Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing.

We used ultra-deep sequencing to obtain tens of thousands of HIV-1 sequences from regions targeted by CD8+ T lymphocytes from longitudinal samples from three acutely infected subjects, and modeled viral evolution during the critical first weeks of infection. Previous studies suggested that a single virus established productive infection, but these conclusions were tempered because of limited sampling; now, we have greatly increased our confidence in this observation through modeling the observed earliest sample diversity based on vastly more extensive sampling. Conventional sequencing of HIV-1 from acute/early infection has shown different patterns of escape at different epitopes; we investigated the earliest escapes in exquisite detail. Over 3-6 weeks, ultradeep sequencing revealed that the virus explored an extraordinary array of potential escape routes in the process of evading the earliest CD8 T-lymphocyte responses--using 454 sequencing, we identified over 50 variant forms of each targeted epitope during early immune escape, while only 2-7 variants were detected in the same samples via conventional sequencing. In contrast to the diversity seen within epitopes, non-epitope regions, including the Envelope V3 region, which was sequenced as a control in each subject, displayed very low levels of variation. In early infection, in the regions sequenced, the consensus forms did not have a fitness advantage large enough to trigger reversion to consensus amino acids in the absence of immune pressure. In one subject, a genetic bottleneck was observed, with extensive diversity at the second time point narrowing to two dominant escape forms by the third time point, all within two months of infection. Traces of immune escape were observed in the earliest samples, suggesting that immune pressure is present and effective earlier than previously reported; quantifying the loss rate of the founder virus suggests a direct role for CD8 T-lymphocyte responses in viral containment after peak viremia. Dramatic shifts in the frequencies of epitope variants during the first weeks of infection revealed a complex interplay between viral fitness and immune escape.

The impact of host immune status on the within-host and population dynamics of antigenic immune escape.

Antigenically evolving pathogens such as influenza viruses are difficult to control owing to their ability to evade host immunity by producing immune escape variants. Experimental studies have repeatedly demonstrated that viral immune escape variants emerge more often from immunized hosts than from naive hosts. This empirical relationship between host immune status and within-host immune escape is not fully understood theoretically, nor has its impact on antigenic evolution at the population level been evaluated. Here, we show that this relationship can be understood as a trade-off between the probability that a new antigenic variant is produced and the level of viraemia it reaches within a host. Scaling up this intra-host level trade-off to a simple population level model, we obtain a distribution for variant persistence times that is consistent with influenza A/H3N2 antigenic variant data. At the within-host level, our results show that target cell limitation, or a functional equivalent, provides a parsimonious explanation for how host immune status drives the generation of immune escape mutants. At the population level, our analysis also offers an alternative explanation for the observed tempo of antigenic evolution, namely that the production rate of immune escape variants is driven by the accumulation of herd immunity. Overall, our results suggest that disease control strategies should be further assessed by considering the impact that increased immunity--through vaccination--has on the production of new antigenic variants.

Preexisting compensatory amino acids compromise fitness costs of a HIV-1 T cell escape mutation.

BACKGROUND: Fitness costs and slower disease progression are associated with a cytolytic T lymphocyte (CTL) escape mutation T242N in Gag in HIV-1-infected individuals carrying HLA-B*57/5801 alleles. However, the impact of different context in diverse HIV-1 strains on the fitness costs due to the T242N mutation has not been well characterized. To better understand the extent of fitness costs of the T242N mutation and the repair of fitness loss through compensatory amino acids, we investigated its fitness impact in different transmitted/founder (T/F) viruses. RESULTS: The T242N mutation resulted in various levels of fitness loss in four different T/F viruses. However, the fitness costs were significantly compromised by preexisting compensatory amino acids in (Isoleucine at position 247) or outside (glutamine at position 219) the CTL epitope. Moreover, the transmitted T242N escape mutant in subject CH131 was as fit as the revertant N242T mutant and the elimination of the compensatory amino acid I247 in the T/F viral genome resulted in significant fitness cost, suggesting the fitness loss caused by the T242N mutation had been fully repaired in the donor at transmission. Analysis of the global circulating HIV-1 sequences in the Los Alamos HIV Sequence Database showed a high prevalence of compensatory amino acids for the T242N mutation and other T cell escape mutations. CONCLUSIONS: Our results show that the preexisting compensatory amino acids in the majority of circulating HIV-1 strains could significantly compromise the fitness loss due to CTL escape mutations and thus increase challenges for T cell based vaccines.

