Ecology and Evolutionary Biology Commons^™

Mobile Genetic Elements Shape Microbial Diversity And Functions In Thawing Permafrost Soils, Jiarong Guo, Samuel T. N. Aroney, Guillermo Domínguez-Huerta, Derek Smith, Dean Vik, Carlos Owusu-Ansah, Akbar Adjie Pratama, Sergei Solonenko, Funing Tian, Cristina Howard-Varona, Zhi-Ping Zhong, Aminata Fofana, Garrett J. Smith, Suzanne B. Hodgkins, Dylan Cronin, Isogenie Field Teams 2010–2017, 2019, Emerge Coordinators, Ben J. Woodcroft, Gene W. Tyson, Virginia I. Rich, Matthew B. Sullivan, Simon Roux, Sarah C. Bagby, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Ecosystems are shaped by communities of microorganisms whose niches and impacts depend on functional profiles influenced by gene gains and losses. Culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, but quantitative understanding of these dynamics in natural systems remains limited. Here we develop and apply a systematic, meta-omic framework to investigate MGEs in a complex natural system using an 8-year soil time series collected at Stordalen Mire, in Sweden’s thawing permafrost margin. In this climate-critical peatland, we identify ~2.1 million MGE recombinases across 89 microbial phyla and assess ecological distributions, affected functions, past mobility and current …

Dimensional Welfare Beyond Pain: Extending The Precautionary Principle In Birch’S “The Edge Of Sentience”, Willa M. Lane, Nicola S. Clayton

Animal Sentience

Birch's (2024) The Edge of Sentience identifies sentience candidates primarily through the pain-focused LSE Criteria. Yet, as Birch himself notes in Proposal 17, sentience is not pain. We argue that statutory welfare protections must therefore reach beyond pain, and that the right tool for doing so is Birch et al.’s (2020) dimensionality framework, which characterises conscious experience across five domains. Used together, the LSE Criteria establish that welfare is at stake, while the dimensionality framework maps what is at stake beyond pain to provide a taxon-specific profile of where captivity impoverishes experience. We apply this approach to invertebrate welfare and …

History And Distribution Of The Dark Ibises (Glossy Ibis Plegadis Falcinellus And White-Faced Ibis P. Chihi) In Arkansas, R. Tumlison, P. D. Rodriguez

Journal of the Arkansas Academy of Science

The Glossy Ibis (Plegadis falcinellus) and White-faced Ibis (P. chihi) sometimes are reported simply as Dark Ibises due to difficulty in identifying them when mature characters are not clearly visible. We evaluated reports verified on citizen science websites to examine the origins and distributions of these migratory species in Arkansas. The Glossy Ibis was first documented in Arkansas in 1956, has been reported in 21 of our 75 counties, and is found more commonly in eastern Arkansas. The White-faced Ibis was first reported in Arkansas in 1971, has been reported in 41 of our 75 counties, …

Testing The Accuracy Of A Bear-Tracking Satellite Transmitter Collar Under Natural Conditions, K. A. Watson, K. Phipps, C. Drexler, C. R. Middaugh, M. Means, M. Hooks

Journal of the Arkansas Academy of Science

The Arkansas Game and Fish Commission tracks American black bears (Ursus americanus) using Global Positioning System (GPS) satellite telemetry collars in southeastern Arkansas to assess habitat use and behaviors. Companies test the accuracy of their devices, but researchers have found that natural environments, such as the forested habitat of black bears, can cause an increase in spatial error rates. We therefore tested 1 GPS collar in realistic conditions to help refine data interpretation. We placed the collar at 20 random locations in Columbia County, AR, stratifying habitat type based on data collected from black bears. We determined the …

House Sparrow Invasion Success Across Ecological, Immunological, And Molecular Scales, Kailey Marie Mccain

USF Tampa Graduate Theses and Dissertations

Biological invasions offer natural experiments for studying how organisms cope with ecological novelty. Although invasion success is often attributed to enemy release, introduced organisms do not enter enemy-free environments. Instead, they enter heterogeneous landscapes in which some familiar enemies are absent, others remain, and entirely novel enemies may be encountered. The question, then, is how invaders (hereafter non-natives) are poised to respond to these threats? This dissertation examines whether successful invasions in house sparrows (Passer domesticus) is associated with shifts in pathogen exposure, immune dynamics in blood, gut physiology, and gene co-expression network structure.

