Alex Dornburg

North Carolina Museum of Natural Sciences · Research and Collections

Background: Analyses of phylogenetic informativeness represent an important step in screening potential or existing datasets for their proclivity toward convergent or parallel evolution of molecular sites. However, while new theory has been developed from which to predict the utility of sequence data, adoption of these advances have been stymied b...

Significance Madagascar is a conservation priority because of its unique and threatened biodiversity. Lemurs, by acting as seed dispersers, are essential to maintaining healthy and diverse forests on the island. However, in the past few thousand years, at least 17 lemur species, many of which were inferred seed dispersers, have gone extinct. We out...

Understanding the promotion and regulation of circadian rhythms in marine fishes is important for studies spanning conservation, evolutionary biology, and physiology. Given numerous challenges inherent to quantifying behavioral activity across the full spectrum of marine environments and fish biodiversity, case studies offer a tractable means of ga...

Predicting the response of endemic species to urbanization has emerged as a fundamental challenge in 21st century conservation biology. The factors that underlie population declines of reptiles are particularly nebulous, as these are often the least understood class of vertebrates in a given community. In this study, we assess correlations between...

Background COVID-19 booster vaccinations mitigate transmission and reduce the morbidity and mortality associated with infection. However, the optimal date for booster administration remains uncertain. Geographic variation in infection rates throughout the year makes it challenging to intuit the best yearly booster administration date to effectively...

Holosteans (gars and bowfins) have emerged as valuable models for understanding early vertebrate evolution, offering insights into diverse topics ranging from genomic architecture to molecular processes. These lineages also exhibit unusual features in their immune response, combining molecular elements seen in both tetrapods and ray-finned fishes....

Sister lineage comparisons provide a valuable tool for understanding evolutionary origins of species-rich clades. Percomorpha, comprising over 18,900 species, represents one of the most species-rich vertebrate clades. However, the phylogenetic resolution of its sister lineage remains unclear, obscuring whether contrasts in histories of diversificat...

Multiple sclerosis patients treated with disease-modifying therapies experience varying immune responses to COVID-19 vaccinations. However, guidance regarding the impact of treatments on infection risks remains sparse. Integrating vaccine-based and long-term coronavirus infection-based antibody data, we calculated cumulative probabilities of breakt...

Complex patterns of genome evolution associated with the end-Cretaceous [Cretaceous-Paleogene (K–Pg)] mass extinction limit our understanding of the early evolutionary history of modern birds. Here, we analyzed patterns of avian molecular evolution and identified distinct macroevolutionary regimes across exons, introns, untranslated regions, and mi...

COVID-19 booster vaccinations mitigate transmission and reduce the morbidity and mortality associated with infection. However, the optimal date for booster administration remains uncertain. Geographic variation in infection rates throughout the year make it challenging to intuit the best yearly booster administration date to effectively prevent inf...

The advent of generative AI models holds tremendous potential for aiding teachers in the generation of pedagogical materials. However, numerous knowledge gaps concerning the behavior of these models obfuscate the generation of research-informed guidance for their effective usage. Here we assess trends in prompt specificity, variability, and weaknes...

Across the Tree of Life, most studies of phenotypic disparity and diversification have been restricted to adult organisms. However, many lineages have distinct ontogenetic phases that differ from their adult forms in morphology and ecology. Focusing disproportionately on the evolution of adult forms unnecessarily hinders our understanding of the pr...

Major ecological transitions are thought to fuel evolutionary radiations, but whether they are contingent on the evolution of certain traits is unclear. We show that the rapid ecological transition of anglerfishes into pelagic habitats during a period of major global warming coincided with the origins of sexual parasitism, in which male anglerfishe...

Transposable elements (TEs) can make up more than 50% of any given vertebrate's genome, with substantial variability in TE composition among lineages. TE variation is often linked to changes in gene regulation, genome size, and speciation. However, the role that genome duplication events have played in generating abrupt shifts in the composition of...

Successive waves of infection by SARS-CoV-2 have left little doubt that this virus will transition to an endemic disease. Foreknowledge of when to expect seasonal surges is crucial for healthcare and public health decision-making. However, the future seasonality of COVID-19 remains uncertain. Evaluating its seasonality is complicated due to the lim...

