Biology subjects

Metzler, D.

Publications and source records attributed to Metzler, D..

6 recordsLinked to original sources

bioRxiv2023

German Ixodes inopinatus samples may not actually represent this tick species

Ticks are important vectors of human and animal pathogens, but many questions remain unanswered regarding their taxonomy. Molecular sequencing methods have allowed research to start understanding the evolutionary history of even closely related tick species. Ixodes inopinatus is considered a sister species and highly similar to Ixodes ricinus, an important vector of many tick-borne pathogens in Europe, but identification between these species remains ambiguous with disagreement on the geographic extent of I. inopinatus. In 2018-2019, 1583 ticks were collected from breeding great tits (Parus major) in southern Germany, of which 45 were later morphologically identified as I. inopinatus. We aimed to confirm morphological identification using molecular tools. Utilizing two genetic markers (16S rRNA, TROSPA) (n=37) and whole genome sequencing of specific ticks (n=8), we were able to determine that German samples morphologically identified as I. inopinatus, genetically represent I. ricinus regardless of previous morphological identification and most likely are not I. ricinus/I. inopinatus hybrids. Further, our results showed that the entire mitochondrial genome, let alone singular mitochondrial genes (i.e., 16S), is unable to distinguish between I. ricinus and I. inopinatus. As most examples of I. inopinatus in Germany were based on morphology and mitochondrial sequences, the results of the current study brings into question whether I. inopinatus was properly identified in previous research and if this species exists in Central Europe. Our results highlight the power of utilizing genomic data in answering questions regarding tick taxonomy even when closely related species are considered. HighlightsO_LIGerman Ixodes inopinatus samples represent I. ricinus based on genomic data C_LIO_LIThe mitochondrial genome is not sufficient for delineation of I. inopinatus and I. ricinus C_LIO_LIGerman samples most likely do not represent I. ricinus/I. inopinatus hybrids C_LI

evolutionary biology↗

bioRxiv2020

Fluffy feathers: how neoptile feathers contribute to camouflage in precocial chicks

Camouflage is a widespread strategy to increase survival. The plumage of precocial chicks often contains elements of disruptive colouration and background matching to enhance concealment. Chick plumage also features fringed feathers as appendages that may contribute to camouflage. Here, we examine whether and how neoptile feathers conceal the outline of chicks. We first conducted a digital experiment to test two potential mechanisms for outline diffusion through appendages: 1) edge intensity reduction and 2) luminance transition. Local Edge Intensity Analysis (LEIA) showed that appendages decreased edge intensity and a mean luminance comparison revealed that the appendages created an intermediate transition zone to conceal the objects outline. The outline was most diffused through an intermediate number of interspersed thin appendages. Increased appendage thickness resulted in fewer appendages improving camouflage, whereas increased transparency required more appendages for best concealment. For edge intensity, the outline diffusion was strongest for a vision system with low spatial acuity, which is characteristic of many mammalian predators. We then analysed photographs of young snowy plover (Charadrius nivosus) chicks to examine whether neoptile feathers increase outline concealment in a natural setting. Consistent with better camouflage, the outline of digitally cropped chicks with protruding feathers showed lower edge intensities than the outline of chicks cropped without those feathers. However, the observed mean luminance changes were not consistent with better concealment. Taken together, our results suggest that thin skin appendages such as neoptile feathers improve camouflage. As skin appendages are widespread, this mechanism may apply to a large variety of organisms.

ecology↗

bioRxiv2020

Frequency dependent sexual selection, mating trait architecture and preference function govern spatio-temporal hybrid zone dynamics

