1,720,973 research outputs found
Sex differences in spiders: from phenotype to genomics
No full textSexual reproduction is pervasive in animals and has led to the evolution of sexual dimorphism. In most animals, males and females show marked differences in primary and secondary sexual traits. The formation of sex-specific organs and eventually sex-specific behaviors is defined during the development of an organism. Sex determination processes have been extensively studied in a few well-established model organisms. While some key molecular regulators are conserved across animals, the initiation of sex determination is highly diverse. To reveal the mechanisms underlying the development of sexual dimorphism and to identify the evolutionary forces driving the evolution of different sexes, sex determination mechanisms must thus be studied in detail in many different animal species beyond the typical model systems. In this perspective article, we argue that spiders represent an excellent group of animals in which to study sex determination mechanisms. We show that spiders are sexually dimorphic in various morphological, behavioral, and life history traits. The availability of an increasing number of genomic and transcriptomic resources and functional tools provides a great starting point to scrutinize the extensive sexual dimorphism present in spiders on a mechanistic level. We provide an overview of the current knowledge of sex determination in spiders and propose approaches to reveal the molecular and genetic underpinnings of sexual dimorphism in these exciting animals
Intraspezifische phänotypische Variation und deren genetische Basis in Daphnia
No full textOrganismen leben in einer dynamischen und häufig herausfordernden Welt. Wechselnde Umweltbedingungen zu bewältigen, ist eine wesentliche Fähigkeit von Organismen um ihr Überleben zu sichern und somit eine wichtige Fähigkeit, diese an ihre Nachkommen weiterzugeben. Organismen entwickelten eine Reihe verschiedener Mechanismen wie z. B. Veränderungen in der Morphologie, ihrem Verhalten oder in Merkmalen ihrer Lebensgeschichte ('life history traits') um Umweltveränderungen zu bewältigen. Diese phänotypisch plastischen Antworten ermöglichen den Lebewesen, sich schnell einen neuen Lebensstil anzueignen, wenn eine neue Umweltsituation eintritt. Phänotypisch plastische Antworten auf Prädatoren wurden für den ökologischen und genomischen Modellorganismus Daphnia berichtet. Dieser ist ein Zooplankter, der als Weidegänger im Süsswasser eine Schlüsselposition in aquatischen Nahrungsnetzen einnimmt. Allerdings
wurde bisher die Variabilität innerhalb von Daphnia-Populationen selten explizit
adressiert. Des Weiteren ist die genetische Basis dieser Räuber-induzierten Antworten
bisher nicht gut verstanden.
Die vorgelegte Arbeit hat zum Ziel, die intraspezifische phänotypische Variation sowie ihre genetische Basis in der europäischen Art Daphnia galeata zu untersuchen. 'life history traits' von insgesamt 24 klonalen Linien wurden in An- und Abwesenheit von
Fischkairomonen dokumentiert und zeigten hohe intraspezifische phänotypische Variation innerhalb und zwischen den vier untersuchten D. galeata Populationen. Die Ergebnisse zeigten weiter, dass das Potential zur lokalen Anpassung an die Anwesenheit von Prädatoren gegeben ist und dass Fischkairomone einen Einfluss auf die Morphologie von D. galeata haben. Um Licht ins Dunkel der genetischen Basis von Räuber-induzierten Antworten zu bringen, wurden Transkriptionsprofile von zwei klonalen Linien, die Fischkairomonen ausgesetzt waren, erstellt und Kandidaten-Transkripte identifiziert, die in Räuber-induzierte Veränderungen von 'life history traits' involviert waren. Die differenzierende Genexpressionsanalyse zeigte eine hohe Varianz zwischen den klonalen Linien, die die konträre Strategie der 'life history traits' reflektiert. Insgesamt wurden 125 unterschiedlich exprimierte Transkripte in der Anwesenheit von Fischkairomonen identifiziert. Die zusätzliche Gen-Co-Expressionsanalyse identifizierte Gruppen von eng verbunden Transkripten (Module), die genetische Pfade in Räuber-induzierten Antworten aufzeigen. Sie beinhalten Transkripte, die in der Remodellierung der Kutikula, in Wachstum und Verdauung involviert sind. Bei der Anwendung einer genom-weiten Assoziationsanalyse auf die Genotypen und Phänotypen der 24 untersuchten klonalen Linien wurden zwei 'life history traits' entdeckt, die eine genetische Basis auf der Sequence Ebene in der An- und Abwesenheit von Räubern hat. Des Weiteren identifizierte die GenCo-Expressionsanalyse 44 Module, von dem eines mit dem 'life history trait' Gesamtanzahl von Bruten korrelierte. Durch Integration einer transkriptom-weiten Assoziationsanalyse und einer Gen-Co-Expressionsanalyse konnte eine Liste mit 156 Kandidaten-Transkripten erstellt werden. Um das Verständnis der funktionalen Rolle der Transkripte zu verbessern, wurden orthologe und paraloge Transkripte von verwandten Arten hinzugezogen und gemeinsame Gruppen orthologer Transkripte verwendet, um interessante Kandidaten
Transkripte zu annotieren.
