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Progressive levels of trait divergence along a 'speciation transect' in the Lake Victoria cichlid fish Pundamilia
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Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Genomics of adaptation revealed in threespine stickleback
Full text linkNatural selection is the ultimate, but not only force underlying organismal diversity. Despite this general biological insight, our understanding of how selection targets and shapes the genome during adaptation remains incomplete and is the central quest of this thesis. My main model organism is the threespine stickleback fish (Gasterosteus aculeatus). Stickleback provide an outstanding opportunity to study adaptive evolutionary change, because marine ancestors have repeatedly colonized and adapted to different freshwater environments all over the northern hemisphere since the last glacial retreat about 12,000 years ago. Besides wild populations, I also make use of lab-raised stickleback hybrids from controlled crosses for this thesis work.
Thousands of genome-wide genetic polymorphisms (i.e., genetic markers) called in marine, but predominantly in distinct lake and stream stickleback populations from different geographic locations allow me to decipher the number and position of genomic targets of selection in the early phase of adaptive divergence. I find that selection acts on many loci distributed widely across the genome. On a genomic scale, the recombination landscape along chromosomes proves to be - in concert with selection - an important factor in driving heterogeneous genetic differentiation among populations.
To investigate the rate of recombination across the stickleback's genome in more detail, I use an artificially crossed second-generation (F2) population. This reveals constraints in the frequency and location of detectable recombination events (i.e., cross-overs) within the genome. For example, cross-overs prove to be more frequent in chromosome peripheries than centers. This, together with selection, results in decreased within-population genetic diversity and increased between-population differentiation in the centers of chromosomes as opposed to the peripheries. Furthermore, I show that the cessation of recombination between the heterogametic sex chromosomes occurred in independent bouts. As a consequence, I find extended genomic regions distinct in their degree of degeneration between the X and Y chromosome, so called evolutionary strata. Finally, recombination reveals to be an important determinant of other aspects of a genome, such as its nucleotide composition.
Integrating theoretical modeling with targeted and genome-wide sequencing, my research further demonstrates that the inference and interpretation of genomic regions exhibiting particularly high and low population differentiation is not as straightforward as commonly believed. This is because the type of genetic variation available to selection (i.e., pre-existing vs. de novo variation) as well as the mode of adaptation (i.e., divergent vs. parallel adaptation) influence the way neutral variation is shaped by selection across the genome. I demonstrate that a genomic region of high differentiation may not necessarily be indicative of divergent selection when populations adapt in parallel to similar environments from a shared pool of genetic variation.
Based on several hundreds of F2 specimens reared under standardized conditions in the laboratory, I also link variation in heritable phenotypic traits to genetic variation, a research program generally referred to as quantitative trait locus (QTL) mapping. Corroborating with the results from my genome scans within and between wild populations (indicating that adaptive divergence involves many loci widespread across the genome), QTL mapping reveals that most phenotypic traits are controlled by numerous genetic loci. In general, each of these loci explains a small fraction of the entire phenotypic trait variation.
I also use high resolution SNP data to infer the demographic history of several lake and stream stickleback populations from the Lake Constance watershed (Central Europe) and demonstrate that the repeated occurrence of similar stream phenotypes are, in this particular system, better explained by an evolutionary scenario of 'ecological vicariance' rather than repeated parallel divergence. I then show how selection has shaped local and broad-scale linkage, diversity and differentiation across the genome in these populations. Interestingly, I find evidence for strong divergent selection acting on large chromosomal rearrangements I had previously detected to be important for marine vs. freshwater adaptation. This finding provides a strong case for the re-use of pre-existing genetic variation in stickleback and demonstrates that the same genomic regions can be involved in adaptive divergence between disparate ecotype pairs.
Overall, I come to conclude that signatures of selection are - at various physical scales - frequent within the stickleback genome. Stickleback repeatedly use pre-existing genetic variation, shared across various geographic ranges, to adapt to similar or disparate environments. Yet, there is a substantial degree of genetic non-parallelism - at least at the level of neutral markers - that goes along with parallel phenotypic evolution. My thesis emphasizes that the reliable detection and interpretation of genomic signatures of selection requires integrating many replicate study populations within a clear-cut ecological and demographic framework, as well as complementary analytical approaches. Controlled crossing experiments and theoretical modeling are key to deriving predictions about the genomics of adaptation in the wild and to facilitate our understanding of complex biological processes and patterns
Variations on the Author
Full text link“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
Full text linkWe 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
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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