39 research outputs found
Data for: Atypical singing is associated with developmental stress and zero fitness in a male white-throated sparrow (Zonotrichia albicollis)
No full text<p>Here we provide data for a manuscript in which we describe the atypical song of a male white-throated sparrow (<em>Zonotrichia albicollis</em>). We observed this male over multiple breeding seasons at our Cranberry Lake study site (Adirondack Mountains; New York; 44.15N, 74.78W). We recorded the male singing, and also made observations regarding his failure to obtain reproductive success. In addition, as the male was banded as a nestling, we were able to compare his morphometric measurements at the time to the population average. Our observations of this unique individual support a connection between developmental stress, atypical song, and fitness outcomes.</p>
Comparative BAC-based mapping in the white-throated sparrow, a novel behavioral genomics model, using interspecies overgo hybridization
No full textBACKGROUND
The genomics era has produced an arsenal of resources from sequenced organisms allowing researchers to target species that do not have comparable mapping and sequence information. These new "non-model" organisms offer unique opportunities to examine environmental effects on genomic patterns and processes. Here we use comparative mapping as a first step in characterizing the genome organization of a novel animal model, the white-throated sparrow (Zonotrichia albicollis), which occurs as white or tan morphs that exhibit alternative behaviors and physiology. Morph is determined by the presence or absence of a complex chromosomal rearrangement. This species is an ideal model for behavioral genomics because the association between genotype and phenotype is absolute, making it possible to identify the genomic bases of phenotypic variation.
FINDINGS
We initiated a genomic study in this species by characterizing the white-throated sparrow BAC library via filter hybridization with overgo probes designed for the chicken, turkey, and zebra finch. Cross-species hybridization resulted in 640 positive sparrow BACs assigned to 77 chicken loci across almost all macro-and microchromosomes, with a focus on the chromosomes associated with morph. Out of 216 overgos, 36% of the probes hybridized successfully, with an average number of 3.0 positive sparrow BACs per overgo.
CONCLUSIONS
These data will be utilized for determining chromosomal architecture and for fine-scale mapping of candidate genes associated with phenotypic differences. Our research confirms the utility of interspecies hybridization for developing comparative maps in other non-model organisms
Behavioral genomics in the white-throated sparrow
No full textMost behavioral traits are complex and are the product of interactions between multiple genes and/or environments. Therefore, ideal models in which to examine the relative roles of genetic effects should have, 1) variation in behavioral phenotypes, 2) the potential to identify the genetic bases of these behavioral traits, 3) an obvious association between phenotype and genotype, 4) the potential to identify relevant environmental conditions contributing to the establishment of behavioral phenotypes so that partitioning of gene-by-environment effects is possible, and 5) a strong understanding of the evolutionary forces influencing the system. Given these desires, an unexpected new animal model emerges for the study of behavioral genomics – morphs of the white-throated sparrow (Zonotrichia albicollis) exhibit alternative strategies of monogamy/high parental effort vs. promiscuity/low parental effort. These behaviors are absolutely correlated with the presence or absence of a large chromosomal rearrangement. We have amassed 22+ years of detailed behavioral, physiological, ecological, and evolutionary data on this species making it possible to identify the genetic, epigenetic, and environmental bases of behavior. Here we further outline the utility of the species, as well as present current cytogenetic and molecular data showing that rearrangements and linkage in multiple chromosomes are key to the evolution of alternative phenotypes. In addition, comparative analyses among the Zonotrichia suggest an interesting and slightly counterintuitive evolutionary pathway in this group. Genomic studies in the white-throated sparrow will identify the gene(s) associated with complex behaviors, as well as provide us with information on how environment interacts with genetic architecture to affect aggressive, social, sexual, and parental phenotypes. Morphs of the sparrow provide us with a unique opportunity to study intraspecific genomic differences, which have resulted from two separate, yet linked evolutionary trajectories. Such results can transform our understanding of the evolution of genomes
Developmental stress and telomere dynamics in a genetically polymorphic species