Dieser integrative Ansatz von verschiedenen Methoden bestärkte, dass die Identität einer klonale Linie an sich wichtig ist, sowohl auf phänotypischer als auch genetischer Ebene. Dies wurde in den 24 untersuchten klonalen Linien der europäischen Daphnia galeata gezeigt, die dem Risiko einem Räuber zu begegnen ausgesetzt waren. Die Daten dieser Doktorarbeit stellen wertvolle Information über Räuber-induzierte Antworten in Daphnia zur Verfügung, während sie gleichzeitig wesentlich zum Verständnis der Bedeutung der genetischen Basis zur intraspezifischen phänotypischen Variation beiträgt.Organisms live in a dynamic and often challenging world. Coping with stress due to
environmental changes is a vital skill for organisms to ensure their survival as well as a valuable capability to pass on to their progeny. Organisms evolved a variety of
mechanisms such as changes in morphology, life history traits or behavior to cope with environmental changes. These phenotypic plastic responses allow organisms to rapidly adjust their lifestyle to a new environmental situation. Phenotypic plastic responses to vertebrate and invertebrate predators are reported for the ecological and genomic model organism Daphnia, a grazing freshwater zooplankter occupying a key position within aquatic food webs. However, the inter- and intra-population variation in Daphnia is rarely addressed explicitly. Furthermore, the genetic basis of these predator-induced responses is not well understood.
The present thesis aims to assess the intraspecific phenotypic variation and its genetic basis in European Daphnia galeata. Life history traits were recorded in the presence and absence of fish kairomones for a total of 24 clonal lines consisting of four populations with six clonal lines each. High intraspecific phenotypic variation was revealed within and between all four D. galeata populations. In addition, the potential to locally adapt to a vertebrate predator regime as well as an effect of the fish kairomones on morphology of D. galeata was investigated. To bring light into the genetic level of predator-induced response, the transcriptional profile of two D. galeata clonal lines exposed to fish kairomones were established identifying candidate transcripts being involved in predatorinduced shifts of life history traits. The differential gene expression analysis revealed a surprisingly high variance between clonal lines reflecting their opposing life history strategies. A total of 125 differentially expressed transcripts (DETs) were identified to be related to fish kairomone exposure. The additional gene co-expression network analysis identified clusters of tightly linked transcripts. Genetic pathways of predator-induced responses were thereby revealed including transcripts being involved in remodeling of the cuticle, growth and digestion. By applying a genome-wide association approach to genotypes and phenotypes of all 24 clonal lines, two life history traits were discovered to have a genetic basis at sequence level in the presence and absence of fish kairomones.
Furthermore, a gene co-expression network analysis of all 24 clonal lines in the absence of fish kairomones identified 44 gene clusters of which one module correlated to one life history trait, the total number of broods. By integrating a transcriptome-wide association analysis and a gene co-expression analysis a list of 156 candidate transcripts was established. To enhance the understanding of the functional roles of the transcripts, orthologs and paralogs from related species were identified using common ontologies to annotate the candidate transcripts of interest.
Interestingly, the integrative approach emphasized the importance of the identity of a
clonal line both at the phenotypic and genetic level in the studied 24 clonal lines of
European D. galeata in an environment of predation risk. The data of the present thesis provides valuable information for predator-induced responses in Daphnia, while contributing substantially to our understanding of the genetic basis of intraspecific phenotypic variation
Genomic architecture in the Daphnia longispina species complex
No full textHybridization between species across the tree of life is an important evolutionary force that shapes the species’ genomes. The short- and long-term evolutionary consequences of hybridization vary among taxa and are affected by neutral processes, recombination, or selection. The impact of these processes can vary between populations and individuals and lead to diverse outcomes, such as the erosion of reproductive barriers or the introduction of new genetic material for adaptation. The overarching questions addressed in this thesis are about the causes and frequency of recent hybridization in hybrid zones, and how genomic patterns vary among populations and species. I examine these questions in taxa of the zooplankton Daphnia longispina species complex, which is known to hybridize frequently and form freshwater mosaic hybrid zones. To facilitate this, I apply, adapt, and develop appropriate genomic methods to investigate genome-wide hybridization and introgression.
Daphnia resting eggs accumulate over time in freshwater ecosystems and are particularly well suited for population genomic studies of hybrid zones and the temporal changes they experience. However, methods were hindered by small amounts of potentially degraded DNA. In Chapter 2, I introduce and test a cost-saving method for whole-genome sequencing of Daphnia resting eggs from the resting egg bank using whole genome amplification and a pre-sequencing contamination screening. This allows us, for the first time, to directly investigate genomic diversity and hybridization in Daphnia populations over several decades.
Previous studies of the Daphnia longispina species complex have found frequent hybridization, but lacked a reference genome to characterize genome-wide variability. The D. galeata reference genome I present in Chapter 3, allowed us to identify extensive hybridization and introgression in ecologically diverse habitats. In total, we resequenced and analyzed 49 genomes from the three species and their hybrids, from genotypes sampled in the water column and from single resting eggs extracted from sediment cores. Introgression patterns revealed a complex history reflecting multiple generations of hybridization and backcrossing.