Patients undergoing antineoplastic therapies often exhibit reduced immune response to COVID-19 vaccination, necessitating assessment of alternate booster vaccination frequencies. However, data on reinfection risks to guide clinical decision-making is limited. Here we quantified reinfection risks for patients undergoing distinct antineoplastic thera...

Since its initial discovery over 50 years ago, understanding the evolution of the vertebrate RAG- mediated adaptive immune response has been a major area of research focus for comparative geneticists. However, how the evolutionary novelty of an adaptive immune response impacted the diversity of receptors associated with the innate immune response h...

Over the past two decades the pace of spillovers from animal viruses to humans has accelerated, with COVID-19 becoming the most deadly zoonotic disease in living memory. Prior to zoonosis, it is conceivable that the virus might largely be subjected to purifying selection, requiring no additional selective changes for successful zoonotic transmissio...

Patients undergoing antineoplastic therapies often exhibit reduced immune response to COVID-19 vaccination, necessitating assessment of alternate boosting frequencies for these patients. However, data on reinfection risks to guide clinical decision-making is limited. We quantified reinfection risks of SARS-CoV-2 at different mRNA boosting frequenci...

Holosteans (gars and bowfins) represent the sister lineage to teleost fishes, the latter being a clade that comprises over half of all living vertebrates and includes important models for comparative genomics and human health. A major distinction between the evolutionary history of teleosts and holosteans is that all teleosts experienced a genome d...

Since its initial discovery over 50 years ago, understanding the evolution of the vertebrate adaptive immune response has been a major area of research focus for comparative geneticists. However, how the evolutionary novelty of an adaptive immune response impacted the diversity of receptors associated with the innate immune response has received co...

One of the most consequential unknowns of the COVID‐19 pandemic is the frequency at which vaccine boosting provides sufficient protection from infection. We quantified the statistical likelihood of breakthrough infections over time following different boosting schedules with mRNA‐1273 (Moderna) and BNT162b2 (Pfizer‐BioNTech) by integration of anti‐...

Holosteans (gars and bowfins) represent the sister lineage to teleost fishes, the latter being a clade that comprises over half of all living vertebrates and includes important models for comparative genomics and human health. A major distinction between the evolutionary history of teleosts and holosteans is that all teleosts experienced a genome d...

Following the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational relevance to specific diseases. However, staggering sequence complexity has also challenged the development of a more comprehensive understanding of human genome bi...

Complex patterns of genome and life-history evolution associated with the end-Cretaceous (K– Pg) mass extinction event limit our understanding of the early evolutionary history of crown group birds. Here, we assess molecular heterogeneity across living birds using a technique enabling inferred sequence substitution models to transition across the h...

Evolutionary transitions in water column usage have played a major role in shaping ray-finned fish diversity. However, the extent to which vision-associated trait complexity and water column usage is coupled remains unclear. Here we investigate the relationship between depth niche, eye size, and the molecular basis of light detection across the Ant...

The durability of vaccine-mediated immunity to SARS-CoV-2, the durations to breakthrough infection, and the optimal timings of booster vaccination are crucial knowledge for pandemic response. Here, we applied comparative evolutionary analyses to estimate the durability of immunity and the likelihood of breakthrough infections over time following va...

Briefly considered extinct in the wild, the future of the Wyoming toad (Anaxyrus baxteri) continues to rely on captive breeding to supplement the wild population. Given its small natural geographic range and history of rapid population decline at least partly due to fungal disease, investigation of the diversity of key receptor families involved in...

Spiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and account for more than a quarter of all living vertebrate species. Previous time-calibrated phylogenies and patterns from the fossil record explain this dominance by correlating the origin of major acanthomorph lineages with the Cretaceous–Palaeogene mass extinction. Here we infe...

Multiple novel immunoglobulin-like transcripts (NILTs) have been identified from salmon, trout, and carp. NILTs typically encode activating or inhibitory transmembrane receptors with extracellular immunoglobulin (Ig) domains. Although predicted to provide immune recognition in ray-finned fish, we currently lack a definitive framework of NILT divers...

The ecological theory of adaptive radiation has profoundly shaped our conceptualization of the rules that govern diversification. However, while many radiations follow classic early-burst patterns of diversification as they fill ecological space, the longer-term fates of these radiations depend on many factors, such as climatic stability. In system...

