1,721,032 research outputs found
MHC class I variation among wild, domestic and insular populations of the zebra finch (Taeniopygia guttata)
No full textThe zebra finch (Taeniopygia guttata) is a passerine bird native to Australia and the Lesser Sunda Islands, with domesticated populations derived from each of these localities. The Lesser Sundas and domesticated zebra finches have undergone historic bottlenecks and previous analyses using neutral markers have reported striking genetic differences among these populations. However, comparisons utilizing functional loci are lacking. Immune genes are thought to strongly rely on genetic variation to convey a greater resistance to pathogens. Genes of the major histocompatibility complex (MHC), a component of the vertebrate adaptive immune response involved in antigen presentation, have received considerable attention as a classic example of balancing selection. Here, we characterize the third exon of the highly variable MHC class I [alpha] chain, which encodes the [alpha]2 domain of the peptide binding region (PBR). Despite natural and human-mediated population bottlenecks, we find that high MHC polymorphism persists across all populations. We report higher levels of nucleotide diversity when compared with neutral loci and strong evidence of positive selection acting on important residues forming the PBR. Clear population differentiation is also evident and this may be due to adaptation to captivity and life on islands. Due to its importance in pathogen recognition, selection seems to have maintained variability of the MHC class I [alpha]2 domain, even in the presence of a genetic bottleneck.M.S
Microsatellite analysis of brook trout, Salvelinus fontinalis, in western Pennsylvania
No full textIn western Pennsylvania, the brook trout, Salvelinus fontinalis, has dramatically declined in population due to the environmental stressors of mining, logging, water withdrawal, and acid deposition. Brook trout are game fish and are valued economically in this region which makes their declining populations concerning. To better understand brook trout population dynamics in western Pennsylvania, we conducted a genetic analysis to determine patterns of population connectivity and genetic diversity. Microsatellites are short repeat sequences within the genome, and are highly susceptible to mutation making them suitable as neutral markers for analyzing patterns of regional population variation. Therefore, we conducted a microsatellite analysis of 16 individuals from 4 streams, for a total of 64 samples. Seven tri-and tetranucleotide microsatellite DNA markers were analyzed to investigate allelic diversity of brook trout. Amplified microsatellite loci were analyzed using Geneious 6.0 software that estimated PCR product sizes and converted sizes into estimates of the number of microsatellite repeats at each locus. Genepop 4.2 program was used to obtain the fixation index (FST) to measure levels of population differentiation and connectivity. The results showed moderate divergence (average pairwise divergence FST= 0.24; range of 0.06-0.30) with highly significant differentiation (P < 0.001). My study suggests that even populations that are spatially close to one another show evidence of divergence. This finding suggests limited dispersal between streams and will inform species management strategies for this species
Gene Expression Divergence Between Zebra Finch (Taeniopygia Guttata) Subspecies And Gene Regulation In Hybrids
No full textSince the publication of Mayr's Systematics and the Origin of Species, birds have been important model organisms for studies regarding evolutionary processes such as sexual selection and speciation. In this study, I will examine patterns of expression divergence in two subspecies of the zebra finch Taeniopygia guttata. These two zebra finch populations have been allopatrically isolated for about one million years, thus allowing for divergence in aspects of morphology, genetics and behavior. Based on previous research, we have a detailed portrait of the timing and demographic components of divergence in these birds. However, little is known about how gene expression may contribute to genomic divergence. Among sexually reproducing organisms, the conclusion of the speciation process is thought to be evidenced by the buildup of genomic incompatibilities. The two zebra finch subspecies can mate and generate viable hybrids, allowing the use of expression data from hybrids to test for such genomic incompatibilities. Here, I will use RNA sequencing technology to quantify genome-scale patterns of expression divergence, highlighting patterns of functional divergence in the zebra finch genome.M.S
Behavioral and genetic divergence among wild and domesticated populations of the zebra finch (Taeniopygia guttata)
No full textZebra finches (Taeniopygia guttata) have been the subject of extensive neurological and behavioral research having served as the dominant model for vocal learning over half a century. Learned vocal communication, or vocal learning, is a trait that is shared by humans and songbirds but is rare or less well developed in other animals. Unlike innate communication, learned vocalizations are acquired early on by juveniles listening and copying what they hear from adults. Little, however, has been done to characterize the intraspecific variation in song behavior in the zebra finch model system. Other systems, such as the lab mouse, Mus musculus, have begun to take advantage of inbred and natural populations to assess genetic variation and to link genotype and behavior. The opportunity exists to do the same in the zebra finch. The first step to better able study song learning in a genetics context is to define trait variation within and among populations. The majority of research conducted on these birds relies on domesticated populations of Taeniopygia guttata castanotis (T. g. castanotis), but wild populations are also available for study, as is a second subspecies, T. g. guttata. With the sequencing of the zebra finch genome a decade ago, zebra finches have risen in importance in the field of population genomics so there is an opportunity to investigate the genetic variation in this system as well. I compared patterns genetic and song variation among these populations to examine how these features have