Potent and broad neutralizing activity of a single chain antibody fragment against cell-free and cell-associated HIV-1.

Several human monoclonal antibodies (hmAbs) exhibit relatively potent and broad neutralizing activity against HIV-1, but there has not been much success in using them as potential therapeutics. We have previously hypothesized and demonstrated that small engineered antibodies can target highly conserved epitopes that are not accessible by full-size antibodies. However, their potency has not been comparatively evaluated with known HIV-1-neutralizing hmAbs against large panels of primary isolates. We report here the inhibitory activity of an engineered single chain antibody fragment (scFv), m9, against several panels of primary HIV-1 isolates from group M (clades A-G) using cell-free and cell-associated virus in cell line-based assays. M9 was much more potent than scFv 17b, and more potent than or comparable to the best-characterized broadly neutralizing hmAbs IgG(1) b12, 2G12, 2F5 and 4E10. It also inhibited cell-to-cell transmission of HIV-1 with higher potency than enfuvirtide (T-20, Fuzeon). M9 competed with a sulfated CCR5 N-terminal peptide for binding to gp120-CD4 complex, suggesting an overlapping epitope with the coreceptor binding site. M9 did not react with phosphatidylserine (PS) and cardiolipin (CL), nor did it react with a panel of autoantigens in an antinuclear autoantibody (ANA) assay. We further found that escape mutants resistant to m9 did not emerge in an immune selection assay. These results suggest that m9 is a novel anti-HIV-1 candidate with potential therapeutic or prophylactic properties, and its epitope is a new target for drug or vaccine development.

Eco-evolutionary trophic dynamics: loss of top predators drives trophic evolution and ecology of prey.

Ecosystems are being altered on a global scale by the extirpation of top predators. The ecological effects of predator removal have been investigated widely; however, predator removal can also change natural selection acting on prey, resulting in contemporary evolution. Here we tested the role of predator removal on the contemporary evolution of trophic traits in prey. We utilized a historical introduction experiment where Trinidadian guppies (Poecilia reticulata) were relocated from a site with predatory fishes to a site lacking predators. To assess the trophic consequences of predator release, we linked individual morphology (cranial, jaw, and body) to foraging performance. Our results show that predator release caused an increase in guppy density and a "sharpening" of guppy trophic traits, which enhanced food consumption rates. Predator release appears to have shifted natural selection away from predator escape ability and towards resource acquisition ability. Related diet and mesocosm studies suggest that this shift enhances the impact of guppies on lower trophic levels in a fashion nuanced by the omnivorous feeding ecology of the species. We conclude that extirpation of top predators may commonly select for enhanced feeding performance in prey, with important cascading consequences for communities and ecosystems.

Minor Moves: Growth, Fugitivity, and Children's Physical Movement

From tendencies to reduce the Underground Railroad to the imperative "follow the north star" to the iconic images of Ruby Bridges' 1960 "step forward" on the stairs of William Frantz Elementary School, America prefers to picture freedom as an upwardly mobile development. This preoccupation with the subtractive and linear force of development makes it hard to hear the palpable steps of so many truant children marching in the Movement and renders illegible the nonlinear movements of minors in the Underground. Yet a black fugitive hugging a tree, a white boy walking alone in a field, or even pieces of a discarded raft floating downstream like remnants of child's play are constitutive gestures of the Underground's networks of care and escape. Responding to 19th-century Americanists and cultural studies scholars' important illumination of the child as central to national narratives of development and freedom, "Minor Moves" reads major literary narratives not for the child and development but for the fugitive trace of minor and growth.

In four chapters, I trace the physical gestures of Nathaniel Hawthorne's Pearl, Harriet Beecher Stowe's Topsy, Harriet Wilson's Frado, and Mark Twain's Huck against the historical backdrop of the Fugitive Slave Act and the passing of the first compulsory education bills that made truancy illegal. I ask how, within a discourse of independence that fails to imagine any serious movements in the minor, we might understand the depictions of moving children as interrupting a U.S. preoccupation with normative development and recognize in them the emergence of an alternative imaginary. To attend to the movement of the minor is to attend to what the discursive order of a development-centered imaginary deems inconsequential and what its grammar can render only as mistakes. Engaging the insights of performance studies, I regard what these narratives depict as childish missteps (Topsy's spins, Frado's climbing the roof) as dances that trouble the narrative's discursive order. At the same time, drawing upon the observations of black studies and literary theory, I take note of the pressure these "minor moves" put on the literal grammar of the text (Stowe's run-on sentences and Hawthorne's shaky subject-verb agreements). I regard these ungrammatical moves as poetic ruptures from which emerges an alternative and prior force of the imaginary at work in these narratives--a force I call "growth."