Chapter 1 is at the population/ecological …

On The Edge Of Science?, Mark Briffa, Lynne U. Sneddon

Animal Sentience

In The Edge of Sentience, Jonathan Birch (2024) provides a thought-provoking synthesis of current perspectives on animal (and artificial) sentience. He addresses the question from conceptual, ethical, regulatory and empirical viewpoints. Here we focus on some of the scientific issues raised, including defining and operationalising the concept of sentience and the implications for policy and regulation. Despite unresolved conceptual challenges, the book makes a compelling case for the continued scientific investigation of animal sentience.

Butterfly Taxa Discovery Via Genomic Analysis, Jing Zhang, Qian Cong, Jinhui Shen, Leina Song, Nick V. Grishin

The Taxonomic Report of the International Lepidoptera Survey

Expanding a genomics-guided assessment of butterfly taxonomy, we integrate phylogenetic evidence from all protein-coding genes with morphological considerations to refine our understanding of butterfly systematics and discover new taxa. As a result, 2 subgenera, 39 species, and 5 subspecies are proposed as new (type species in original combinations or type localities are listed in parentheses): Erebia (Magda) magdalena uintana Grishin, ssp. n. (USA: Utah, Uintah Co.) in Nymphalidae Rafinesque, 1815; Myselasia rondea Grishin, sp. n. (Brazil: Rondônia), Myselasia pseudocrinon Grishin, sp. n. (Ecuador: Pastaza), Myselasia paramatuta Grishin, sp. n. (Ecuador: Morona-Santiago), Euselasia anapellos Grishin, sp. n. (Peru: Loreto), …

From The Edge To The Grounds Of “Sentientism”, David Degrazia

Animal Sentience

Birch’s book is a remarkable exploration of the nature of sentience, its moral salience, evidence for its presence, and how to arrive at humane policies regarding our treatment of human beings, animals, brain organoids, and AI systems of uncertain sentience. Although Birch endorses the view that sentience is of fundamental moral importance, he endeavors to remain neutral among reasonable moral views and work out how to navigate through uncertainty—both ethical and epistemological—to arrive at defensible policies. While making common cause with Birch’s project, my own recent book advances a developed case in favor of the “sentientism” Birch endorses.

Natural Behavior Vs. Subjective Experience In Fish Welfare Assessments, Ronald G. Oldfield

Animal Sentience

Several commentaries on the Oldfield & Bonano (2024) target article proposed that natural behavior should play a larger role in assessing the welfare of fishes in zoos and aquariums. However, the natural-behavior concept of animal welfare has been widely criticized because natural behaviors do not necessarily improve welfare, and unnatural behaviors do not necessarily reduce it. I review the three major concepts of animal welfare — physical health, natural behavior, and affect/feelings — and argue that behavior patterns, whether natural or otherwise, should be evaluated according to their effects on health and subjective experience. Using the affect/feelings concept and the …

The Palm Farm Next-Door: Land Concessions, Livelihoods, And Nutrition In Plantation-Adjacent Communities, Julia Entwistle

Electronic Theses and Dissertations

Large-scale land concessions have reshaped agrarian landscapes globally, yet their implications for community land tenure, livelihoods, and nutrition remain unevenly understood. This dissertation examines how plantation agriculture and foreign investment have transformed land access, labor relations, and food systems in Liberia, a country with one of the highest proportions of land under concession globally. Guided by a political ecology framework, the study employs a mixed-methods design integrating policy analysis, in-depth interviews, and household surveys across two palm oil concession sites. The findings show that ambiguous land policies historically facilitated dispossession, while recent legal reforms have enabled communities to strategically mobilize …

Unveiling The Complexity Of Post-Roman Polity Formation In Pannonia Using Ancient Dna, Yijie Tian, István Koncz, Norbert Faragó, Corina Knipper, Ronny Friedrich, Deven N. Vyas, Levente Samu, Olga Spekker, Tamás Szeniczey, Tamás Hajdu, Balázs Gusztáv Mende, Péter Tomka, Ildikó Katalin Pap, Dávid Czigány, Rita Radzeviciute, Luca Traverso, Guido Alberto Gnecchi-Ruscone, Paolo Francalacci, Bernd Schöne, Gábor Tóth, Anna Szécsényi-Nagy, Petrus Le Roux, Kurt W. Alt, Zuzana Hofmanová, Walter Pohl, Johannes Krause, Tivadar Vida, Patrick J. Geary, Krishna R. Vereramah

Ecology & Evolution Faculty Publications

The transformation of the Roman world [fourth to ninth centuries common era (CE)], culminating in the Western Roman Empire’s fall, marked a fundamental transition in European history. Key questions persist regarding the regionally specific nature of this transformation. We generated a paleogenomic dataset to reconstruct post-Roman organizations in the Little Hungarian Plain at microregional resolution. Genetic and archaeological analyses of two Roman (n = 68) and five post-Roman (n = 246) sites reveal a rise in Northern European ancestry, reflecting large-scale population movements into this region. Moreover, despite post-Roman sites sharing similar genetic profiles, material culture, and burial …

