Founder niche constrains evolutionary adaptive radiation

Adaptive radiation of a lineage into a range of organisms with different niches underpins the evolution of life’s diversity. Although the role of the environment in shaping adaptive radiation is well established, theory predicts that the evolvability and niche of the founding ancestor are also of importance. Direct demonstration of a causal link requires resolving the independent effects of these additional factors. Here, we accomplish this using experimental bacterial populations and demonstrate how the dynamics of adaptive radiation are constrained by the niche of the founder. We manipulated the propensity of the founder to undergo adaptive radiation and resolved the underlying causal changes in both its evolvability and niche. Evolvability did not change, but the propensity for adaptive radiation was altered by changes in the position and breadth of the niche of the founder. These observations provide direct empirical evidence for a link between the niche of organisms and their propensity for adaptive radiation. This general mechanism may have rendered the evolutionary dynamics of extant adaptive radiations dependent on chance events that determined their founding ancestors.Rapid diversification of a single lineage into organisms with different niches—adaptive radiation—underpins the evolution of biodiversity (1–4). Here, we define a niche as the complex of reciprocal ecological interactions between an organism and its environment that governs organismal fitness (following refs. 5–7). Although the dynamics of adaptive radiation are determined by the interplay of many factors, two universal prerequisites are sufficiency of founder evolvability and availability of ecological opportunity (1–4, 8–12). Founder evolvability concerns the maximal range of derived organisms with different niches that can be accessed from the founding ancestor by mutation and recombination over an interval of evolutionary time (3, 8, 13–16). Ecological opportunity for adaptive radiation emerges when the environment allows the possibility of invasion and persistence of multiple derived organisms with different niches (17). Spectacular adaptive radiations, such as those of the Galapagos finches (18), African Rift Lake cichlids (15) or Caribbean Anolis lizards (19), can occur when evolvability and ecological opportunity interact to facilitate generation of niche specialists while precluding superior generalists, which might otherwise usurp ecological opportunity.Since Simpson (2) formulated the requirements for adaptive radiation in the 1950s, the environment has been established as a major determinant of ecological opportunity (3). This is supported by a large body of work on extant adaptive radiations (3, 8, 9, 11, 15, 18, 19). In addition, evolutionary experiments with bacteria have provided direct evidence that links environmental components of ecological opportunity to patterns of adaptive radiation (20–30).However, because ecological opportunity emerges from the interaction between the organism and the environment, it is also influenced by the niche of the (prospective) founder [e.g., positively by key innovations and negatively by resource usurpation (3)]. Compared with the role of the environment, relatively little is known about the effects of the founder’s niche on the dynamics of adaptive radiation. Comparative studies reveal differences in the tempo and outcome of parallel adaptive radiations that may have arisen from ecological differences among the founding ancestors (31, 32). In contrast, phylogenetic reconstruction of the niche of founders of extant adaptive radiations is yet to resolve significant correlations with patterns of diversification (4, 8). An effect of founder niche on evolutionary branching has been observed in experimental bacterial populations, demonstrating that founder specialization can increase the likelihood of diversification (33).In addition to its niche, a second property of the founder that shapes adaptive radiation is evolvability (3, 8, 13–16). Founder evolvability places an upper limit on the number of organisms with different niches that can emerge by adaptive radiation over an interval of evolutionary time. Moreover, for adaptive radiation to occur, founder evolvability must facilitate generation of diverse niche specialists but preclude “Darwinian demons” with superior, generalist niches that would impede adaptive radiation (10, 34). Studies on extant adaptive radiations have begun to probe the impact of evolvability (16, 35, 36), and its importance for diversification in general is supported by evidence from experimental evolution (e.g., refs. 37, 38).The ecological theory of adaptive radiation predicts that founder evolvability and niche have an impact on the dynamics of diversification (8). An important step toward further establishment of these factors is direct demonstration of their effects. To achieve this, it is necessary to manipulate the evolvability and niche of the founder experimentally and resolve their independent effects on adaptive radiation. Here, we accomplish this using experimental populations of the bacterium Pseudomonas fluorescens SBW25. First, we exploit a previously described evolutionary selection regime to manipulate the propensity for adaptive radiation of the founder (39). We then apply a combination of analyses to resolve the underlying causal changes in evolvability and niche. The results provide a direct demonstration of the founder-niche effect on the dynamics of adaptive radiation.     

