Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is in MXL, in CLM, and in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern America ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas thousand years ago (kya), supports that the MXL Ancestors split kya, with a subsequent split of the ancestors to CLM and PUR kya. The model also features effective populations of in Mexico, in Colombia, and in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations.     

Mating interference of glassy‐winged sharpshooters,Homalodisca vitripennis

Animal communication is a complex behavior that is influenced by abiotic and biotic factors of the environment. Glassy‐winged sharpshooters (GWSS), Homalodisca vitripennis (Germar) (Hemiptera: Cicadellidae), primarily use vibrational signaling for courtship communication. Because GWSS is a major pest, transmitting the plant pathogenic bacterium Xylella fastidiosa Wells et al., interruption of communication is a possible avenue for control. Playback of white noise, pre‐recorded female signals, and artificial female noise (continuously overlapping female signals) significantly reduced mating of GWSS when compared to silent control mating trials. Furthermore, to begin to determine the mechanism underlying playback control, female signaling activity was recorded in the presence of stimuli. In response to playback of female signals, females signaled (duet‐like) more often than females tested in the absence of playback. After the first playback, almost two‐thirds of females signaled a response within 3 s. Additionally, one‐third of the females signaled within 1 s after cessation of white noise, and significantly more in the time periods following noise termination. Results highlight how GWSS responds to differing competitive disturbances in the environment and lays important ground work that possibly could be used to develop pesticide‐free control methods.     

Nitric oxide induces apoptosis in a human colonic epithelial cell line, T84

Chronic inflammation is associated with inducible nitric oxide synthase expression in infiltrating and resident cells (epithelia, neurons) and an exaggerated release of nitric oxide. NO can induce apoptosis in macrophages and tumour cell lines. We investigated whether NO induced cell death in an epithelial (T84) cell fine via apoptosis. Culture T84 cells were exposed to a bolus of NO (40 or 80 muM) dissolved in Hank's balanced salt solution (HBSS) supplemented with 10% fetal calf serum (FCS). After incubation for 4 h at 37( degrees )C in 5% CO(2), cells were either stained for DNA fragmentation with the TdT-mediated dUTP-biotin nick end labelling (TUNEL) method, or cytosolic DNA fragments quantified by a cell death detection ELISA assay. Nitric oxide induced apoptosis in a dose-dependent manner which preceded frank cell death (failure to exclude Trypan blue). These data suggest that epithelial cell death may be NO dependent and via apoptosis, in states of gut inflammation.     

A graphical method for detecting recombination in phylogenetic data sets

Current phylogenetic tree reconstruction methods assume that there is a single underlying tree topology for all sites along the sequence. The presence of mosaic sequences due to recombination violates this assumption and will cause phylogenetic methods to give misleading results due to the imposition of a single tree topology on all sites. The detection of mosaic sequences caused by recombination is therefore an important first step in phylogenetic analysis. A graphical method for the detection of recombination, based on the least squares method of phylogenetic estimation, is presented here. This method locates putative recombination breakpoints by moving a window along the sequence. The performance of the method is assessed by simulation and by its application to a real data set.      

Leaf Phenology and Leaf Damage of Saplings in the Luquillo Experimental Forest,Puerto Rico1

Changes in light or water availability can result in synchronous leaf production, concentrating food availability for herbivores of young leaves to only a few months. To determine the importance of food availability on herbivory, leaf phenology and leaf damage were studied in the Luquillo Experimental Forest (LEF) of Puerto Rico. We studied 20 individuals of eight species for two years. Every month, new leaves were marked; the following month, leaf area and area of damage were measured. Over two years, comparison of leaf production and percent herbivory were performed for each species, and for all species taken together. More than 30 percent of the annual leaf production occurred in May and June. Leaf production was associated with an increase in PFD (photon flux density) and was not related to the patterns of rainfall. Although leaf production was synchronous, there were no differences in herbivory between the peak and non‐peak periods of leaf production. Possible explanations for the constant levels of herbivory throughout the year are the presence of a generalist herbivore community, the ability of herbivores to track changes in food availability, or high densities of herbivore predators that control herbivore populations.