Michael E Pfrender

Michael E Pfrender
University of Notre Dame | ND · Department of Biological Sciences

Ph.D.

About

361
Publications
49,976
Reads
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9,867
Citations
Citations since 2016
86 Research Items
6337 Citations
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Introduction
Michael E Pfrender currently works at the Department of Biological Sciences, University of Notre Dame. Michael does research in Evolutionary Biology and Genetics.
Additional affiliations
January 2011 - December 2012
University of Notre Dame
July 2009 - June 2016
University of Notre Dame
Position
  • Professor (Associate)
August 2001 - June 2009
Utah State University

Publications

Publications (361)
Article
Full-text available
Background: Formalin-fixed, paraffin-embedded (FFPE) tissues have many advantages for identification of risk biomarkers, including wide availability and potential for extended follow-up endpoints. However, RNA derived from archival FFPE samples has limited quality. Here we identified parameters that determine which FFPE samples have the potential...
Article
Objectives The impact and risk of SARS-CoV-2 transmission from asymptomatic and presymptomatic hosts remains an open question. This study measured the secondary attack rates (SARs) and relative risk (RR) of SARS-CoV-2 transmission from asymptomatic and presymptomatic index cases as compared with symptomatic index cases. Methods We used COVID-19 te...
Article
Full-text available
The repeated evolution of tetrodotoxin (TTX) resistance provides a model for testing hypotheses about the mechanisms of convergent evolution. This poison is broadly employed as a potent antipredator defense, blocking voltage‐gated sodium channels (Nav) in muscles and nerves, paralyzing and sometimes killing predators. Resistance in taxa bearing thi...
Article
Importance: The COVID-19 pandemic led many higher education institutions to close campuses during the 2020-2021 academic year. As campuses prepared for a return to in-person education, many institutions were mandating vaccines for students and considering the same for faculty and staff. Objective: To determine the association between vaccination...
Article
Full-text available
Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been vitally important during the COVID-19 pandemic. There are a variety of methods for testing for this virus, and it is important to understand their accuracy in choosing which one might be best suited for a given application.
Article
Full-text available
Although obligately asexual lineages are thought to experience selective disadvantages associated with reduced efficiency of fixing beneficial mutations and purging deleterious mutations, such lineages are phylogenetically and geographically widespread. However, despite several genome-wide association studies, little is known about the genetic elem...
Preprint
Spread of nonindigenous organisms by shipping is one of the largest threats to coastal ecosystems. Limited monitoring and understanding of this phenomenon currently hinder development of effective prevention policies. Surveying ports in North America, South America, Europe, Southeast Asia, and Australia we explored environmental DNA community profi...
Preprint
Full-text available
Importance. The COVID—19 pandemic led many higher education institutions to close campuses during the 2020—21 academic year. As campuses prepared for a return to in—person education, many institutions were mandating vaccines for students and considering the same for faculty and staff. This paper demonstrates the effectiveness of such a strategy bas...
Article
Full-text available
Bacteriocins are a highly diverse group of antimicrobial peptides that have been identified in a wide range of commensal and probiotic organisms, especially those resident in host microbiomes. Rising antibiotic resistance have fueled renewed research into new drug scaffolds such as antimicrobial peptides for use in therapeutics. In this investigati...
Preprint
Full-text available
Despite increasing empirical evidence that chromosomal rearrangements may play an important role in adaptive divergence and speciation, the degree to which divergent genomic regions are associated with chromosomal rearrangements remains unclear. In this study, we provide the first whole-genome analyses of ecological speciation and chromosomal evolu...
Preprint
Full-text available
Accurate tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been critical in efforts to control its spread. The accuracy of molecular tests for SARS-CoV-2 has been assessed numerous times, usually in reference to a gold standard diagnosis. One major disadvantage of that approach is the possibility of error due to inaccuracy...
Preprint
Full-text available
Importance: Asymptomatic and presymptomatic carriers of SARS-CoV-2 are an ongoing and significant risk for community spread of the virus, especially with the majority of the world still unvaccinated and new variants emerging. Objective: To quantify the presence and effects of symptom presentation (or lack thereof) on the community transmission ofSA...
Article
Full-text available