Accelerated regulatory gene evolution in an adaptive radiation

The disparity between rates of morphological and molecular evolution remains a key paradox in evolutionary genetics. A proposed resolution to this paradox has been the conjecture that morphological evolution proceeds via diversification in regulatory loci, and that phenotypic evolution may correlate better with regulatory gene divergence. This conjecture can be tested by examining rates of regulatory gene evolution in species that display rapid morphological diversification within adaptive radiations. We have isolated homologues to the Arabidopsis APETALA3 (ASAP3/TM6) and APETALA1 (ASAP1) floral regulatory genes and the CHLOROPHYLL A/B BINDING PROTEIN9 (ASCAB9) photosynthetic structural gene from species in the Hawaiian silversword alliance, a premier example of plant adaptive radiation. We have compared rates of regulatory and structural gene evolution in the Hawaiian species to those in related species of North American tarweeds. Molecular evolutionary analyses indicate significant increases in nonsynonymous relative to synonymous nucleotide substitution rates in the ASAP3/TM6 and ASAP1 regulatory genes in the rapidly evolving Hawaiian species. By contrast, no general increase is evident in neutral mutation rates for these loci in the Hawaiian species. An increase in nonsynonymous relative to synonymous nucleotide substitution rate is also evident in the ASCAB9 structural gene in the Hawaiian species, but not to the extent displayed in the regulatory loci. The significantly accelerated rates of regulatory gene evolution in the Hawaiian species may reflect the influence of allopolyploidy or of selection and adaptive divergence. The analyses suggest that accelerated rates of regulatory gene evolution may accompany rapid morphological diversification in adaptive radiations.     

Experimental evidence that predation promotes divergence in adaptive radiation

Adaptive radiation is the evolution of ecological and phenotypic diversity within a rapidly multiplying lineage. Recent studies have identified general patterns in adaptive radiation and inferred that resource competition is a primary factor driving phenotypic divergence. The role and importance of other processes, such as predation, remains controversial. Here we use Timema stick insects to show that adaptive radiation can be driven by divergent selection from visual predators. Ecotypes using different host-plant species satisfy criteria for the early stages of adaptive radiation and differ in quantitative aspects of color, color pattern, body size, and body shape. A manipulative field experiment demonstrates that the direction and strength of divergent selection on these traits is strongly positively correlated with the direction and magnitude of their population divergence in nature but only when selection is estimated in the presence of predation. Our results indicate that both competition and predation may commonly serve as mechanisms of adaptive radiation.     

Evidence for adaptive radiation from a phylogenetic study of plant defenses

One signature of adaptive radiation is a high level of trait change early during the diversification process and a plateau toward the end of the radiation. Although the study of the tempo of evolution has historically been the domain of paleontologists, recently developed phylogenetic tools allow for the rigorous examination of trait evolution in a tremendous diversity of organisms. Enemy-driven adaptive radiation was a key prediction of Ehrlich and Raven''s coevolutionary hypothesis [Ehrlich PR, Raven PH (1964) Evolution 18:586–608], yet has remained largely untested. Here we examine patterns of trait evolution in 51 North American milkweed species (Asclepias), using maximum likelihood methods. We study 7 traits of the milkweeds, ranging from seed size and foliar physiological traits to defense traits (cardenolides, latex, and trichomes) previously shown to impact herbivores, including the monarch butterfly. We compare the fit of simple random-walk models of trait evolution to models that incorporate stabilizing selection (Ornstein-Ulenbeck process), as well as time-varying rates of trait evolution. Early bursts of trait evolution were implicated for 2 traits, while stabilizing selection was implicated for several others. We further modeled the relationship between trait change and species diversification while allowing rates of trait evolution to vary during the radiation. Species-rich lineages underwent a proportionately greater decline in latex and cardenolides relative to species-poor lineages, and the rate of trait change was most rapid early in the radiation. An interpretation of this result is that reduced investment in defensive traits accelerated diversification, and disproportionately so, early in the adaptive radiation of milkweeds.     