Reading these "minor moves" holds open the possibility of thinking about a generative association between blackness and childishness, one that neither supports racist ideas of biological inferiority nor mandates in the name of political uplift the subsequent repudiation of childishness. I argue that recognizing the fugitive force of growth indicated in the interplay between the conceptual and grammatical disjunctures of these minor moves opens a deeper understanding of agency and dependency that exceeds notions of arrested development and social death. For once we interrupt the desire to picture development (which is to say the desire to picture), dependency is no longer a state (of social death or arrested development) of what does not belong, but rather it is what Édouard Glissant might have called a "departure" (from "be[ing] a single being"). Topsy's hard-to-see pick-pocketing and Pearl's running amok with brown men in the market are not moves out of dependency but indeed social turns (a dance) by way of dependency. Dependent, moving and ungrammatical, the growth evidenced in these childish ruptures enables different stories about slavery, freedom, and childishness--ones that do not necessitate a repudiation of childishness in the name of freedom, but recognize in such minor moves a fugitive way out.

Informatic Opacity: Biometric Facial Recognition and the Aesthetics and Politics of Defacement

Confronting the rapidly increasing, worldwide reliance on biometric technologies to surveil, manage, and police human beings, my dissertation Informatic Opacity: Biometric Facial Recognition and the Aesthetics and Politics of Defacement charts a series of queer, feminist, and anti-racist concepts and artworks that favor opacity as a means of political struggle against surveillance and capture technologies in the 21st century. Utilizing biometric facial recognition as a paradigmatic example, I argue that today's surveillance requires persons to be informatically visible in order to control them, and such visibility relies upon the production of technical standardizations of identification to operate globally, which most vehemently impact non- normative, minoritarian populations. Thus, as biometric technologies turn exposures of the face into sites of governance, activists and artists strive to make the face biometrically illegible and refuse the political recognition biometrics promises through acts of masking, escape, and imperceptibility. Although I specifically describe tactics of making the face unrecognizable as "defacement," I broadly theorize refusals to visually cohere to digital surveillance and capture technologies' gaze as "informatic opacity," an aesthetic-political theory and practice of anti- normativity at a global, technical scale whose goal is maintaining the autonomous determination of alterity and difference by evading the quantification, standardization, and regulation of identity imposed by biometrics and the state. My dissertation also features two artworks: Facial Weaponization Suite, a series of masks and public actions, and Face Cages, a critical, dystopic installation that investigates the abstract violence of biometric facial diagramming and analysis. I develop an interdisciplinary, practice-based method that pulls from contemporary art and aesthetic theory, media theory and surveillance studies, political and continental philosophy, queer and feminist theory, transgender studies, postcolonial theory, and critical race studies.

The Ontogeny of Mucosal and Systemic Antibody Responses to HIV-1 Infection

The humoral immune system plays a critical role in the clearance of numerous pathogens. In the setting of HIV-1 infection, the virus infects, integrates its genome into the host's cells, replicates, and establishes a reservoir of virus-infected cells. The initial antibody response to HIV-1 infection is targeted to non-neutralizing epitopes on HIV-1 Env gp41, and when a neutralizing response does develop months after transmission, it is specific for the autologous founder virus and the virus escapes rapidly. After continuous waves of antibody mediated neutralization and viral escape, a small subset of infected individuals eventually develop broad and potent heterologous neutralizing antibodies years after infection. In this dissertation, I have studied the ontogeny of mucosal and systemic antibody responses to HIV-1 infection by means of three distinct aims: 1. Determine the origin of the initial antibody response to HIV-1 infection. 2. Characterize the role of restricted VH and VL gene segment usage in shaping the antibody response to HIV-1 infection. 3. Determine the role of persistence of B cell clonal lineages in shaping the mutation frequencies of HIV-1 reactive antibodies.

