Paul F. Gugger

Paul F. Gugger
Ronin Institute

Ph.D.

About

185
Publications
19,856
Reads
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2,533
Citations
Citations since 2016
59 Research Items
2158 Citations
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Introduction
I am a bioinformatician in the private sector with broad experience ranging from population genomics in non-model trees to single-cell transcriptomics in biomedicine. In my "free" time, I continue past research on evolutionary responses of tree populations to environmental change and related topics in ecology, evolution, and genomics.
Additional affiliations
May 2019 - present
NYU Langone Medical Center
Position
  • Senior Researcher
May 2019 - present
University of Maryland Center for Environmental Science
Position
  • Professor (Assistant)
April 2019 - present
Ronin Institute
Position
  • Researcher
Education
September 2004 - June 2010
University of Minnesota Twin Cities
Field of study
  • Ecology, Evolution and Behavior
August 2000 - December 2003
Duke University
Field of study
  • Biology

Publications

Publications (185)
Article
Full-text available
DNA methylation in plants affects transposon silencing, transcriptional regulation and thus phenotypic variation. One unanswered question is whether DNA methylation could be involved in local adaptation of plant populations to their environments. If methylation alters phenotypes to improve plant response to the environment, then methylation sites o...
Article
Full-text available
Identifying and quantifying the importance of environmental variables in structuring population genetic variation can help inform management decisions for conservation, restoration, or reforestation purposes, in both current and future environmental conditions. Landscape genomics offers a powerful approach for understanding the environmental factor...
Article
Full-text available
Climate change over the next century is predicted to cause widespread maladaptation in natural systems. This prediction, as well as many sustainable management and conservation practices, assumes that species are adapted to their current climate. However, this assumption is rarely tested. Using a large-scale common garden experiment combined with g...
Article
Full-text available
Obesity and diabetes are leading causes of cardiovascular morbidity and mortality. Although extensive strides have been made in the treatments for non-diabetic atherosclerosis and its complications, for patients with diabetes, these therapies provide less benefit for protection from cardiovascular disease (CVD). These considerations spur the concep...
Article
Full-text available
The genus Quercus , which emerged ∼55 million years ago during globally warm temperatures, diversified into ∼450 extant species. We present a high-quality de novo genome assembly of a California endemic oak, Quercus lobata , revealing features consistent with oak evolutionary success. Effective population size remained large throughout history desp...
Article
Full-text available
Amyotrophic lateral sclerosis (ALS) is an incurable disease characterized by proteinaceous aggregate accumulation and neuroinflammation culminating in rapidly progressive lower and upper motor neuron death. To interrogate cell-intrinsic and inter-cell type perturbations in ALS, single-nucleus RNA sequencing was performed on the lumbar spinal cord i...
Article
Full-text available
Aim Adaptation, migration and extinction of species is closely associated with climate changes and shape the distribution of biodiversity. The adaptive responses of species in the biodiversity hotspot, the Hengduan Mountains, to climate change remain poorly understood. Location The Hengduan Mountains, southeast of the Qinghai-Tibet Plateau. Metho...
Article
Full-text available
Background Burgeoning evidence highlights seminal roles for microglia in the pathogenesis of neurodegenerative diseases including amyotrophic lateral sclerosis (ALS). The receptor for advanced glycation end products (RAGE) binds ligands relevant to ALS that accumulate in the diseased spinal cord and RAGE has been previously implicated in the progre...
Article
Full-text available
Fundamental modulation of energy metabolism in immune cells is increasingly being recognized for the ability to impart important changes in cellular properties. In homeostasis, cells of the innate immune system, such as monocytes, macrophages and dendritic cells (DCs), are enabled to respond rapidly to various forms of acute cellular and environmen...
Preprint
The genus Quercus, which emerged ~55 million years ago during globally warm temperatures, diversified into ~450 species. We present a high-quality de novo genome assembly of a California endemic oak, Quercus lobata , revealing features consistent with oak evolutionary success. Effective population size remained large throughout history despite decl...
Article
Understanding how the environment shapes genetic variation provides critical insight about the evolution of local adaptation in natural populations. At multiple spatial scales and multiple geographic contexts within a single species, such information could address a number of fundamental questions about the scale of local adaptation and whether or...
