the livebearing fish Poeciliopsis baenschiAndrea J. Roth-Monzón, Laura E. Scott, Ashley A. Camargo, Eliza I. Clark, Eric E. Schott & Jerald B. Johnson
In this study, we explored the possibility that differences in pigmentation patterns among populations of the fish Poeciliopsis baenschi were associated with the presence or absence of the closely related species P. turneri. If reproductive character displacement is responsible, spotting patterns in these two species should diverge in sympatry, but not allopatry. We predicted that female P. baenschi from sympatric sites should show a preference for associating with conspecifics vs. heterospecific males, but females from...
Data from: Why does it take two to tango? lifetime fitness consequences of parental care in a burying beetleAshlee N. Smith, J. Curtis Creighton & Mark C. Belk
In species that require parental care, each parent can either care for their offspring or leave them in the care of the other parent. For each parent this creates three possible parental care strategies: biparental care, uniparental (male or female) care, and uniparental desertion by either the male or female. The burying beetle, Nicrophorus orbicollis, typically exhibits biparental care of offspring, and thus provides a unique system that allows us to compare the fitness benefits...
Data from: Root morphology and mycorrhizal type strongly influence root production in nutrient hot spots of mixed forestsWeile Chen, Roger T. Koide & David M. Eissenstat
1. Plants compete for nutrients using a range of strategies. We investigated nutrient foraging within nutrient hot-spots simultaneously available to plant species with diverse root traits. We hypothesized that there would be more root proliferation by thin-root species than by thick-root species, and that root proliferation by thin-root species would limit root proliferation by thick-root species. 2. We conducted a root ingrowth experiment in a temperate forest in eastern USA where root systems of different...
Data from: Sexual dimorphism, phenotypic integration, and the evolution of head structure in casque-headed lizardsGregory W. Taylor, Juan C. Santos, Benjamin J. Perrault, Mariana Morando, Carlos Roberto Vásquez Almazán, & Jack W. Sites
Sexes can differ in features associated with differential reproduction, which can be used during courtship or aggressive encounters. Some traits tend to evolve independently between sexes and emerge as sexually dimorphic within the organismal phenotype. We characterize such a relationship by estimating the phenotypic integration of the head morphology and modularity of the crest in the casque-headed lizards (Corytophanidae). In this clade, some species show extreme sexual dimorphism (e.g., head crests in the genus Basiliscus)...
Comparable taxonomic ranks within clades can facilitate more consistent classifications and objective comparisons among taxa. Here we use a temporal approach to identify taxonomic ranks. This is an extension of the temporal banding approach including a Temporal Error Score that finds an objective cut-off for each taxonomic rank using information for the current classification. We illustrate this method using a data set of the lichenized fungal family Parmeliaceae. To assess its performance, we simulated the...
Data from: Detecting hybridization by likelihood calculation of gene tree extra lineages given explicit modelsMelisa Olave, Luciano J. Avila, , Mariana Morando & Jack W. Sites
Explanations for gene tree discordance with respect to a species tree are commonly attributed to deep coalescence (also known as incomplete lineage sorting [ILS]), as well as different evolutionary processes such as hybridization, horizontal gene transfer and gene duplication. Among these, deep coalescence is usually quantified as the number of extra lineages and has been studied as the principal source of discordance among gene trees, while the other processes that could contribute to gene tree...
Data from: Genome-wide sensitivity analysis of the microsymbiont Sinorhizobium meliloti to symbiotically important, defensin-like host peptidesMarkus F. F. Arnold, Mohammed Shabab, Jon Penterman, Kevin L. Boehme, Joel S. Griffitts & Graham C. Walker
The model legume species Medicago truncatula expresses more than 700 nodule-specific cysteine-rich (NCR) signaling peptides that mediate the differentiation of Sinorhizobium meliloti bacteria into nitrogen-fixing bacteroids. NCR peptides are essential for a successful symbiosis in legume plants of the inverted-repeat-lacking clade (IRLC) and show similarity to mammalian defensins. In addition to signaling functions, many NCR peptides exhibit antimicrobial activity in vitro and in vivo. Bacterial resistance to these antimicrobial activities is likely to be important...
Brigham Young University10
National Scientific and Technical Research Council2
St. John's University1
Field Museum of Natural History1
Federal University of Paraíba1
University of San Carlos of Guatemala1
Federal University of Amazonas1
Complutense University of Madrid1
Colorado State University1