Cryptococcus neoformans is responsible for life-threatening infections that primarily affect immunocompromised individuals and has an estimated worldwide burden of 220,000 new cases each year—with 180,000 resulting deaths—mostly in sub-Saharan Africa. Surprisingly, little is known about the ecological niches occupied by C . neoformans in nature. To...
Article
Full-text available
Environmental DNA (eDNA) analysis methods permit broad yet detailed biodiversity sampling to be performed with minimal field effort. However, considerable uncertainty remains regarding the spatial resolution necessary for effective sampling, especially in aquatic environments. Also, contemporary plant communities are under-investigated with eDNA me...
Article
Full-text available
Background: Island systems offer excellent opportunities for studying the evolutionary histories of species by virtue of their restricted size and easily identifiable barriers to gene flow. However, most studies investigating evolutionary patterns and processes shaping biotic diversification have focused on more recent (emergent) rather than ancie...
Preprint
Full-text available
Cryptococcus neoformans is responsible for life-threatening infections that primarily affect immunocompromised individuals and has an estimated worldwide burden of 220,000 new cases each year—with 180,000 resulting deaths—mostly in sub-Saharan Africa. Surprisingly, little is known about the ecological niches occupied by C. neoformans in nature. To...
Article
Full-text available
The ability to properly identify species present in a landscape is foundational to ecology and essential for natural resource management and conservation. However, many species are often unaccounted for due to ineffective direct capture and visual surveys, especially in aquatic environments. Environmental DNA metabarcoding is an approach that overc...
Preprint
Full-text available
Background: Island systems offer excellent opportunities for studying the evolutionary histories of species by virtue of their restricted size and easily identifiable barriers to gene flow. However, most studies investigating evolutionary patterns and processes shaping biotic diversification have focused on more recent (emergent) rather than ancien...
Preprint
Full-text available
Background: Island systems offer excellent opportunities for studying the evolutionary histories of species by virtue of their restricted size and easily identifiable barriers to gene flow. However, most studies investigating evolutionary patterns and processes shaping biotic diversification have focused on more recent (emergent) rather than ancien...
Preprint
Full-text available
Background: Island systems offer excellent opportunities for studying the evolutionary histories of species by virtue of their restricted size and easily identifiable barriers to gene flow. However, most studies investigating evolutionary patterns and processes shaping biotic diversification have focused on more recent (emergent) rather than ancien...
Preprint
Full-text available
Background: Island systems offer excellent opportunities for studying the evolutionary histories of species by virtue of their restricted size and easily identifiable barriers to gene flow. However, most studies investigating evolutionary patterns and processes shaping biotic diversification have focused on more recent (emergent) rather than ancien...
Article
Full-text available
The Geographic Mosaic Theory of Coevolution (GMTC) predicts that coevolutionary arms races will vary over time and space because of the diverse ecological settings and population histories of interacting species across the landscape. Thus, understanding coevolution may require investigating broad sets of populations sampled across the range of the...
Article
Full-text available
The advent of next-generation sequencing has allowed for higher-throughput determination of which species live within a specific location. Here we establish that three analysis methods for estimating diversity within samples-namely, Operational Taxonomic Units; the newer Amplicon Sequence Variants; and a method commonly found in sequence analysis,...
Article
Full-text available
Background: Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding gen...
Article
Full-text available
Background: Daphnia species reproduce by cyclic parthenogenesis involving both sexual and asexual reproduction. The sex of the offspring is environmentally determined and mediated via endocrine signalling by the mother. Interestingly, male and female Daphnia can be genetically identical, yet display large differences in behaviour, morphology, life...
Article
Full-text available
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Article
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The small cabbage white butterfly, Pieris rapae , is a major agricultural pest of cruciferous crops and has been introduced to every continent except South America and Antarctica as a result of human activities. In an effort to reconstruct the near-global invasion history of P. rapae , we developed a citizen science project, the “Pieris Project,” a...
Article