Effect Of Temperature On The Defensive And Predatory Behavior Of The Scorpion Hadrurus Obscurus (Scorpiones: Hadruridae), Zia Nisani, Megan Bennett, Audrey Enriquez, Mel Iniquez, Emilia Martinez Rios, Brooklyn Stone

Euscorpius

Scorpions employ their stinging mechanism both for defense and predation, and being ectothermic, temperature influences their physiology and behavior. As such, we hypothesized that temperature both affects defensive stinging and prey-capture behavior in scorpions. We tested the effects of body temperature on these behaviors in the desert hairy scorpion, Hadrurus obscurus Williams, 1970. In the first experiment, scorpions were placed in temperature-controlled chambers with either high (26-28°C) or low (21- 22°C) temperatures and probed to elicit a defensive sting. We recorded the reaction time and the number of probes needed to elicit a sting. In the second experiment, we observed …

Terrestrial Abiotic Synthesis Of Simple Precursor Molecules Starting From Two Approaches: The Universality Of Carbon Reduction, Eloi Camprubi, Ben K.D. Pearce, Martina Preiner

School of Integrative Biological & Chemical Sciences Faculty Publications

To address the chemistry responsible for life’s emergence, we examine the simple chemicals accessible on early Earth and the processes that could have transformed them. We focus on carbon reduction as a process central to the direct precursors of life. Two main approaches for the emergence of life’s building blocks and their associated functions are discussed. One approach investigates chemical routes for forming life’s building blocks via processes that worked differently from those of extant life, referred to as “unrestricted” prebiotic chemistries. The other approach establishes a direct mechanistic connection between prebiotic building blocks and extant biochemistry, referred to as …

Scientific Note: Here The Whole Time: A Revised Understanding Of White Alumroot (Heuchera Alba, Saxifragaceae) In The Susquehanna River Valley., Anais Barnes, Madeline Wickers, Scott Schuette, Tanisha M. Williams, Ryan Folk, Christopher T. Martine

Faculty Journal Articles

Heuchera alba and H. pubescens (Saxifragaceae) are closely related species of alumroot endemic to the Appalachian region of eastern North America that can be difficult to distinguish morphologically. Heuchera pubescens has been understood to occupy a range from Kentucky to Pennsylvania, with the distribution of H. alba restricted to Virginia and West Virginia—plus a recently-recorded extension into Pennsylvania discovered with the help of social media. The uncovering of H. alba in Pennsylvania has challenged historical perceptions of Heuchera distributions in the state, particularly as this relates to the current concept of H. pubescens which may be in need of revision. …

Exploring The Effects Of Pest-Induced Hemlock Mortality On Growth In Neighboring Trees, Sidney L. Booher

McNair Culminating Research Projects

Trees provide many important products and services to humans. In particular, tree growth is critical to carbon storage, air and water quality, and helps determine demographic processes like population growth and reproductive success. Importantly, tree growth is sensitive to both abiotic (environmental) and biotic factors and is vulnerable to ecological disturbances. Understanding how tree populations respond to disturbances, like invasive pests, is therefore crucial to formulating timely and effective forest management practices.

Here, I used tree ring analysis to investigate how competition for water between neighboring trees changes following the decline of Eastern and Carolina Hemlock(ECH) trees due to the …

Movement And Space Use Of Weaned Northern Elephant Seal (Mirounga Angustirostris) Pups During Their First At-Sea Foraging Migration, Katie Saenger

Master's Theses

The northern elephant seal (Mirounga angustirostris) is a marine mammal known for engaging in long foraging migrations at sea. Adult male northern elephant seals follow pathways along the western coast of North America towards Alaska and adult female northern elephant seals follow pathways to open ocean in the North Pacific. However, there is little information on weaned northern elephant seal pup foraging behavior during their first foraging migration. This lack of knowledge is significant because northern elephant seals have a mortality rate of >50% in the first year. This project aimed to better understand the at-sea migratory movement …

Recreational Fishing Location Guide, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Occasional Publications

Please note: this version (6th edition) published in 2026 replaces the version published in 2023.

This guide has been developed to help you identify the fishing locations that you may visit. The purpose of this guide is to enhance consistent and accurate identification of fishing locations and block numbers within each Bioregion. If you are unsure about a particular location, please discuss it with a representative of the Department of Primary Industries and Regional Development, Western Australia.