After the introduction (Chapter 1) and methods (Chapter 2), Chapter 3 of this dissertation describes a study of the antibody response of terminal ileum B cells to HIV-1 envelope (Env) in early and chronic HIV-1 infection and provides evidence for the role of environmental antigens in shaping the repertoire of B cells that respond to HIV-1 infection. Previous work by Liao et al. demonstrated that the initial plasma cell response in the blood to acute HIV-1 infection is to gp41 and is derived from a polyreactive memory B cell pool. Many of these antibodies cross-reacted with commensal bacteria, Therefore, in Chapter 3, the relationship of intestinal B cell reactivity with commensal bacteria to HIV-1 infection-induced antibody response was probed using single B cell sorting, reverse transcription and nested polymerase chain reaction (RT- PCR) methods, and recombinant antibody technology. The dominant B cell response in the terminal ileum was to HIV-1 envelope (Env) gp41, and 82% of gp41- reactive antibodies cross-reacted with commensal bacteria whole cell lysates. Pyrosequencing of blood B cells revealed HIV-1 antibody clonal lineages shared between ileum and blood. Mutated IgG antibodies cross-reactive with both Env gp41 and commensal bacteria could also be isolated from the terminal ileum of HIV-1 uninfected individuals. Thus, the antibody response to HIV-1 can be shaped by intestinal B cells stimulated by commensal bacteria prior to HIV-1 infection to develop a pre-infection pool of memory B cells cross-reactive with HIV-1 gp41.

Chapter 4 details the study of restricted VH and VL gene segment usage for gp41 and gp120 antibody induction following acute HIV-1 infection; mutations in gp41 lead to virus enhanced neutralization sensitivity. The B cell repertoire of antibodies induced in a HIV-1 infected African individual, CAP206, who developed broadly neutralizing antibodies (bnAbs) directed to the HIV-1 envelope gp41 membrane proximal external region (MPER), is characterized. Understanding the selection of virus mutants by neutralizing antibodies is critical to understanding the role of antibodies in control of HIV-1 replication and prevention from HIV-1 infection. Previously, an MPER neutralizing antibody, CAP206-CH12, with the binding footprint identical to that of MPER broadly neutralizing antibody 4E10, that like 4E10 utilized the VH1-69 and VK3-20 variable gene segments was isolated from this individual (Morris et al., 2011). Using single B cell sorting, RT- PCR methods, and recombinant antibody technology, Chapter 4 describes the isolation of a VH1-69, Vk3-20 glycan-dependent clonal lineage from CAP206, targeted to gp120, that has the property of neutralizing a neutralization sensitive CAP206 transmitted/founder (T/F) and heterologous viruses with mutations at amino acids 680 or 681 in the MPER 4E10/CH12 binding site. These data demonstrate sites within the MPER bnAb epitope (aa 680-681) in which mutations can be selected that lead to viruses with enhanced sensitivity to autologous and heterologous neutralizing antibodies.

In Chapter 5, I have completed a comparison of evolution of B cell clonal lineages in two HIV-1 infected individuals who have a predominant VH1-69 response to HIV-1 infection--one who produces broadly neutralizing MPER-reactive mAbs and one who does not. Autologous neutralization in the plasma takes ~12 weeks to develop (Gray et al., 2007; Tomaras et al., 2008b). Only a small subset of HIV-1 infected individuals develops high plasma levels of broad and potent heterologous neutralization, and when it does occur, it typically takes 3-4 years to develop (Euler et al., 2010; Gray et al., 2007; 2011; Tomaras et al., 2011). The HIV-1 bnAbs that have been isolated to date have a number of unusual characteristics including, autoreactivity and high levels of somatic hypermutations, which are typically tightly regulated by immune control mechanisms (Haynes et al., 2005; 2012b; Kwong and Mascola, 2012; Scheid et al., 2009a). The VH mutation frequencies of bnAbs average ~15% but have been shown to be as high as 32% (reviewed in Mascola and Haynes, 2013; Kwong and Mascola, 2012). The high frequency of somatic hypermutations suggests that the B cell clonal lineages that eventually produce bnAbs undergo high-levels of affinity maturation, implying prolonged germinal center (GC) reactions and high levels of T cell help. To study the duration of HIV-1- reactive B cell clonal persistence, HIV-1 reactive and non HIV-1- reactive B cell clonal lineages were isolated from an HIV-1 infected individual that produces bnAbs, CAP206, and an HIV-1 infected individual who does not produce bnAbs, 004-0. Single B cell sorting, RT-PCR and recombinant antibody technology was used to isolate and produce monoclonal antibodies from multiple time points from each individual. B cell sequences clonally related to mAbs isolated by single cell PCR were identified within pyrosequences of longitudinal samples of these two individuals. Both individuals produced long-lived B cell clones that persisted from 0-232 weeks in CAP206, and 0-238 weeks in 004-0. The average length of persistence of clones containing members isolated from two separate time points was 91.5 weeks both individuals. Examples of the continued evolution of clonal lineages were observed in both the bnAb and non-bnAb individual. These data indicated that the ability to generate persistent and evolving B cell clonal lineages occurs in both bnAb and non-bnAb individuals, suggesting that some alternative host or viral factor is critical for the generation of highly mutated broadly neutralizing antibodies.