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Metabarcoding helps to quickly assess biodiversity. In this study, we discuss popular metabarcoding analytical tools and parameter settings. We also develop a metabarcoding bioinformatics pipeline, EPPS, to process data from quality control of raw reads to biodiversity comparisons between samples using a pipeline building program, Nextflow. EPPS pi...
Preprint
Full-text available
A major goal of invasion and climate change biology research is to understand the ecological and evolutionary responses of organisms to anthropogenic disturbance, especially over large spatial and temporal scales. One significant, and sometimes unattainable, challenge of these studies is garnering sufficient numbers of relevant specimens, especiall...
Poster
Full-text available
Three common methods, normalization, log transformation , and rarefaction, for handling outliers and erroneous abundances in Operational Taxonomic Unit (OTU) tables are tested for effects in K-means and PCA clustering as well as effects in NMF. We find that of the three methods, log transformation is closest to the unmodified OTUs data, also indica...
Conference Paper
Full-text available
The advent of next-generation barcode sequencing has allowed for more high-throughput determination of which species live within an area. Relationships, which are a computed distance, are determined by inferred occupancy of the species in one location relative to another. Here we establish that two analysis methods, namely the established Operation...
Article
Full-text available
The analysis of environmental DNA (eDNA) using metabarcoding has increased in use as a method for tracking biodiversity of ecosystems. Little is known about eDNA in marine human-modified environments, such as commercial ports, which are key sites to monitor for anthropogenic impacts on coastal ecosystems. To optimise an eDNA metabarcoding protocol...
Preprint
Full-text available
Background Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genom...
Article
Full-text available
DNA methylation is an evolutionary ancient epigenetic modification that is phylogenetically widespread. Comparative studies of the methylome across a diverse range of non-conventional and conventional model organisms is expected to help reveal how the landscape of DNA methylation and its functions have evolved. Here we explore the DNA methylation p...
Article
Full-text available
Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, beha...
Article
Full-text available
Environmental DNA (eDNA) metabarcoding can greatly enhance our understanding of global biodiversity and our ability to detect rare or cryptic species. However, sampling effort must be considered when interpreting results from these surveys. We explored how sampling effort influenced biodiversity patterns and nonindigenous species (NIS) detection in...
Article
Full-text available
Environmental DNA (eDNA) metabarcoding has been increasingly applied to biodiversity surveys in stream ecosystems. In stream networks, the accuracy of eDNA-based biodiversity assessment depends on whether the upstream eDNA influx affects downstream detection. Biodiversity assessment in low-discharge streams should be less influenced by eDNA transpo...
Article
Full-text available
Significance The biological consequences of climate change are determined by the responses of individual species and interactions among species. Hybridization, or interbreeding between related species, is an interaction that affects how species evolve in response to environmental change. Here we provide evidence that climatic warming has caused a g...
Preprint
Full-text available
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. 2. Using sample to sample similarities based on MinHash similarities we use hierarchal clustering to generate...
Article
Full-text available
The spread of blood-borne pathogens by mosquitoes relies on their taking a blood meal; if there is no bite, there is no disease transmission. Although many species of mosquitoes never take a blood meal, identifying genes that distinguish blood feeding from obligate nonbiting is hampered by the fact that these different lifestyles occur in separate,...
Article
Increasing effects of anthropogenic stressors and those of natural origin on aquatic ecosystems have intensified the need for predictive and functional models of their effects. Here, we use gene expression patterns in combination with weighted gene co-expression networks and generalized additive models to predict effects on reproduction in the aqua...
Article
Full-text available
Background: The primary energy-producing pathway in eukaryotic cells, the oxidative phosphorylation (OXPHOS) system, comprises proteins encoded by both mitochondrial and nuclear genes. To maintain the function of the OXPHOS system, the pattern of substitutions in mitochondrial and nuclear genes may not be completely independent. It has been sugges...
Article
Full-text available
Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here, we used RAD sequencing across the entire MPB ran...
Article
Full-text available
The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing (‘HTS’) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed ‘environmental DNA’ or ‘eDNA’). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called ‘...