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"Biology Classsification."
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The New Foundations of Evolution
This book presents a history of microbial evolutionary biology from the 19th century to the present. It follows the research of molecular evolutionists who explore the origins of the genetic system and the primary life forms: three domains and multiple kingdoms, created by mechanisms very unlike those considered by Darwin and his followers.
eBook
Environmental Niche Equivalency versus Conservatism: Quantitative Approaches to Niche Evolution
Environmental niche models, which are generated by combining species occurrence data with environmental GIS data layers, are increasingly used to answer fundamental questions about niche evolution, speciation, and the accumulation of ecological diversity within clades. The question of whether environmental niches are conserved over evolutionary time scales has attracted considerable attention, but often produced conflicting conclusions. This conflict, however, may result from differences in how niche similarity is measured and the specific null hypothesis being tested. We develop new methods for quantifying niche overlap that rely on a traditional ecological measure and a metric from mathematical statistics. We reexamine a classic study of niche conservatism between sister species in several groups of Mexican animals, and, for the first time, address alternative definitions of “niche conservatism” within a single framework using consistent methods. As expected, we find that environmental niches of sister species are more similar than expected under three distinct null hypotheses, but that they are rarely identical. We demonstrate how our measures can be used in phylogenetic comparative analyses by reexamining niche divergence in an adaptive radiation of Cuban anoles. Our results show that environmental niche overlap is closely tied to geographic overlap, but not to phylogenetic distances, suggesting that niche conservatism has not constrained local communities in this group to consist of closely related species. We suggest various randomization tests that may prove useful in other areas of ecology and evolutionary biology.
Journal Article
TESTING FOR DIFFERENT RATES OF CONTINUOUS TRAIT EVOLUTION USING LIKELIHOOD
Rates of phenotypic evolution have changed throughout the history of life, producing variation in levels of morphological, functional, and ecological diversity among groups. Testing for the presence of these rate shifts is a key component of evaluating hypotheses about what causes them. In this paper, general predictions regarding changes in phenotypic diversity as a function of evolutionary history and rates are developed, and tests are derived to evaluate rate changes. Simulations show that these tests are more powerful than existing tests using standardized contrasts. The new approaches are distributed in an application called Brownie and in r8s.
Journal Article
Vom Bildstimulus zur Emotion AI: Zur Sichtbarkeit und Unsichtbarkeit technischer Affektbilder
Science has always produced and processed images that are not only used for illustration purposes, regardless of whether they are historical drawings of biological or technical objects, more recent computer simulations, or the multiple use of photographs (cf. Rheinberger; Weigel; Galison). From this abundance of images, the following article singles out the scientific photographs of emotion psychology. For a long time, this special type of scientific photography in emotion research received little attention in comparison to other cases, such as photographs from psychiatry (cf. Didi-Huberman) and evolutionary biology (cf. Prodger; Voss). However, technical affect pictures have been decisive for the classification, the rating and the computing of the emotion in the sense of bodily phenomena. In the development of Emotion AI and Affective Computing, they still play a key role for the technical identification of individual affects, which is to be highlighted here.
Journal Article
Evolutionary and Biogeographic Origins of High Tropical Diversity in Old World Frogs (Ranidae)
Differences in species richness between regions are ultimately explained by patterns of speciation, extinction, and biogeographic dispersal. Yet, few studies have considered the role of all three processes in generating the high biodiversity of tropical regions. A recent study of a speciose group of predominately New World frogs (Hylidae) showed that their low diversity in temperate regions was associated with relatively recent colonization of these regions, rather than latitudinal differences in diversification rates (rates of speciation-extinction). Here, we perform parallel analyses on the most species-rich group of Old World frogs (Ranidae; ∼1300 species) to determine if similar processes drive the latitudinal diversity gradient. We estimate a time-calibrated phytogeny for 390 ranid species and use this phytogeny to analyze patterns of biogeography and diversification rates. As in hylids, we find a strong relationship between the timing of colonization of each region and its current diversity, with recent colonization of temperate regions from tropical regions. Diversification rates are similar in tropical and temperate clades, suggesting that neither accelerated tropical speciation rates nor greater temperate extinction rates explain high tropical diversity in this group. Instead, these results show the importance of historical biogeography in explaining high species richness in both the New World and Old World tropics.
Journal Article
EVOLUTION IN EXTREME ENVIRONMENTS: REPLICATED PHENOTYPIC DIFFERENTIATION IN LIVEBEARING FISH INHABITING SULFIDIC SPRINGS
We investigated replicated ecological speciation in the livebearing fish Poecilia mexicana and P. sulphuraria (Poeciliidae), which inhabit freshwater habitats and have also colonized multiple sulfidic springs in southern Mexico. These springs exhibit extreme hypoxia and high concentrations of hydrogen sulfide, which is lethal to most metazoans. We used phylogenetic analyses to test whether springs were independently colonized, performed phenotypic assessments of body and gill morphology variation to identify convergent patterns of trait differentiation, and conducted an eco-toxicological experiment to detect differences in sulfide tolerances among ecotypes. Our results indicate that sulfidic springs were colonized by three different lineages, two within P. mexicana and one representing P. sulphuraria. Colonization occurred earlier in P. sulphuraria, whereas invasion of sulfidic springs in P. mexicana was more recent, such that each population is more closely related to neighboring populations from adjacent nonsulfidic habitats. Sulfide spring fish also show divergence from nonsulfidic phenotypes and a phenotypic convergence toward larger heads, larger gills, and increased tolerance to H₂S. Together with previous studies that indicated significant reproductive isolation between fish from sulfidic and nonsulfidic habitats, this study provides evidence for repeated ecological speciation in the independent sulfide spring populations of P. mexicana and P. sulphuraria.