Together the studies described in Chapter 3-5 show that multiple factors influence the antibody response to HIV-1 infection. The initial antibody response to HIV-1 Env gp41 can be shaped by a B cell response to intestinal commensal bacteria prior to HIV-1 infection. VH and VL gene segment restriction can impact the B cell response to multiple HIV-1 antigens, and virus escape mutations in the MPER can confer enhanced neutralization sensitivity to autologous and heterologous antibodies. Finally, the ability to generate long-lived HIV-1 clonal lineages in and of itself does not confer on the host the ability to produce bnAbs.

Due to her tender age: Black girls and childhood on trial in South Carolina, 1885-1920

Drawing on local criminal court records in western and central South Carolina, this dissertation follows the legal experiences of black girls in South Carolina courts between 1885 and 1920, a time span that includes the aftermath of Reconstruction and the foundational years of Jim Crow. While scholars continue to debate the degree to which black children were included in evolving conversations about childhood and child protection, this dissertation argues that black girls were critical to turn-of-the century debates about all children's roles in society. Far from invisible in the courts and jails of their time, black girls found themselves in the crosshairs of varying forms of power --including intraracial community surveillance, burgeoning local government, Progressive reform initiatives and military policy -- particularly when it came to matters of sexuality and reproduction. Their presence in South Carolina courts established boundaries between early childhood, adolescence and womanhood and pushed legal stakeholders to consider the legal implication of age, race, and gender in criminal proceedings. Age had a complicated effect on black girls' legal encounters; very young black girls were often able to claim youth and escape harsher punishments, while courts often used judicial discretion to levy heavier sentences to adolescents and violent girl offenders. While courts helped to separate early childhood from the middle years, they also provided a space for African-American children and family to engage a legal system that was moving rapidly toward disenfranchising blacks.

A dimensionless number for understanding the evolutionary dynamics of antigenically variable RNA viruses.

Antigenically variable RNA viruses are significant contributors to the burden of infectious disease worldwide. One reason for their ubiquity is their ability to escape herd immunity through rapid antigenic evolution and thereby to reinfect previously infected hosts. However, the ways in which these viruses evolve antigenically are highly diverse. Some have only limited diversity in the long-run, with every emergence of a new antigenic variant coupled with a replacement of the older variant. Other viruses rapidly accumulate antigenic diversity over time. Others still exhibit dynamics that can be considered evolutionary intermediates between these two extremes. Here, we present a theoretical framework that aims to understand these differences in evolutionary patterns by considering a virus's epidemiological dynamics in a given host population. Our framework, based on a dimensionless number, probabilistically anticipates patterns of viral antigenic diversification and thereby quantifies a virus's evolutionary potential. It is therefore similar in spirit to the basic reproduction number, the well-known dimensionless number which quantifies a pathogen's reproductive potential. We further outline how our theoretical framework can be applied to empirical viral systems, using influenza A/H3N2 as a case study. We end with predictions of our framework and work that remains to be done to further integrate viral evolutionary dynamics with disease ecology.

Global Rates of Free Hydrogen (H2) Production by Serpentinization and other Abiogenic Processes within Young Ocean Crust

The main conclusion of this dissertation is that global H2 production within young ocean crust (<10 Mya) is higher than currently recognized, in part because current estimates of H2 production accompanying the serpentinization of peridotite may be too low (Chapter 2) and in part because a number of abiogenic H2-producing processes have heretofore gone unquantified (Chapter 3). The importance of free H2 to a range of geochemical processes makes the quantitative understanding of H2 production advanced in this dissertation pertinent to an array of open research questions across the geosciences (e.g. the origin and evolution of life and the oxidation of the Earth’s atmosphere and oceans).