Article
The escalating problem of obesity and its multiple metabolic and cardiovascular complications threatens the health and longevity of humans throughout the world. The cause of obesity and one of its chief complications, insulin resistance, involves the participation of multiple distinct organs and cell types. From the brain to the periphery, cell-int...
Article
Full-text available
For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation and functional constraints...
Article
Full-text available
For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation and functional constraints...
Article
Full-text available
Within the scope of this study, current distribution areas and habitat preferences of Kasnak oak (Quercus vulcanica [Boiss. et Heldr. ex] Kotschy) species, which is known as one of the most rarest oak species in the world, have been revealed and a new distribution area has been determined around Ankara-Nallıhan-Sarıcali Mountain for the distributio...
Article
Full-text available
Within the scope of this study, current distribution areas and habitat preferences of kasnak oak (Quercus vulcanica [Boiss. et Heldr. ex] Kotschy) species, which is known as one of the most rarest oak species in the world, have been revealed and a new distribution area has been determined around Ankara-Nallıhan-Sarıcali Mountain for the distributio...
Article
Full-text available
The eastern North American white oaks, a complex of approximately 16 potentially interbreeding species, have become a classic model for studying the genetic nature of species in a syngameon. Genetic work over the past two decades has demonstrated the reality of oak species, but gene flow between sympatric oaks raises the question of whether there a...
Article
Climate refugia are locations where plants are able to survive periods of regionally adverse climate. Such refugia may affect evolutionary processes and the maintenance of biodiversity. Numerous refugia have been identified in the context of Quater-nary climate oscillations. With climate warming, there is an increasing need to apply insights from t...
Article
Full-text available
Climate refugia are locations where plants are able to survive periods of regionally adverse climate. Such refugia may affect evolutionary processes and the maintenance of biodiversity. Numerous refugia have been identified in the context of Quater-nary climate oscillations. With climate warming, there is an increasing need to apply insights from t...
Preprint
Full-text available
The eastern North American white oaks, a complex of approximately 16 potentially interbreeding species, have become a classic model for studying the genetic nature of species in a syngameon. Genetic work over the past two decades has demonstrated the reality of oak species, but gene flow between sympatric oaks raises the question of whether there a...
Article
Full-text available
Quercus magnoliifolia and Q. resinosa are two Mexican white oak species that have been taxonomically reported to exhibit morphological similarities and possible hybridization. The objective of this study was to compare the variation in Q. magnoliifolia and Q. resinosa throughout their distribution range to identify the degree of species differentia...
Article
Front cover: The cover image of lace lichen (Ramalina menziesii) growing on California valley oak (Quercus lobata), in California, Hastings UC Reserve is based on the Research Paper Historical interactions are predicted to be disrupted under future climate change: The case of lace lichen and valley oak by Jian‐Li Zhao et al., DOI: 10.1111/jbi.13442...
Article
Aim The distributions and interactions of co‐occurring species may change if their ranges shift asymmetrically in response to rapid climate change. We aim to test whether two currently interacting taxa, valley oak (Quercus lobata) and lace lichen (Ramalina menziesii), have had a long‐lasting historical association and are likely to continue to asso...
Article
Full-text available
Background: Hybridization and introgression are common phenomena among oak species. These processes can be beneficial by introducing favorable genetic variants across species (adaptive introgression). Given that drought is an important stress, impacting physiological and morphological variation and limiting distributions, our goal was to identify d...
Article
Full-text available
A long‐term debate in evolutionary biology is the extent to which reproductive isolation is a necessary element of speciation. Hybridizing plants in general are cited as evidence against this notion and oaks specifically have been used as the classic example of species maintenance without reproductive isolation. Here, we use thousands of SNPs gener...
Article
Carcasses provide an important resource for assessing the vulnerability of bat species and sexes to threats, but the reliability of sex data derived from the external morphology (sexmorph) of bat carcasses remains uncertain. We used genetic‐based assessment of sex (sexgen) to evaluate the effect of carcass age and searcher identity on sexmorph‐base...
Article
Full-text available
Local adaptation is a critical evolutionary process that allows plants to grow better in their local compared to nonnative habitat and results in species‐wide geographic patterns of adaptive genetic variation. For forest tree species with a long generation time, this spatial genetic heterogeneity can shape the ability of trees to respond to rapid c...