Journal Article
Molekulare Klassifikation des Endometriumkarzinoms – ein kurzer Überblick
Zusammenfassung
Hintergrund
Die histopathologische Diagnostik ist die Basis der Diagnostik und Therapie des Endometriumkarzinoms (EC). Die initial binäre Einteilung in Typ-1-EC (histopathologischer Prototyp endometrioid) bzw. Typ-2-EC (serös) hat sich als unzureichend trennscharf erwiesen.
Material und Methoden
Es erfolgte eine selektive Recherche der Literatur und Analyse der Neuerungen der überarbeiteten Version der S3-Leitlinie Endometriumkarzinom.
Ergebnisse und Schlussfolgerung
Basierend auf initialen Untersuchungen des The Cancer Genome Atlas Project (TCGA) sind 4 distinkte molekulare Subtypen des EC identifiziert worden: EC mit POLE-Mutation (POLEmut), mit Defizienz der Mismatch-Repair-Proteine (dMMR) oder mit p53-Mutation (p53mut) sowie solche ohne eine der genannten Veränderungen, NSMP („no special molecular profile“). Diese molekulare Klassifikation des EC erfolgt histologisch (Tumordiagnose, histologischer Subtyp, Grading), immunhistochemisch (MMR, p53) sowie molekularpathologisch (POLE) und stellt somit eine morphomolekulare Klassifikation dar. Entsprechend den Empfehlungen der Weltgesundheitsorganisation (WHO) sowie zahlreicher nationaler und internationaler Gesellschaften findet die molekulare Klassifikation des EC zunehmend Eingang in die klinische Versorgung. Bis dato unzureichend charakterisiert ist die große Gruppe der NSMP-EC.
Journal Article
Molekulare Klassifikation des Endometriumkarzinoms – ein kurzer Überblick
Zusammenfassung
Hintergrund
Die histopathologische Diagnostik ist die Basis der Diagnostik und Therapie des Endometriumkarzinoms (EC). Die initial binäre Einteilung in Typ-1-EC (histopathologischer Prototyp endometrioid) bzw. Typ-2-EC (serös) hat sich als unzureichend trennscharf erwiesen.
Material und Methoden
Es erfolgte eine selektive Recherche der Literatur und Analyse der Neuerungen der überarbeiteten Version der S3-Leitlinie Endometriumkarzinom.
Ergebnisse und Schlussfolgerung
Basierend auf initialen Untersuchungen des The Cancer Genome Atlas Project (TCGA) sind 4 distinkte molekulare Subtypen des EC identifiziert worden: EC mit POLE-Mutation (POLEmut), mit Defizienz der Mismatch-Repair-Proteine (dMMR) oder mit p53-Mutation (p53mut) sowie solche ohne eine der genannten Veränderungen, NSMP („no special molecular profile“). Diese molekulare Klassifikation des EC erfolgt histologisch (Tumordiagnose, histologischer Subtyp, Grading), immunhistochemisch (MMR, p53) sowie molekularpathologisch (POLE) und stellt somit eine morphomolekulare Klassifikation dar. Entsprechend den Empfehlungen der Weltgesundheitsorganisation (WHO) sowie zahlreicher nationaler und internationaler Gesellschaften findet die molekulare Klassifikation des EC zunehmend Eingang in die klinische Versorgung. Bis dato unzureichend charakterisiert ist die große Gruppe der NSMP-EC.
Journal Article
Origins and Evolution of a Transmissible Cancer
Canine transmissible venereal tumor (CTVT) is an infectious disease of dogs. Remarkably, the infectious agent is the cancerous cell itself. To investigate its origin and spread, we collected 37 tumor samples from four continents and determined their evolutionary relationships using microsatellite length differences and microarray-based comparative genomic hybridization (aCGH). The different tumors show very little microsatellite variation, and the pattern of variation that does exist is consistent with a purely asexual mode of transmission. Approximately one quarter of the loci scored by aCGH show copy number variation relative to normal dogs, again with little variation among different tumor samples. Sequence analysis of the RPPH1 gene indicates an origin from either dogs or wolves, and microsatellite analysis indicates that the tumor is more than 6000 years old, and perhaps originated when dogs were first domesticated. By contrast, the common ancestor of extant tumors lived within the last few hundred years, long after the first tumor. The genetic and genomic patterns we observe are typical of those expected of asexual pathogens, and the extended time since first origin may explain the many remarkable adaptations that have enabled this mammalian cell lineage to live as a unicellular pathogen.
Journal Article