No full textAbstract: A central objective of evolutionary biology is understanding variation in life-history trajectories and the rate of aging, or senescence. Senescence can be affected by trade-offs and behavioural strategies in adults but may also be affected by developmental stress. Developmental stress can accelerate telomere degradation, with long-term longevity and fitness consequences. Little is known regarding whether variation in developmental stress and telomere dynamics contributes to patterns of senescence during adulthood. We investigated this question in the dimorphic white-throated sparrow (Zonotrichia albicollis), a species in which adults of the two morphs exhibit established differences in behavioural strategy and patterns of senescence, and also evaluated the relationship between oxidative stress and telomere length. Tan morph females, which exhibit high levels of unassisted parental care, display faster reproductive senescence than white females, and faster actuarial senescence than all of the other morph-sex classes. We hypothesized that high oxidative stress and telomere attrition in tan female nestlings could contribute to this pattern, since tan females are small and potentially at a competitive disadvantage even as nestlings. Nestlings that were smaller than nest mates had higher oxidative stress, and nestlings with high oxidative stress and fast growth rates displayed shorter telomeres. However, we found no consistent morph-sex differences in oxidative stress or telomere length. Results suggest that oxidative stress and fast growth contribute to developmental telomere attrition, with potential ramifications for adults, but that developmental oxidative stress and telomere dynamics do not account for morph-sex differences in senescence during adulthood
An Intersection of Computational Biology and Functional Genomics to identify Transcriptional Gene Enhancers and Their Role in Cancer
No full textDespite the critical role of gene regulation in cell development and differentiation, the major challenge remains to identify the cis-regulatory modules (CRMs). Mainly, these CRMs include enhancers, promoters and insulators that governs the spatiotemporal gene regulation. The gene regulatory networks are highly dependent on their CRMs and mostly consist of DNA motifs and epigenetic landmarks. The recent advancements in high-throughput sequencing techniques and comparative genomics analysis accelerate the discovery of enhancers, however the major obstacles are to identify the genome-wide location of these CRMs, their dynamic nature of interactions, and cis/trans location which could be hundred to thousands base pairs away from the target gene location. The goal of this literature review is to provide an insight into the CRMs specifically enhancers, how they modulate gene expression, mutations that converts normal cell into a disease-state such as cancer. Also, this embedded review article is focused on the use of computational strategies coupled with the biochemical assays to predict functional gene enhancers. The computational strategies such as window clustering, probabilistic modeling, phylogenetic footprinting and discriminative modeling are briefly discussed to scan and locate the putative gene enhancers. Besides theses, biochemical techniques such as ChIP-seq, DNA footprinting, and deletion mapping are briefly reviewed in Drosophila to predict functional gene enhancers and dissecting gene regulatory networks. In addition, this review article may help bench scientists to incorporate bioinformatics tools with biochemical techniques to scan, locate and verify gene enhancer regions within a cell. With best of our knowledge, this is a first-time effort to combine insilico, in vitro and in vivo techniques to explore the connections between CRMs and gene regulation
Partial incubation during egg laying reduces eggshell microbial loads in a temperate‐breeding passerine
No full textData for: Breeding synchrony and extrapair paternity in a species with alternative reproductive strategies
No full textThis excel file contains information about the levels of extrapair paternity found in clutches of a polymorphic species, the white-throated sparrow (Zonotrichia albicollis). Levels of breeding synchrony are given for each clutch (nesting attempt). Each line contains data on one nestling, and nestlings are grouped into clutches. Information about male characteristics, breeding density, number of territorial neighbors, date, and clutch number (e.g., first or second nesting attempt) is also provided. PercentW is the proportion of the population consisting of white morph (versus the alternative tan morph) males
Oxidative stress data for nestling white-throated sparrows
No full textThis data file contains levels of total antioxidant capacity (OXY), reactive oxygen metabolites (ROM), and oxidative stress (OS) measured in nestling white-throated sparrows (Zonotrichia albicollis). OS was calculated as: mM ROMs/mM TAC x 1000. Also provided are nestling morph (white (W) or tan (T)), nestling sex, day in the nestling stage, basic body measurements, growth rates, and the time and date of blood sampling