Article
Full-text available
Many plant species exhibit different leaf morphologies within a single plant, or heterophylly. The molecular mechanisms regulating this phenomenon, however, have remained elusive. In this study, the transcriptomes of submerged and floating leaves of an aquatic heterophyllous plant, Potamogeton octandrus Poir, at different stages of development, wer...
Article
Here we study hybridization, introgression and lineage diversification in the widely distributed canyon live oak (Quercus chrysolepis) and the relict island oak (Q. tomentella), two Californian golden cup oaks with an intriguing biogeographical history. We employed restriction-site-associated DNA sequencing and integrated phylogenomic and populatio...
Technical Report
Full-text available
Koa (Acacia koa) is a valuable tree species economically, ecologically, and culturally in Hawaii. A vascular wilt disease of koa, caused by the fungal pathogen Fusarium oxysporum f. sp. koae (FOXY), causes high rates of mortality in field plantings and threatens native koa forests in Hawaii. Producing seeds with genetic resistance to FOXY is vital...
Preprint
Full-text available
Many plant species exhibit heterophylly, displaying different leaves upon a single plant. The molecular mechanisms regulating this phenomenon, however, have remained elusive. In this study, the transcriptomes of submerged and floating leaves of an aquatic heterophyllous plant, Potamogeton octandrus Poir, were sequenced using a high-throughput seque...
Preprint
Full-text available
Many plant species exhibit heterophylly, displaying different leaves upon a single plant. The molecular mechanisms regulating this phenomenon, however, have remained elusive. In this study, the transcriptomes of submerged and floating leaves of an aquatic heterophyllous plant, Potamogeton octandrus Poir, were sequenced using a high-throughput seque...
Article
Full-text available
Background. Abiotic constraints, historical effects of the last glaciation, and differential dispersal, have been proposed as potential explanations to account for the latitudinal decrease in acorn size of wide-ranging oak species distributed in the U.S. and Canada. Hypothesis. We specifically tested the abiotic constraints hypothesis on oak acorn...
Article
Full-text available
Natural hybridization, which can be involved in local adaptation and in speciation processes, has been linked to different sources of anthropogenic disturbance. Here, we use genotypic data to study range-wide patterns of genetic admixture between the serpentine-soil specialist leather oak (Quercus durata) and the widespread Californian scrub oak (Q...
Article
Full-text available
Reduced water availability during drought can create major stress for many plant species. Within a species, populations with a history of seasonal drought may have evolved the ability to tolerate drought more than those in areas of high precipitation and low seasonality. In this study, we assessed response to water stress in a California oak specie...
Article
Full-text available
Oaks represent a valuable natural resource across Northern Hemisphere ecosystems attracting a large research community studying its genetics, ecology, conservation, and management. Here we introduce a draft genome assembly of valley oak (Quercus lobate) using Illumina sequencing of adult leaf tissue of an tree found in an accessible, well-studied,...
Article
Full-text available
The lotus (Nelumbonaceae: Nelumbo Adans.) is a highly desired ornamental plant, comprising only two extant species, the sacred lotus (N. nucifera Gaerten.) with red flowers and the American lotus (N. lutea Willd.) with yellow flowers. Flower color is the most obvious difference of two species. To better understand the mechanism of flower color diff...
Data
Alignment of bHLH domain of NnbHLH1 and other anthocyanin-related bHLHs from other species. Identical residues are shown in black, conserved residues in dark grey and similar residues in light grey.
Data
GenBank accessions of all contigs used for the identification of 95 MYB, 10 bHLH and 17 WD40 transcription factors in lotus genome.
Data
Details of sample locations, sample size (n) and haplotypes of 16 populations of N. lutea (NlP1-8) and N. nucifera (NnP1-8) surveyed for DNA sequence variation in the second exon of MYB5 gene. tru.
Data
Phylogenetic tree showing relationships between the 92 lotus MYB TFs with MYBs of other species. Numbers close to the nodes indicate bootstrap values, with only values above 50 shown, and scale shows 0.1 amino acid substitutions per site. Black circles represent lotus MYB TFs that were clustered MYBs with other species known to be involved in the r...
Article
Full-text available
Phylogeography documents the spatial distribution of genetic lineages that result from demographic processes, such as population expansion, population contraction, and gene movement, shaped by climate fluctuations and the physical landscape. Because most phylogeographic studies have used neutral markers, the role of selection may have been underval...