The first component of this dissertation (Chapter 2) examines H2 produced within young ocean crust [e.g. near the mid-ocean ridge (MOR)] by serpentinization. In the presence of water, olivine-rich rocks (peridotites) undergo serpentinization (hydration) at temperatures of up to ~500°C but only produce H2 at temperatures up to ~350°C. A simple analytical model is presented that mechanistically ties the process to seafloor spreading and explicitly accounts for the importance of temperature in H2 formation. The model suggests that H2 production increases with the rate of seafloor spreading and the net thickness of serpentinized peridotite (S-P) in a column of lithosphere. The model is applied globally to the MOR using conservative estimates for the net thickness of lithospheric S-P, our least certain model input. Despite the large uncertainties surrounding the amount of serpentinized peridotite within oceanic crust, conservative model parameters suggest a magnitude of H2 production (~1012 moles H2/y) that is larger than the most widely cited previous estimates (~1011 although previous estimates range from 1010-1012 moles H2/y). Certain model relationships are also consistent with what has been established through field studies, for example that the highest H2 fluxes (moles H2/km2 seafloor) are produced near slower-spreading ridges (<20 mm/y). Other modeled relationships are new and represent testable predictions. Principal among these is that about half of the H2 produced globally is produced off-axis beneath faster-spreading seafloor (>20 mm/y), a region where only one measurement of H2 has been made thus far and is ripe for future investigation.

In the second part of this dissertation (Chapter 3), I construct the first budget for free H2 in young ocean crust that quantifies and compares all currently recognized H2 sources and H2 sinks. First global estimates of budget components are proposed in instances where previous estimate(s) could not be located provided that the literature on that specific budget component was not too sparse to do so. Results suggest that the nine known H2 sources, listed in order of quantitative importance, are: Crystallization (6x1012 moles H2/y or 61% of total H2 production), serpentinization (2x1012 moles H2/y or 21%), magmatic degassing (7x1011 moles H2/y or 7%), lava-seawater interaction (5x1011 moles H2/y or 5%), low-temperature alteration of basalt (5x1011 moles H2/y or 5%), high-temperature alteration of basalt (3x1010 moles H2/y or <1%), catalysis (3x108 moles H2/y or <<1%), radiolysis (2x108 moles H2/y or <<1%), and pyrite formation (3x106 moles H2/y or <<1%). Next we consider two well-known H2 sinks, H2 lost to the ocean and H2 occluded within rock minerals, and our analysis suggests that both are of similar size (both are 6x1011 moles H2/y). Budgeting results suggest a large difference between H2 sources (total production = 1x1013 moles H2/y) and H2 sinks (total losses = 1x1011 moles H2/y). Assuming this large difference represents H2 consumed by microbes (total consumption = 9x1011 moles H2/y), we explore rates of primary production by the chemosynthetic, sub-seafloor biosphere. Although the numbers presented require further examination and future modifications, the analysis suggests that the sub-seafloor H2 budget is similar to the sub-seafloor CH4 budget in the sense that globally significant quantities of both of these reduced gases are produced beneath the seafloor but never escape the seafloor due to microbial consumption.

The third and final component of this dissertation (Chapter 4) explores the self-organization of barchan sand dune fields. In nature, barchan dunes typically exist as members of larger dune fields that display striking, enigmatic structures that cannot be readily explained by examining the dynamics at the scale of single dunes, or by appealing to patterns in external forcing. To explore the possibility that observed structures emerge spontaneously as a collective result of many dunes interacting with each other, we built a numerical model that treats barchans as discrete entities that interact with one another according to simplified rules derived from theoretical and numerical work, and from field observations: Dunes exchange sand through the fluxes that leak from the downwind side of each dune and are captured on their upstream sides; when dunes become sufficiently large, small dunes are born on their downwind sides (“calving”); and when dunes collide directly enough, they merge. Results show that these relatively simple interactions provide potential explanations for a range of field-scale phenomena including isolated patches of dunes and heterogeneous arrangements of similarly sized dunes in denser fields. The results also suggest that (1) dune field characteristics depend on the sand flux fed into the upwind boundary, although (2) moving downwind, the system approaches a common attracting state in which the memory of the upwind conditions vanishes. This work supports the hypothesis that calving exerts a first order control on field-scale phenomena; it prevents individual dunes from growing without bound, as single-dune analyses suggest, and allows the formation of roughly realistic, persistent dune field patterns.