Multiple novel immunoglobulin-like transcripts (NILTs) have been identified from salmon, trout and carp. NILTs typically encode activating or inhibitory transmembrane receptors with extracellular immunoglobulin (Ig) domains. Although predicted to provide immune recognition in ray-finned fish, we currently lack a definitive framework of NILT diversi...

The ecological theory of adaptive radiation has profoundly shaped our conceptualization of the rules that govern diversification. However, while many radiations follow classic early burst patterns of diversification as they fill ecological space, the longer-term fates of these radiations depend on many factors, such as climatic stability. In system...

For over half a century, deciphering the origins of the genomic loci that form the jawed vertebrate adaptive immune response has been a major topic in comparative immunogenetics. Vertebrate adaptive immunity relies on an extensive and highly diverse repertoire of tandem arrays of variable (V), diversity (D), and joining (J) gene segments that recom...

Importance Successive waves of infection by SARS-CoV-2 have left little doubt that COVID-19 will transition to an endemic disease, yet the future seasonality of COVID-19 remains one of its most consequential unknowns. Foreknowledge of spatiotemporal surges would have immediate and long-term consequences for medical and public health decision-making...

Briefly considered extinct in the wild, the future of the wild population of the Wyoming toad ( Anaxyrus baxteri ) continues to rely on captive breeding to supplement the wild population. Given its small natural geographic range and history of rapid population decline at least partly due to fungal disease, investigation of the diversity of key rece...

Across the Tree of Life, most studies of phenotypic disparity and diversification have been restricted to adult organisms. However, many lineages have distinct ontogenetic phases that do not reflect the same traits as their adult forms. Non-adult disparity patterns are particularly important to consider for coastal ray-finned fishes, which often ha...

Abstract Historical records from museums or government agencies are of tremendous utility for illuminating the factors that shape the spatial distribution of the planet’s biodiversity. However, these data were often collected under heterogeneous and opportunistic sampling designs and therefore likely contain significant sampling biases that change...

Hemidactylus mabouia is one of the most successful, widespread invasive reptile species and has become ubiquitous across tropical urban settings in the Western Hemisphere. Its ability to thrive in close proximity to humans has been linked to the rapid disappearance of native geckos. However, aspects of Hemidactylus mabouia natural history and ecomo...

The emergence of a new phylogeny of ray-finned fishes at the turn of the twenty-first century marked a paradigm shift in understanding the evolutionary history of half of living vertebrates. We review how the new ray-finned fish phylogeny radically departs from classical expectations based on morphology. We focus on evolutionary relationships that...

The progression of cancer is an evolutionary process that is challenging to monitor between sampling timepoints. However, investigation of cancer evolution over specific time periods is crucial to the elucidation of key events such as the acquisition of therapeutic resistance and subsequent fatal metastatic spread of therapy-resistant cell populati...

Background Among the most consequential unknowns of the devastating COVID-19 pandemic are the durability of immunity and time to likely reinfection. There are limited direct data on SARS-CoV-2 long-term immune responses and reinfection. The aim of this study is to use data on the durability of immunity among evolutionarily close coronavirus relativ...

Over 99% of ray-finned fishes (Actinopterygii) are teleosts, a clade that comprises half of all living vertebrate species that have diversified across virtually all fresh and saltwater ecosystems. This ecological breadth raises the question of how the immunogenetic diversity required to persist under heterogeneous pathogen pressures evolved. The te...

The bowfin ( Amia calva ) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central specie...

Allopatry has traditionally been viewed as the primary driver of speciation in marine taxa, but the geography of the marine environment and the larval dispersal capabilities of many marine organisms render this view somewhat questionable. In marine fishes, one of the earliest and most highly cited empirical examples of ecological speciation with ge...

Spiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and comprise more than a quarter of all living vertebrate species1-3. It is believed that this dominance resulted from explosive lineage and phenotypic diversification coincident with the Cretaceous-Paleogene (K-Pg) mass-extinction event4. It remains unclear, however, if living acan...

Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously-undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have th...

Over 99% of ray-finned fishes (Actinopterygii) are teleosts, a clade that comprises half of all living vertebrates that have diversified across virtually all fresh and saltwater ecosystems. This ecological diversity raises the question of how the immunogenetic diversity required to persist under heterogeneous pathogen pressures evolved. The teleost...