Article
Aim: Ecological differentiation of closely related species has attracted wide attention to explore its evolutionary significance in speciation. In particular, the prevalence of ecological speciation of sister species driven by Quaternary climate changes is debated. Here, we used two parapatric sister species, Roscoea humeana and R. cautleoides, to...
Article
Full-text available
A fundamental goal of evolutionary biology is to understand how environment shapes genetic variation through its effect on demographic processes and through natural selection. In non-model species, transcriptome sequencing generates large single nucleotide polymorphism (SNP) panels to disentangle these influences. Quercus lobata (valley oak) offers...
Article
Full-text available
Premise of the study: Geography and climate shape the distribution of organisms, their genotypes, and their phenotypes. To understand historical and future evolutionary and ecological responses to climate, we compared the association of geography and climate of three oak species (Quercus engelmannii, Quercus berberidifolia, and Quercus cornelius-m...
Article
Full-text available
Premise of the study: The ability of California tree populations to survive anthropogenic climate change will be shaped by the geographic structure of adaptive genetic variation. Our goal is to test whether climate-associated candidate genes show evidence of spatially divergent selection in natural populations of valley oak, Quercus lobata, as pre...
Article
Full-text available
The taxonomy of oaks (Quercus) is always a challenge because many species exhibit variable phenotypes that overlap with other species. The scrub White Oaks of California are no exception. In California, Quercus section Quercus (i.e., White Oaks) includes six species of scrub oaks plus four tree oak species. Field identification utilizes leaf traits...
Chapter
Landscape genomic studies analyze spatial patterns of genetic variation to test hypotheses about how demographic history, gene flow, and natural selection have shaped populations. For decades, angiosperm trees have served as outstanding model systems for landscape-scale genetic studies due to their extensive geographic ranges, large effective popul...
Article
Full-text available
Reference transcriptomes provide valuable resources for understanding evolution within and among species. We de novo assembled and annotated a reference transcriptome for Quercus lobata and Q. garryana and identified single-nucleotide polymorphisms (SNPs) to provide resources for forest genomicists studying this ecologically and economically import...
Article
Understanding the factors promoting species formation is a major task in evolutionary research. Here, we employ an integrative approach to study the evolutionary history of the Californian scrub white oak species complex (genus Quercus). To infer the relative importance of geographical isolation and ecological divergence in driving the speciation p...
Technical Report
Full-text available
California oaks exhibit tremendous phenotypic variation throughout their range. This variation reflects phenotypic plasticity in tree response to local environmental conditions as well as genetic differences underlying those phenotypes. In this study, we analyze phenotypic variation in leaf traits for valley oak adults sampled along three elevation...
Technical Report
Full-text available
We present the methods used to establish a provenance test in valley oak, Quercus lobata. Nearly 11,000 acorns were planted and 88 percent of those germinated. The resulting seedlings were measured after 1 and 2 years of growth, and were outplanted in the field in the winter of 2014-2015. This test represents a long-term resource for both research...
Article
It has long been known that adaptive evolution can occur through genetic mutations in DNA sequence, but it is unclear whether adaptive evolution can occur through analogous epigenetic mechanisms, such as through DNA methylation. If epigenetic variation contributes directly to evolution, species under threat of disease, invasive competition, climate...
Article
AimWe studied which factors shape contemporary patterns of genetic structure, diversity and admixture in the canyon live oak (Quercus chrysolepis). Specifically, we tested two alternative hypotheses: (1) that areas with high habitat suitability and stability since the Last Glacial Maximum (LGM) sustain higher effective population sizes, resulting i...
Conference Paper
Background/Question/Methods Climate change is a particularly challenging threat to tree species because their long generation time can delay their evolutionary response. Tolerating the projected rapid rate of 21st Century climate warming and drying will require that tree populations utilize existing local adaptation to climate for the survival of...
Conference Paper
Full-text available
Background/Question/Methods Identifying phenotypes and genes in natural populations that are under selection by local climate is an important goal for evaluating local adaptation in response to climate. Elevational gradients offer a rare opportunity to evaluate the extent of local adaptation in response to climate over small spatial scales. We sam...
Conference Paper
Background/Question/Methods Acacia koa is a keystone tree species native to the Hawaiian Islands. It provides food and habitat for a range of native birds and insects. Climate change is anticipated to impact the Hawaiian Islands. We focused on the landscape genomics of A. koa in Hawaiʻi to identify geographic patterns of genetic differentiation a...