Biology subjects

Pfrender, M.

Publications and source records attributed to Pfrender, M..

3 recordsLinked to original sources

bioRxiv2025

QTL identification and characterization of the recombination landscape of the mountain pine beetle (Dendroctonus ponderosae)

Insect pests can rapidly accumulate in number and thrive in diverse environments, making them valuable models for studying phenotypic plasticity and the genetic basis of local adaptation. The mountain pine beetle (Dendroctonus ponderosae) is a major forest pest and adult body size and generation time are two traits that vary among populations and directly influence reproductive success and outbreak dynamics. To identify regions of the genome linked to these two traits, we generated ddRAD sequencing data from an F2 intercross, using populations from two Y haplogroups with phenotypic and genetic differences in these traits. A high-density linkage map was generated and QTL analyses performed. We identified a single large effect QTL for generation time, associated with an adult diapause. The QTL spans the entire X chromosome, peaking over the evolutionarily conserved portion of the X. We were unable to detect a significant QTL for body size. Our linkage map identified putative inversions shared by parents that are absent in the published reference genome, with three putative inversions on chromosomes 2, 3, and the X. We also detected extensive regions of low recombination that were associated with low gene density, indicative of large pericentromeric regions. Surprisingly, we found that in our cross, F2 males inherited X chromosomes with significantly fewer crossover events than F2 females. Our findings provide information about the recombination landscape, the sex-biased inheritance of recombined Xs, and the genomic location of a key trait in a major forest pest.

genetics↗

bioRxiv2018

The Effects of Normalization, Transformation, and Rarefaction on Clustering of OTU Abundance

Introduction Introduction Methods Discussion Data and Code Availability References Metagenomic clustering presents a unique opportunity to associate and understand communities. Working with Operational Taxonomic Units (OTUs), however, often requires a strategy for handling OTUs that may be over or under represented in a given sample, which is thought of as \"erroneous\". PCR amplification, for example, is known to sometimes non-linearly over-represent more common species Gonzalez et al. 2012. Strategies dealing with this bias include Normalization, Rarefaction, and Log Transformation. Here, we examine how methods to handle potential outlier observations affect de novo estimation of groups using both clustering and matrix factorization methods.\n\nWhile log transformations may affect parametric tests ...

ecology↗

bioRxiv2017

Methods in Description and Validation of Local Metagenetic Microbial Communities

1. We propose MinHash (as implemented by MASH) and NMF as alternative methods to estimate similarity between metagenetic samples. We further describe these results with cluster analysis and correlations with independent ecological metadata.\n\n2. Using sample to sample similarities based on MinHash similarities we use hierarchal clustering to generate clusters, simultaneously we generate groups based on NMF, and we compare groups generated from the MinHash similarity derived clusters and from NMF to those determined by the environment, looking to Silhouette Width for an assessment of the quality of the cluster.\n\n3. We analyze existing data from the Atacama Desert to determine the relationship between ecological factors and group membership, and using the generated groups from MASH and NMF we run an ANOVA to uncover links between metagenetic samples and known environmental variables such as pH and Soil Conductivity.

bioinformatics↗