diverged during the early stages of domestication as well as during divergence in allopatry. When comparing the wild and domesticated populations, I find that overall levels of genetic differentiation are low (FST = ~0.02); I also find evidence of selection acting on portions of the genome. Genetic drift also appears to have played a role in shaping patterns of genetic variation. While genetic drift has led to reduced diversity and a loss of rare alleles in domestic populations, it has also done so in the island subspecies, T. g. guttata: I found further support for a dramatic bottleneck in the island subspecies as the two subspecies have diverged, as there is an overall reduction in diversity. Among the most highly diverged regions of the genome are two genes associated with color. I have identified fixed differences in two well-known pigmentation genes, SLC45A2 and CDKN2A that may contribute to plumage color differences between subspecies. In addition to genetic divergence, I also characterized divergence in song behavior among populations. I find that the island subspecies shows less variation in song among individuals than the mainland birds. Though the island subspecies, T. g. guttata, shows a reduction in variation in song among individuals possibly due to the bottleneck during speciation, the domestication process has actually led to increased variability in song structure in domesticated birds. It is possible that domesticated birds have been freed from the constraints on song structure imposed by mate choice and the need for accurate species recognition. Finally, in order to differentiate between genetic or cultural controls of this difference in variation, I cross-fostered both subspecies to the Bengalese finch, Lonchura striata domestica, to test for differences in song copying behavior. I cannot reject the null hypothesis that zebra finch subspecies copy tutor songs equally well, but it does appear that the high variability in song structure in T. g. castanotis remains following controlled tutoring. Overall, I have begun to characterize the intraspecific behavioral and genetic variation in zebra finches, which has the potential to further our ability to study gene-environment influences on behavior, particularly with regards to the genetic contributions to song copying ability
The Genetic Basis of Pigmentation Variation in Domesticated Zebra Finches
No full textThe zebra finch is the most common estrildid finch native to Australia and Southeast Asia. The zebra finch has also been domesticated and is now a common pet and experimental model system for research. As part of the domestication process, multiple color variants have been generated, providing an opportunity to examine the genetic basis of these traits. For this study I focused on two genes whose single nucleotide polymorphisims have been associated with natural variation in pigmentation traits within both human and animal populations. Thus, I set out to examine the SLC45A2 and TYRP1 gene patterns between several morphs of the domesticated zebra finch. To examine pigmentation variations, both TYRP1 and SLC45A2 genes were sequenced from three different color morphs of the domesticated zebra finch. Sequencing the two genes was limited to the first seven exons of each individual DNA sample to approximate the number of substitutions observed between the morphs. Results from this study gave the first characterization of the two pigmentation genes between the different morphs of the domesticated zebra finch. Through genomic analysis of the candidate genes, we were able to locate non-synonymous mutations in SLC45A2 that differentiate the Chestnut Flanked White Continental (CFW-C), lightback and timor morphs from each other. Though our samples were limited, Exons 1, 2 and 7 showed prominent nucleotide substitutions that could potentially be of functional significance. In contrast, Exons 2, 7 and 6 of the TYRP1 gene showed no significant variations among morphs. Changes in SLC45A2 therefore may contribute to the observed phenotypic differences
The effects of stress on avian gene expression and microbiomes
No full textOrganisms must cope with stressors throughout their lifetime. Stressors are broad and come from both intrinsic and extrinsic sources. In this era of rapid global change, exposure to stressors will become more unpredictable and frequent. Thus, it is imperative we begin to understand how organisms respond to these stimuli. Birds are useful models to investigate responses to stress, as they are a diverse taxonomic group encompassing both well studied ecological and laboratory models. Here, I use several bird species and sources of stress to investigate how birds respond from a transcriptomic and microbiome perspective. The first two chapters investigate how infection and androgens impact gene expression of the avian immune system. In Chapter 1, I explore the avian immune transcriptomic response to West Nile virus, a common avian pathogen that has had devastating effects on birds since its emergence in North America. In Chapter 2, I test the Immunocompetence Handicap Hypothesis, which states that androgen-dependent sexually selected traits are costly to produce because androgens are simultaneously immunosuppressive. I used previously published transcriptome data and found support for the hypothesis. In Chapters 3 & 4, I turn my focus to early-life stress and white-throated sparrows (WTSPs). WTSPs exhibit two stable alternative parental care strategies, biparental care and female-biased parental care. In Chapter 3, I show that female-biased care induces a transcriptomic stress response in nestlings. In Chapter 4, I investigate the microbiome of WTSP nestlings and find no differences between individuals raised under the different parental care strategies. However, I do find some evidence of host genetic control of the microbiome. Overall, I have begun to explore how birds cope with various stressors, including infection, androgen induced immunosuppression, and developmental stress. Through primarily gene expression approaches, I uncover the molecular pathways affected by these stimuli. Each chapter will set the stage for future integrative work to explore organismal responses to their environment
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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