The progression of cancer—including the acquisition of therapeutic resistance and the fatal metastatic spread of therapy-resistant cell populations—is an evolutionary process that is challenging to monitor between sampling timepoints. Here we apply mutational signature analysis to clinically correlated cancer chronograms to detect and describe the...

Multiple novel immunoglobulin-like transcripts (NILTs) have been identified from salmon, trout and carp. NILTs typically encode activating or inhibitory transmembrane receptors with extracellular immunoglobulin (Ig) domains. Although predicted to provide some level of immune recognition in ray-finned fish, we currently lack a definitive framework o...

Understanding the role of ecological processes in speciation has become one of the most active areas of research in marine population biology in recent decades. The traditional view was that allopatry was the primary driver of speciation in marine taxa, but the geography of the marine environment and the dispersal capabilities of many marine organi...

Understanding the role of ecological processes in speciation has become one of the most active areas of research in marine population biology in recent decades. The traditional view was that allopatry was the primary driver of speciation in marine taxa, but the geography of the marine environment and the dispersal capabilities of many marine organi...

Species distribution models (SDMs) are frequently used to predict the effects of climate change on species of conservation concern. Biases inherent in the process of constructing SDMs and transferring them to new climate scenarios may result in undesirable conservation outcomes. We explore these issues and demonstrate new methods to estimate biases...

Background: Advances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptomic sequencing has driven the public accumulation of a wealth of data for phylogenomic analyses, however lack of tools aimed towa...

Comparative genomic analyses have enormous potential for identifying key genes central to human health phenotypes, including those that promote cancers. In particular, the successful development of novel therapeutics using model species requires phylogenetic analyses to determine molecular homology. Accordingly, we investigate the evolutionary hist...

The bowfin fish ( Amia calva ) diverged before the genome duplication in teleost fishes, and its archetypical body plan and slow rate of molecular evolution make it a key species for genomic exploration as a basal representative of the neopterygian fishes. To investigate the evolution and development of ray-finned fishes, we generated a chromosome-...

Unravelling the phylogenetic relationships among the major groups of living birds has been described as the greatest outstanding problem in dinosaur systematics. Recent work has identified portions of the avian tree of life that are particularly challenging to reconstruct, perhaps as a result of rapid cladogenesis early in crown bird evolutionary h...

An understanding of host–parasite interactions represents an important, but often overlooked, axis for predicting how polar marine biodiversity may be impacted by continued environmental change over the next century. Here, we survey three species of crocodile icefish (Notothenioidei: Channichthyidae) collected from two island archipelagos in the so...

Hemidactylus spp. (House geckos) rank among the most successful invasive reptile species worldwide. Hemidactylus mabouia in particular has become ubiquitous across tropical urban settings in the Western Hemisphere. H. mabouia's ability to thrive in close proximity to humans has led to the rapid displacement of native geckos in urban areas, however...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Background Advances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptomic sequencing has driven the public accumulation of a wealth of data for phylogenomic analyses, however lack of tools aimed toward...

Background Advances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptomic sequencing has driven the public accumulation of a wealth of data for phylogenomic analyses, however lack of tools aimed toward...

Background: Advances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptomic sequencing has driven the public accumulation of a wealth of data for phylogenomic analyses, however lack of tools aimed towar...

An understanding of host-parasite interactions represents an important, but often overlooked, axis for predicting how marine biodiversity may be impacted by continued environmental change over the next century. For host and parasite communities in the Southern Ocean, investigations of many major groups of parasites have largely been limited to taxo...

Leeches (Hirudinida) comprise a charismatic, yet often maligned group of worms. Despite their ecological, economic, and medicalimportance, a general consensus on the phylogenetic relationships of major hirudinidan lineages is lacking. This absence of aconsistent, robust phylogeny of early-diverging lineages has hindered our understanding of the und...

The progression of cancer is an evolutionary process. During this process, evolving populations of cancer cells encounter restrictive ecological niches within the body, such as the primary tumor, the circulatory system, and diverse metastatic sites. Heterogeneous populations of cancer cells undergo selection for adaptive phenotypes, which shapes mo...

Background Advances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptomic sequencing has driven the public accumulation of a wealth of data for phylogenomic analyses, however lack of tools aimed toward...