Biology subjects

Petzold, A.

Publications and source records attributed to Petzold, A..

21 records · Page 2Linked to original sources

bioRxiv2019

A conservative approach for species delimitation based on multi-locus DNA sequences: a case study of the genus Giraffa (Mammalia, Cetartiodactyla)

Molecular data are now commonly used in taxonomy for delimiting cryptic species. In the case of giraffes, which were treated as a single species (Giraffa camelopardalis) during half of a century, several molecular studies have suggested a splitting into four to seven species, but the criteria applied for taxonomic delimitation were not fully described.\n\nIn this study, we have analysed all multi-locus DNA sequences available for giraffes using multispecies coalescent (MSC: *BEAST, BPP and STACEY), population genetic (STRUCTURE, allelic networks, haplotype network and bootstrapping) and phylogenetic (MrBayes, PhyML, SuperTRI) methods to identify the number of species. Our results show that depending on the method chosen, different taxonomic hypotheses, recognizing from two to six species, can be considered for the genus Giraffa. Our results confirm that MSC methods can lead to taxonomic over-splitting, as they delimit geographic structure rather than species. The 3-species hypothesis, which recognizes G. camelopardalis sensu strico, G. giraffa, and G. tippelskirchi, is highly supported by phylogenetic analyses and also corroborated by most population genetic and MSC analyses. The three species show high levels of nucleotide divergence in both nuclear (0.35-0.51 %) and mitochondrial sequences (3-4 %), and they are characterised by 7 to 12 exclusive synapomorphies (ES) detected in nine of the 21 nuclear introns analysed for this study. By contrast, other putative species, such as G. peralta, G. reticulata, G. thornicrofti or G. tippelskirchi sensu stricto, do not exhibit any ES in nuclear genes.\n\nA robust mito-nuclear conflict was found for the position and monophyly of G. giraffa and G. tippelskirchi, which is explained firstly by a mitochondrial introgression from Masai giraffe to southeastern giraffe during the Pleistocene, and secondly, by gene flow mediated by male dispersal between southern populations (subspecies G.g. giraffa and G.g. angolensis).

evolutionary biology↗

bioRxiv2017

Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution

Detecting the genomic changes underlying phenotypic changes between species is a main goal of evolutionary biology and genomics. Evolutionary theory predicts that changes in cis-regulatory elements are important for morphological changes. Here, we combine genome sequencing and functional genomics with genome-wide comparative analyses to investigate the fate of regulatory elements in lineages that lost morphological traits. We first show that limb loss in snakes is associated with widespread divergence of limb regulatory elements. We next show that eye degeneration in subterranean mammals is associated with widespread divergence of eye regulatory elements. In both cases, sequence divergence results in an extensive loss of relevant transcription factor binding sites. Importantly, diverged regulatory elements are associated with key genes required for normal limb patterning or normal eye development and function, suggesting that regulatory divergence contributed to the loss of these phenotypes. Together, our results provide the first evidence that genome-wide decay of the phenotype-specific cis-regulatory landscape is a hallmark of lost morphological traits.

genomics↗

bioRxiv2017

A miRNA catalogue and ncRNA annotation of theshort-living fish Nothobranchius furzeri

Background: The short-lived fish Nothobranchius furzeri is the shortest-lived vertebrate that can be cultured in captivity and was recently established as a model organism for aging research. Small non-coding RNAs, especially miRNAs, are implicated in age-dependent control of gene expression.\n\nResults: Here, we present a comprehensive catalogue of miRNAs and several other non-coding RNA classes (ncRNAs) for Nothobranchius furzeri. Analyzing multiple small RNA-Seq libraries, we show most of these identified miRNAs are expressed in at least one of seven Nothobranchius species. Additionally, duplication and clustering of N. furzeri miRNAs was analyzed and compared to the four fish species Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Takifugu rubripes. A peculiar characteristic of N. furzeri as compared to other teleosts was a duplication of the miR-29 cluster.\n\nConclusion: The completeness of the catalogue we provide is comparable to that of zebrafish. This catalogue represents a basis to investigate the role of miRNAs in aging and development in this species.\n\nAvailability: All supplementary material can be found online at http://www.rna.uni-jena.de/en/supplements/nothobranchius-furzeri-mirnome/.

genomics↗