Brain shape convergence in the adaptive radiation of New World monkeys

Primates constitute one of the most diverse mammalian clades, and a notable feature of their diversification is the evolution of brain morphology. However, the evolutionary processes and ecological factors behind these changes are largely unknown. In this work, we investigate brain shape diversification of New World monkeys during their adaptive radiation in relation to different ecological dimensions. Our results reveal that brain diversification in this clade can be explained by invoking a model of adaptive peak shifts to unique and shared optima, defined by a multidimensional ecological niche hypothesis. Particularly, we show that the evolution of convergent brain phenotypes may be related to ecological factors associated with group size (e.g., social complexity). Together, our results highlight the complexity of brain evolution and the ecological significance of brain shape changes during the evolutionary diversification of a primate clade.Adaptive radiation, defined as the rapid and exceptional adaptive diversification of a single phylogenetic lineage into a variety of different ecological niches (1, 2), is thought to be one of the main evolutionary processes generating biodiversity on Earth (3). Although several adaptive radiations have now been thoroughly studied (e.g., African cichlids, Caribbean anoles, Galapagos finches, etc.), we still need more studies from which generalizations on this process can be drawn (2). Particularly, under what conditions a lineage will undergo adaptive radiation has long been debated, although both empirical and theoretical models point to the existence of ecological opportunity as a major factor (2, 3). This opportunity may appear, among others, through the colonization of a new area, the extinction of a strong ecological competitor, or the evolution of a new trait—a “key innovation”—that allows the utilization of resources in ways that were not previously possible (3, 4). Therefore, a significant dimension of adaptive radiations is the diversification of ecologically relevant phenotypic traits (2, 5). Among the studied cases of adaptive radiations, several ecologically relevant traits have been identified. For example, relative limb size in anoles lizards (6), beak shape in Darwin’s finches (7), or overall body shape in cichlid fishes (8).Remarkably, a trait that has received less attention in the study of adaptive radiations among vertebrate clades is brain morphology. Brains have substantial ecological and adaptive importance because they underlie the behavior that allows an animal to successfully interact with its environment. In this sense, primates constitute a notable example, as the evolution of brain morphology is one of the most prominent features of their diversification (9). Primates generally engage in complex foraging and social behaviors (10), and therefore, the evolution of enhanced cognitive capacities associated with enlarged and/or more complex brains may constitute a major axis of their adaptive ecological diversification. For example, possessing a large brain is perhaps the single most relevant phenotypic trait of our own species, Homo sapiens. Specifically, previous works have pointed out that the evolution of enlarged brains could be important ecologically because these changes are related to the acquisition of the cognitive abilities required to sustain complex social interactions—a behavioral trait probably involved in the origin and maintenance of the evolutionary success of primates (the social brain hypothesis) (11).However, although brain size has been traditionally the preferred measured trait in evolutionary studies, brains are not uniform structures but are constituted by several anatomically distinct functional systems or modules (e.g., neocortex, cerebellum, etc.). Previous work has suggested that these modules can vary in their relative size among species of some mammalian clades (including primates) (12–14) and, moreover, that these mosaic changes can better explain neural diversity than total—absolute or relative—brain size changes alone (e.g., among primates) (14). Additionally, in several vertebrate clades, part of this mosaic variation has been related to particular behavioral capacities (e.g., refs. 15 and 16). Thus, brain diversification is probably a complex process involving several dimensions of change occurring during the divergence of the species and along multiple ecological axes. Moreover, as in previous adaptive radiation studies where shape is the most ecologically relevant trait (6, 7), brain shape (i.e., the relative position and size of individual brain components) is probably a more important aspect of brain evolution than its total relative size. However, despite the potential ecological relevance of brain shape variation for primates, its evolutionary dynamics have been less studied in macroevolution (14).New World monkeys or platyrrhines, one of the three major primate clades, constitute an example of a major mammalian adaptive radiation that unfolded in isolation in Central and South America during the last 25–35 Ma, resulting in broad ecological and morphological diversity (17, 18). Noticeably, previous works have pointed to the putative occurrence of several evolutionary independent processes of increase and decrease in relative brain size (19–21) in this clade, indicating an extensive diversification of brain morphology. However, it is unknown how brain shape has evolved in the context of this primate adaptive radiation.In this study, we investigate the process of brain shape diversification of New World monkeys during their adaptive radiation in relation to different ecological dimensions. We first quantify brain shape variation using virtual reconstructions of cranial endocasts and geometric morphometrics methods, and then explore the evolutionary processes underlying brain diversification using phylogenetic comparative methods. We hypothesized that, if brain shape is an ecologically relevant trait for platyrrhines, a pattern of variation that departs from neutral models of evolution would be expected. To address this hypothesis, we analyzed the relationship between phenotypic variation and the branching process of the species based on a Brownian (random) model of evolution. Next, we investigated whether a model involving changes in adaptive peaks in a macroevolutionary landscape for brain shape can better account for the observed diversity. Moreover, considering that a likely outcome of an adaptive radiation, given the importance of ecological factors in shaping diversity, is the repeated evolution of similar phenotypes (22), we explicitly test for the existence of brain morphological convergence in the platyrrhine radiation. Finally, we explore previously hypothesized ecological factors (e.g., group size) (11) driving brain shape diversification and convergence in this primate clade.     

