TY - THES A1 - Lamanna, Francesco T1 - Adaptive radiation and speciation in African weakly-electric fish T1 - Adaptive Radiation und Artbildung von elektrischen Fischen Afrikas BT - a phylogenetic and transcriptomic perspective BT - eine phylogenetische und transkriptomische Perspektive N2 - The rise of evolutionary novelties is one of the major drivers of evolutionary diversification. African weakly-electric fishes (Teleostei, Mormyridae) have undergone an outstanding adaptive radiation, putatively owing to their ability to communicate through species-specific Electric Organ Discharges (EODs) produced by a novel, muscle-derived electric organ. Indeed, such EODs might have acted as effective pre-zygotic isolation mechanisms, hence favoring ecological speciation in this group of fishes. Despite the evolutionary importance of this organ, genetic investigations regarding its origin and function have remained limited. The ultimate aim of this study is to better understand the genetic basis of EOD production by exploring the transcriptomic profiles of the electric organ and of its ancestral counterpart, the skeletal muscle, in the genus Campylomormyrus. After having established a set of reference transcriptomes using “Next-Generation Sequencing” (NGS) technologies, I performed in silico analyses of differential expression, in order to identify sets of genes that might be responsible for the functional differences observed between these two kinds of tissues. The results of such analyses indicate that: i) the loss of contractile activity and the decoupling of the excitation-contraction processes are reflected by the down-regulation of the corresponding genes in the electric organ; ii) the metabolic activity of the electric organ might be specialized towards the production and turnover of membrane structures; iii) several ion channels are highly expressed in the electric organ in order to increase excitability, and iv) several myogenic factors might be down-regulated by transcription repressors in the EO. A secondary task of this study is to improve the genus level phylogeny of Campylomormyrus by applying new methods of inference based on the multispecies coalescent model, in order to reduce the conflict among gene trees and to reconstruct a phylogenetic tree as closest as possible to the actual species-tree. By using 1 mitochondrial and 4 nuclear markers, I was able to resolve the phylogenetic relationships among most of the currently described Campylomormyrus species. Additionally, I applied several coalescent-based species delimitation methods, in order to test the hypothesis that putatively cryptic species, which are distinguishable only from their EOD, belong to independently evolving lineages. The results of this analysis were additionally validated by investigating patterns of diversification at 16 microsatellite loci. The results suggest the presence of a new, yet undescribed species of Campylomormyrus. N2 - Das übergreifende Ziel dieser Arbeit ist das bessere Verständnis der Bedeutung der schwachen Elektrizität für die adaptive radiation der Mormyriden Afrikas. Das gewählte Modell-Taxon, die Mormyriden-Gattung Campylomormyrus, zeigt eine große Vielfalt an elektrischen Entladungsformen. Diese Entladungsformen sind artspezifisch. Die genetische Basis dieses Merkmales ist allerdings noch unbekannt. In dieser Arbeit habe ich transkriptomische Untersuchungen vom elektrischen Organ und Skelettmuskel durchgeführt. Die Ergebnisse dieser Analysen zeigen, dass die phenotypischen Unterschiede zwischen dem elektrischen Organ und dem Skelettmusckel in den jeweiligen transkriptomen gespiegelt sind. Ich habe auch einen phylogenetischen Stammbaum für die Gattung Campylomormyrus hergestellt, durch die Anwendung von „Multispecies Coalescent Models“-basierten Methoden. Außerdem, durch die Anwendung von Mikrosatellitdaten, die als unabhängiger Beweis dienten, konnte ich zeigen, dass die identifizierten phylogenetischen Gruppen reproduktiv isolierte biologische Arten sind. Auf diese Weise konnte ich ein neuen, noch unbeschriebenen Art nachweisen. KW - evolution KW - transcriptomics KW - phylogeny KW - Evolution KW - Transkriptomik KW - Phylogenese Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-80097 ER - TY - JOUR A1 - Cui, Xiao A1 - Lv, Yang A1 - Chen, Miaolin A1 - Nikoloski, Zoran A1 - Twell, David A1 - Zhang, Dabing T1 - Young Genes out of the Male: An Insight from Evolutionary Age Analysis of the Pollen Transcriptome JF - Molecular plant N2 - The birth of new genes in genomes is an important evolutionary event. Several studies reveal that new genes in animals tend to be preferentially expressed in male reproductive tissues such as testis (Betran et al., 2002; Begun et al., 2007; Dubruille et al., 2012), and thus an "out of testis' hypothesis for the emergence of new genes has been proposed (Vinckenbosch et al., 2006; Kaessmann, 2010). However, such phenomena have not been examined in plant species. Here, by employing a phylostratigraphic method, we dated the origin of protein-coding genes in rice and Arabidopsis thaliana and observed a number of young genes in both species. These young genes tend to encode short extracellular proteins, which may be involved in rapid evolving processes, such as reproductive barriers, species specification, and antimicrobial processes. Further analysis of transcriptome age indexes across different tissues revealed that male reproductive cells express a phylogenetically younger transcriptome than other plant tissues. Compared with sporophytic tissues, the young transcriptomes of the male gametophyte displayed greater complexity and diversity, which included a higher ratio of anti-sense and inter-genic transcripts, reflecting a pervasive transcription state that facilitated the emergence of new genes. Here, we propose that pollen may act as an "innovation incubator' for the birth of de novo genes. With cases of male-biased expression of young genes reported in animals, the "new genes out of the male' model revealed a common evolutionary force that drives reproductive barriers, species specification, and the upgrading of defensive mechanisms against pathogens. KW - pollen KW - evolution KW - young genes KW - transcriptome Y1 - 2015 U6 - https://doi.org/10.1016/j.molp.2014.12.008 SN - 1674-2052 SN - 1752-9867 VL - 8 IS - 6 SP - 935 EP - 945 PB - Cell Press CY - Cambridge ER -