Project description:Divergence in song between allopatric populations can contribute to premating reproductive isolation in territorial birds. Song divergence is typically measured by quantifying divergence in vocal traits using audio recordings, but field playback experiments provide a more direct way to behaviorally measure song divergence between allopatric populations. The White-breasted Wood-Wren (Henicorhina leucosticta; hereafter "WBWW") is an abundant Neotropical species with four mitochondrial clades (in Central America, the Darién, the Chocó and the Amazon) that are deeply divergent (~5-16% sequence divergence). We assessed the possibility that the WBWW as currently defined may represent multiple biological species by conducting both statistical analysis of vocal characters and field playback experiments within three clades (Central America, Chocó and Amazon). Our analysis of vocal traits revealed that Central American songs overlapped in acoustic space with Chocó songs, indicating vocal similarity between these two populations, but that Central American songs were largely divergent from Amazonian songs. Playback experiments in the Caribbean lowlands of Costa Rica revealed that Central American WBWWs typically responded aggressively to songs from the Chocó population but did not respond to playback of songs from the Amazonian population, echoing the results of the vocal trait analysis. This marked difference in behavioral response demonstrates that the songs of Central American and Amazonian WBWWs (but not Central American and Chocó WBWWs) have diverged sufficiently that Central American WBWWs no longer recognize song from Amazonian WBWWs as a signal to elicit territorial defense. This suggests that significant premating reproductive isolation has evolved between these two populations, at least from the perspective of the Central American population, and is consistent with the possibility that Central American and Amazonian populations represent distinct biological species. We conclude by advocating for the further use of field playback experiments to assess premating reproductive isolation (and species limits) between allopatric songbird populations, a situation where behavioral systematics can answer questions that phylogenetic systematics cannot.
Project description:This study aims to investigate the DNA methylation patterns at transcription factor binding regions and their evolutionary conservation with respect to binding activity divergence. We combined newly generated bisulfite-sequencing experiments in livers of five mammals (human, macaque, mouse, rat and dog) and matched publicly available ChIP-sequencing data for five transcription factors (CEBPA, HNF4a, CTCF, ONECUT1 and FOXA1). To study the chromatin contexts of TF binding subjected to distinct evolutionary pressures, we integrated publicly available active promoter, active enhancer and primed enhancer calls determined by profiling genome wide patterns of H3K27ac, H3K4me3 and H3K4me1.
Project description:Whole genome sequencing of the Arabidopsis thaliana dot5-1 transposon insertion line described in Petricka et al 2008 The Plant Journal 56(2): 251-263.
Project description:The analysis identifies differentially occupied genomic regions of H2Bub1, H3K79me3, and H3K27ac by RNF40 silencing in HCC1806 cells
Project description:This study aims to investigate the interactions of mutagenic lesions from diethylnitrosamine (DEN) treatment of mouse livers with such processes as replication, transcription, and interaction of DNA with proteins. Liver samples of 15-day old (P15) untreated C3H/HeOuJ mice were isolated and flash-frozen. ChIP-seq was performed to identify CTCF binding sites in livers of ten pooled individuals. The experiment was done with five biological replicates with a matched input library.