Building on this work, I studied the hybridization dynamics of two populations in more detail in Chapter 4. I further improved the reference genome to a chromosome scale and generated more extensive time-series genomic data. Using a novel junctions approach based on how recombination breaks up genomic blocks of contiguous ancestry over time, I demonstrate how it can be used to estimate the extent and timing of hybridization events. I identified recurrent hybridization across the genome over several decades in both populations and diverse genome-wide hybrid ancestry among individuals. These findings establish the Daphnia longispina species complex as a hybrid system with unique features, such as continuous hybridization between multiple species in a mosaic hybrid zone, not previously described in a natural hybrid population.
These temporal hybridization dynamics are important to consider as changes to hybrid zones are accelerated by anthropogenic changes in Daphnia and other hybrid systems. Ultimately, I show the temporal dynamics and the diverse genomic landscapes of hybrid individuals with unprecedented resolution. This thesis illustrates the evolutionary complexity required to understand all factors that shape mosaic hybrid zones, such as spatial and temporal changes, recurrent hybridization, and the presence of multiple species
Comparative and population transcriptomics of Daphnia galeata
No full textNatural environments are increasingly fragmented through habitat destruction and organisms shift their geographical distribution by altering their growth and reproduction patterns to persist in the habitat. Organisms are subjected to severe selection pressures and they undergo rapid evolutionary changes to avoid extinction. This is particularly evident in aquatic environments especially for species like Daphnia. Therefore, understanding the genetic basis of local adaptation and phenotypic variation and their interplay with the environment are important factors to predict the consequences of ongoing climate change. Daphnia are cyclical parthenogens and they produce resting eggs which make them a well-suited model organism for this purpose.
The aim of the thesis was to assess the impact of transcriptomic basis of local adaptation and phenotypic variation in four European D. galeata populations and identify their ecological roles. To this aim, I used the D. galeata transcriptome data to identify transcripts potentially under local adaptation at the regulatory and sequence level. I revealed candidate transcripts under local adaptation which is influenced by the interplay of forces such as drift, selection and gene flow. Furthermore, I performed a functional annotation of D. galeata transcripts. However, several transcripts identified in D. galeata were “hypothetical” in function. To be able to assess the ecological role and improve the existing annotations of these transcripts, I employed a data mining approach and developed a database based on the expression profiles in Daphnia species from several previous studies. This meta-analysis helped to improve the existing functional annotation of Daphnia by linking them to their ecological roles. Finally, to reveal the transcriptomic basis of phenotypic variation, I performed an association analysis with sequence polymorphisms and ten life-history traits data in the absence and presence of predator-kairomones obtained from another experiment. This study revealed a transcriptomic basis for two life-history traits and the role of plasticity in determining adaptations was inferred.
In conclusion, I detected signs of local adaptation at the transcriptomic level and the association analysis allowed assessing the interplay between the genotype, phenotype and environment. I also improved the existing functional annotation of Daphnia genes/transcripts by developing the Daphnia stressor database. However, further information and work are required to predict the consequences of Daphnia species accurately in the light of environmental fluctuations
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
Impact of climate change on freshwater snail species' ranges
No full textGlobal warming is expected to be associated with diverse changes in freshwater habitats in north-western Europe. Increasing evaporation, lower oxygen concentration due to increased water temperature and changes in precipitation pattern are likely to affect the survival ratio and reproduction rate of freshwater gastropods (Pulmonata, Basommatophora). This work is a comprehensive analyse of the climatic factors influencing their ranges both in the past and in the near future. A macroecological approach showed that for a great proportion of genera the ranges were projected to contract by 2080, even if unlimited dispersal was assumed. The forecasted warming in the cooler northern ranges predicted the emergence of new suitable areas, but also reduced drastically the available habitat in the southern part of the studied region. In order to better understand the ranges dynamics in the past and the post glacial colonisation patterns, an approach combining ecological niche modelling and phylogeography was used for two model species, Radix balthica and Ancylus fluviatilis. Phylogeographic model selection on a COI mtDNA dataset confirmed that R. balthica most likely spread from two central European disjunct refuges after the last glacial maximum. The phylogeographic analysis of A. fluviatilis, using 16S and COI mtDNA datasets, also inferred central European refugia. The absence of niche conservatism (adaptive potential) inferred for A. fluviatilis puts a cautionary note on the use of climate envelope models to predict the future ranges of this species. However, the other model species exhibited strong niche conservatism, which allow putting confidence into such predictions. A profound faunal shift will take place in Central Europe within the next century, either permitting the establishment of species currently living south of the studied region or the proliferation of organisms relying on the same food resources. This study points out the need for further investigations on the dispersal modes of freshwaters snails, since the future range size of the species depend on their ability to establish in newly available habitats. Likewise, the mixed mating system of these organisms gives them the possibility to fund a new population from a single individual. It will probably affect the colonisation success and needs further investigation
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe 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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