Hybrid zones provide a window into the evolutionary processes governing species divergence. While the role of postzygotic isolation has been extensively characterized in the context of hybrid zones, the contribution of prezygotic isolation is less well explored. Here, we investigate the effects of assortative mate choice, the underlying preference function and mating-trait architecture, and the strength of sexual selection on hybrid zone dynamics. We explore this question by means of a mathematical model parameterized with phenotype and genotype data from the hybrid zone between all-black carrion and grey-coated hooded crows. The best-fit model resulted in narrow clines for two mating-trait loci coding for colour phenotype maintained by a moderate degree of assortative mating. Epistasis between the two loci induced hybrid-zone movement in favor of alleles conveying dark plumage followed by a shift in the opposite direction favouring grey-coated phenotypes [~]1,200 generations after secondary contact. Unlinked neutral loci diffused near-unimpeded across the zone. These results were generally robust to the choice of matching rule (self-referencing or parental imprinting) and effects of genetic drift. Overall, this study illustrates under which conditions assortative mating can maintain steep clines in mating-trait loci without generalizing to genome-wide reproductive isolation. It further emphasizes the importance of mating-trait architecture for spatio-temporal hybrid-zone dynamics.

evolutionary biology↗

bioRxiv2019

Selection for altruistic defense in structured populations

We model natural selection for or against an anti-parasite (or anti-predator) defense allele in a host (or prey) population that is structured into many demes. The defense behavior has a fitness cost for the actor compared to non defenders ("cheaters") in the same deme and locally reduces parasite growth rates. Hutzenthaler et al. (2022) have analytically derived a criterion for fixation or extinction of defenders in the limit of large populations, many demes, weak selection and slow migration. Here, we use both individual-based and diffusion-based simulation approaches to analyze related models. We find that the criterion still leads to accurate predictions for settings with finitely many demes and with various migration patterns. A key mechanism of providing a benefit of the defense trait is genetic drift due to randomness of reproduction and death events leading to between-deme differences in defense allele frequencies and host population sizes. We discuss an inclusive-fitness interpretation of this mechanism and present in-silico evidence that under these conditions a defense trait can be altruistic and still spread in a structured population.

evolutionary biology↗

bioRxiv2019

Modeling methylation dynamics with simultaneous changes in CpG islands

MotivationProbabilistic models for methylation dynamics of CpG sites are usually based on sequence evolution models that assume indepedence between sites. In vertebrate genomes, CpG sites can be clustered in CpG islands, and the amount of methylation in a CpG island can change due to gene regulation processes. We propose a probabilistic model of methylation dynamics that accounts for simultaneous methylation changes in multiple CpG sites belonging to the same CpG island. We further propose a Markov-chain Monte-Carlo method to fit this model to methylation data from cell type phylogenies and apply this method to available data from murine haematopoietic cells.\n\nResultsBranch lengths in cell phylogenies show the amount of changes in methylation in the development of one cell type from another. We show that accounting for CpG island wide methylation changes has a strong effect on the inferred branch lengths and leads to a significantly better model fit for the methylation data from murine haematopoietic cells.\n\nAvailabilityAn implementation of the methods presented in this article is freely available as C++ source code on https://github.com//statgenlmu//IWEPoissonPaper under the terms of the GNU general public license (GPLv3).

bioinformatics↗

bioRxiv2018

MARGE: Mutation Analysis for Regulatory Genomic Elements

Cell-specific patterns of gene expression are determined by combinatorial actions of sequence-specific transcription factors at cis-regulatory elements. Studies indicate that relatively simple combinations of lineage-determining transcription factors (LDTFs) play dominant roles in the selection of enhancers that establish cell identities and functions. LDTFs require collaborative interactions with additional transcription factors to mediate enhancer function, but the identities of these factors are often unknown. We have shown that natural genetic variation between individuals has great utility for discovering collaborative transcription factors. Here, we introduce MARGE (Mutation Analysis of Regulatory Genomic Elements), the first publicly available suite of software tools that integrates genome-wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. MARGE is optimized to work with chromatin accessibility assays (such as ATAC-seq or DNase I hypersensitivity), as well as transcription factor binding data collected by ChlP-seq. Herein, we provide investigators with rationale for each step in the MARGE pipeline and key differences for analysis of datasets with different experimental designs. We demonstrate the utility of MARGE using mouse peritoneal macrophages, liver cells, and human lymphoblastoid cells. MARGE provides a powerful tool to identify combinations of cell type-specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation.

bioinformatics↗