One Assay To Rule Them All: Development Of A Global Environmental Dna Tool To Support Range-Wide Surveys Of An Imperiled Sawfish And Its Application In The Eastern Tropical Pacific, Juan C. Cubillos-M, Annmarie Fearing, Demian D. Chapman, Peter M. Kyne, P. Joana Dias, Cindy Gonzalez, Ryan N. Lehman, Yaliana Chichaco, Bryan L. Huerta-Beltrán, Kayla L. Mcculloch, Sarah M. Toepfer, John K. Carlson, Nicole M. Phillips

Faculty Publications

Environmental DNA (eDNA) has emerged as a powerful tool to support the conservation of threatened species. The sawfishes are one of the most imperiled vertebrate groups, with all five species classified as Critically Endangered on the IUCN Red List of Threatened Species. Owing to their toothy rostra, sawfishes are easily entangled in a wide range of fishing gear, with mortalities in fisheries and loss of habitat driving global declines. The Largetooth Sawfish, Pristis pristis, historically had a circumtropical range, but has experienced severe declines in geographic range and abundance. Viable populations are thought to be confined to northern Australia, but …

Kolonialisme Iklim Dan Tercerabutnya Pengetahuan Ekologi Tradisional: Sosio-Bioekonomi Sebagai Reorientasi Epistemologis, Viky Arthiando Putra

Antropologi Indonesia

Abstract The global climate change has brought with it a growing stack of conceptual proposals – from green economy to bioeconomy – each presenting itself as a non-extractive economic alternative. Unfortunately, these conceptual claims continue to reproduce colonial logic that subordinates local knowledge. The loss of Traditional Ecological Knowledge (TEK) is not merely an ecological setback: it is a systematic epistemological violence – a product of climate colonialism operating within the architecture of global green programs. This article traces the discourse of green economy, analyzes the loss of TEK as an epistemological problem, and proposes a socio-bioeconomy reorientation as a …

Pickleweed In The Disappearing Marsh: Population Genetics & Metal Accumulation In Salicornia Depressa, Alice Kaisla

Graduate Doctoral Dissertations

Salicornia is a genus of succulent halophytes found in salt marshes around the world. Salicornia species have a remarkably high tolerance for heavy metal pollution and have been shown to accumulate high concentrations of heavy metals in their tissue under experimental conditions. As a result, they are both a useful system for studying evolution in polluted coastlines and a potential candidate for use in phytoremediation. My research focuses on Salicornia depressa, known as pickleweed, a species commonly found in marshes along the heavily urbanized and industrialized New England coast. I investigate genetic diversity and population structure in S. depressa populations …

Adapting Population Genetics, Practice, And Policy For Plant Conservation In A Changing World, Cooper M. Kimball-Rhines

Graduate Doctoral Dissertations

Biodiversity conservation is an inherently interdisciplinary goal that requires effective collaboration among academics, ecosystem managers, policymakers, and other stakeholders. Codesigning research with these groups ensures experiments are useful and improves adoption of policy and practice recommendations while advancing our understanding of basic science. This dissertation explores the power of codesigned research in shaping plant conservation strategies using stakeholder engagement, causal inference, demographic modeling, and multi-omic sequencing techniques. In chapter 1 I discuss the history of New England ecosystems and the need for research-driven changes to plant conservation policy and practice in the face of global change. In chapter 2, I …

Patents And Technology Evolution: Altering Innovations And Innovators Via Patent Influences, Richard Gruner

Journal of Intellectual Property Law

Technologies improve primarily through evolutionary change not rational optimization. New technologies emerge as attempts to solve practical problems, the technologies are tested in marketplaces to determine if they are superior in cost and function to alternatives, and those that fare well in the testing gain widespread adoption.  Widely adopted technologies, and their problems, form the basis for the next round of technology improvements and evolution.  Through these steps, evolutionary processes lacking rational direction can generate changing technologies matched to the desires and problems of present society.

As they operate to advance diverse technologies, evolutionary processes governing technology change are subject …

Compsobuthus Hadeki Sp. N. From Iraq (Scorpiones: Buthidae), František Kovařík, František Šťáhlavský

Euscorpius

A new species, Compsobuthus hadeki sp. n. from Iraq is described and fully complemented with color photographs and compared with morphologically the most similar species, C. matthiesseni (Birula, 1905). The two species can be unequivocally separated by the following morphological features: in C. hadeki sp. n., movable finger of pedipalp bears 9 rows of granules; telson with aculeus shorter than vesicle, and metasoma III with 10 carinae. Cytogenetic analysis was performed, revealing a diploid chromosome count of 22 in C. hadeki sp. n.

