Biology subjects

Ahrens, D.

Publications and source records attributed to Ahrens, D..

3 recordsLinked to original sources

bioRxiv2023

A transcriptome-based phylogeny of Scarabaeoidea confirms the sister group relationship of dung beetles and phytophagous pleurostict scarabs (Coleoptera)

Scarab beetles (Scarabaeidae) are a diverse and ecologically important group of angiosperm-associated insects. As conventionally understood, scarab beetles comprise two major lineages: dung beetles and the phytophagous Pleurosticti. However, previous phylogenetic analyses have not been able to convincingly answer the question whether or not the two lineages form a monophyletic group. Here we report our results from phylogenetic analyses of more than 4,000 genes mined from transcriptomes of more than 50 species of Scarabaeidae and other Scarabaeoidea. Our results provide convincing support for the monophyly of Scarabaeidae, confirming the debated sister group relationship of dung beetles and phytophagous pleurostict scarabs. Supermatrix-based maximum likelihood and multispecies coalescent phylogenetic analyses strongly imply the subfamily Melolonthinae as currently understood being paraphyletic. We consequently suggest various changes in the systematics of Melolonthinae: Sericinae Kirby, 1837 stat. rest. and sensu n. to include the tribes Sericini, Ablaberini and Diphucephalini, and Sericoidinae Erichson, 1847 stat. rest. and sensu n. to include the tribes Automoliini, Heteronychini, Liparetrini, Maechidiini, Scitalini, Sericoidini, and Phyllotocini. Both subfamilies appear to consistently form a monophyletic sister group to all remaining subfamilies so far included within pleurostict scarabs except Orphninae. Our results represent a major step towards understanding the diversification history of one of the largest angiosperm-associated radiations of beetles.

zoology↗

bioRxiv2021

Standardized nuclear markers advance metazoan taxonomy

Species are the fundamental units of life and their recognition is essential for science and society. DNA barcoding, the use of a single and often mitochondrial gene, has been increasingly employed as a universal approach for the identification of animal species. However, this approach faces several challenges. Here, we demonstrate with empirical data from a number of metazoan animal lineages that multiple nuclear-encoded markers, so called universal single-copy orthologs (USCOs) performs much better than the single barcode gene to discriminate closely related species. Overcoming the general shortcomings of mitochondrial DNA barcodes, USCOs also accurately assign samples to higher taxonomic levels. These loci thus provide a powerful and unifying framework for species delimitation which considerably improves the DNA-based inference of animal species.

molecular biology↗

bioRxiv2020

Genome-wide binding analysis of 195 DNA Binding Proteins reveals "reservoir" promoters and human specific SVA-repeat family regulation

A key aspect in defining cell state is the complex choreography of DNA binding events in a given cell type, which in turn establishes a cell-specific gene-expression program. In the past two decades since the sequencing of the human genome there has been a deluge of genome-wide experiments which have measured gene-expression and DNA binding events across numerous cell-types and tissues. Here we re-analyze ENCODE data in a highly reproducible manner by utilizing standardized analysis pipelines, containerization, and literate programming with Rmarkdown. Our approach validated many findings from previous independent studies, underscoring the importance of ENCODEs goals in providing these reproducible data resources. This approach also revealed several new findings: (i) 1,362 promoters, termed reservoirs, have up to 111 different DNA binding-proteins localized on one promoter yet do not have any expression of steady-state RNA (ii) The human specific SVA repeat element may have been co-opted for enhancer regulation. Collectively, this study performed by the students of a CU Boulder computational biology class (BCHM 5631 - Spring 2020) demonstrates the value of reproducible findings and how resources like ENCODE that prioritize data standards can foster new findings with existing data in a didactic environment.

genomics↗