Dr. Jonathan Velotta Faculty Spotlight, Katelyn Trimble

DU Undergraduate Research Journal Archive

An interview with Dr. Jonathan Velotta of the University of Denver's Department of Biological Sciences.

Phenotypic Plasticity In A Stochastic Environment: Modeling Three Phenotypes And Environments, Sarah P. Williams, Marissa C. K. Douglas, Stephen C. Adolph

Spora: A Journal of Biomathematics

Phenotypically plastic organisms are capable of adjusting their phenotypes in a variable environment. Padilla and Adolph (1996) modeled this process and included a time lag between detection of an environmental change and the responding change in phenotype. We extended the Padilla and Adolph model from two to three discrete environments and phenotypes and analyzed the model computationally. Our results were consistent with their findings: the fitness advantage of phenotypic plasticity is higher when (1) the lag time is shorter, (2) the probability of environmental change is lower, and (3) the fitness disadvantage of mismatched phenotypes and environments is more severe. …

Popgenhelpr: An R Package To Streamline And Facilitate Informed Population Genomic Analyses And Visualization Of Genetic Ancestry, Diversity And Differentiation, Keaka Farleigh, Mason O. Murphy, Christopher Marie Blair, Tereza Jezkova

Publications and Research

Analysing large population genomic datasets requires an interdisciplinary skillset. Beyond a knowledge base in genetics and population biology, population genomic analyses involve computer science and statistics, representing a barrier for researchers without experience in those fields. PopGenHelpR seeks to lower this barrier by enabling researchers to perform population genomic analyses and generate near-publication quality figures in a streamlined and informed fashion. PopGenHelpR allows users to estimate genetic diversity within populations as well as differentiation among populations and individuals from single nucleotide polymorphism data. PopGenHelpR includes commonly used measures such as observed heterozygosity and FST. PopGenHelpR also provides five …

Improving Human-Wildlife Coexistence: An Ecological And Educational Approach To Rewilding Grizzly Bears (Ursus Arctos Horribilis) In California, Amanda C. D. Rosales

Master's Projects and Capstones

Megafauna extinction during the Holocene has been both caused and amplified by climatic changes and human influence. By the last half century, large carnivores were diminished in Europe and the United States, but policies increasingly addressed species decline and their territories expanded. This research examined large carnivore rewilding across the European Union and United States, specifically for rewilding brown bears, Ursus arctos, in historic habitat. Next, case studies for the health status of climate-impacted whitebark pine, Pinus albicaulis, a high energy food for bears, was assessed. Ultimately, research case studies, human perspective surveys, and the California Department of Education content …

Structure And Diversity Of Play Behavior In Juvenile Belding's Ground Squirrels, Paul O'Driscoll Ii

Master's Theses

Play behavior is ubiquitous among juvenile mammals and can promote motor, social, and cognitive development, providing multiple adaptive benefits to young animals in some cases. The structure of play can be linked to the benefits it confers on individuals. I evaluated the structure of play in juvenile Belding’s ground squirrels (Urocitellus beldingi), a species for which multiple adaptive benefits of play have been identified. I compared juvenile play in U. beldingi to adult sexual and aggressive behavior to determine and classify similarities between juvenile play and adult behavior. I evaluated diversity in the behaviors expressed during play interactions and diversity …

Investigating Cryptic Diversity In The Hawaiian Endemic Plant, Psychotria Mariniana (Rubiaceae), Uyen Thi Hoang Nguyen

Master's Theses

Islands, with their isolation and steep environmental gradients, serve as natural laboratories for studying speciation. Molecular phylogenetic and population genetic methods utilizing Next-Generation Sequencing (NGS) have revolutionized our ability to document patterns of genetic divergence and diversity. Cryptic diversity, genetically distinct populations that were previously unrecognized as unique, and cryptic speciation, where divergent genetic populations may be deserving of status as unique species, have been observed in many taxa. The Hawaiian Islands provide an ideal setting for studying divergence and speciation due to their extreme isolation, known ages, and volcanic origin. Previous work has investigated the evolutionary relationships of the …

Watershed Amendments: Assembling New Pervious Ground From Landscape Waste, Sophie Kaplan-Bucciarelli

Masters Theses

In Providence, Rhode Island, much of the downtown area is built over a vast historic tidal estuary. Though we no longer see the salt marshes, wooded bluffs, or meadows that once characterized this landscape, we recognize their absence in contemporary crises of urban heat, flooding, polluted soils and stormwater runoff, and habitat loss. These conditions are particularly acute along the city’s industrialized river corridors, where vacant lots and parking areas sit idle, their history paved over and potential constrained by limited imagination and resources.

These lots - already experiments in fill and land building after centuries of disturbance - can …