Equilibrium speciation dynamics in a model adaptive radiation of island lizards

The relative importance of equilibrium and nonequilibrium processes in shaping patterns of species richness is one of the most fundamental questions in biodiversity studies. If equilibrium processes predominate, then ecological interactions presumably limit species diversity, potentially through diversity dependence of immigration, speciation, and extinction rates. Alternatively, species richness may be limited by the rate at which diversity arises or by the amount of time available for diversification. These latter explanations constitute nonequilibrium processes and can apply only to biotas that are unsaturated or far from diversity equilibria. Recent studies have challenged whether equilibrium models apply to biotas assembled through in situ speciation, as this process may be too slow to achieve steady-state diversities. Here we demonstrate that speciation rates in replicate Caribbean lizard radiations have undergone parallel declines to equilibrium conditions on three of four major islands. Our results suggest that feedback between total island diversity and per-capita speciation rates scales inversely with island area, with proportionately greater declines occurring on smaller islands. These results are consistent with strong ecological controls on species richness and suggest that the iconic adaptive radiation of Caribbean anoles may have reached an endpoint.     

Convergent evolution of behavior in an adaptive radiation of Hawaiian web-building spiders

Species in ecologically similar habitats often display patterns of divergence that are strikingly comparable, suggesting that natural selection can lead to predictable evolutionary change in communities. However, the relative importance of selection as an agent mediating in situ diversification, versus dispersal between habitats, cannot be addressed without knowledge of phylogenetic history. We used an adaptive radiation of spiders within the Hawaiian Islands to test the prediction that species of spiders on different islands would independently evolve webs with similar architectures. Tetragnatha spiders are the only nocturnal orb-weaving spiders endemic to the Hawaiian archipelago, and multiple species of orb-weaving Tetragnatha co-occur within mesic and wet forest habitats on each of the main islands. Therefore, comparison of web architectures spun by spiders on different islands allowed study of replicated evolutionary events of past behavioral diversification. We found that species within each island construct webs with architectures that differ from one another. However, pairs of species on different islands, "ethotypes," share remarkable similarities in web architectures. Phylogenetic analysis demonstrated that the species comprising these ethotypes evolved independent of one another. Our study illustrates the high degree of predictability that can be exhibited by the evolutionary diversification of complex behaviors. However, not all web architectures were shared between islands, demonstrating that unique effects also have played an important role in the historical diversification of behavior.     

Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands

Some of the most spectacular adaptive radiations begin with founder populations on remote islands. How genetically limited founder populations give rise to the striking phenotypic and ecological diversity characteristic of adaptive radiations is a paradox of evolutionary biology. We conducted an evolutionary genomics analysis of genus Metrosideros, a landscape-dominant, incipient adaptive radiation of woody plants that spans a striking range of phenotypes and environments across the Hawaiian Islands. Using nanopore-sequencing, we created a chromosome-level genome assembly for Metrosideros polymorpha var. incana and analyzed whole-genome sequences of 131 individuals from 11 taxa sampled across the islands. Demographic modeling and population genomics analyses suggested that Hawaiian Metrosideros originated from a single colonization event and subsequently spread across the archipelago following the formation of new islands. The evolutionary history of Hawaiian Metrosideros shows evidence of extensive reticulation associated with significant sharing of ancestral variation between taxa and secondarily with admixture. Taking advantage of the highly contiguous genome assembly, we investigated the genomic architecture underlying the adaptive radiation and discovered that divergent selection drove the formation of differentiation outliers in paired taxa representing early stages of speciation/divergence. Analysis of the evolutionary origins of the outlier single nucleotide polymorphisms (SNPs) showed enrichment for ancestral variations under divergent selection. Our findings suggest that Hawaiian Metrosideros possesses an unexpectedly rich pool of ancestral genetic variation, and the reassortment of these variations has fueled the island adaptive radiation.

Adaptive radiations exhibit extraordinary levels of morphological and ecological diversity (1). Although definitions of adaptive radiation vary (2–7), all center on ecological opportunity as a driver of adaptation and, ultimately, diversification (2, 8–10). Divergent selection, the primary mechanism underlying adaptive radiations, favors extreme phenotypes (11) and selects alleles that confer adaptation to unoccupied or under-utilized ecological niches. Differential adaptation results in divergence and, ultimately, reproductive isolation between populations (12). Adaptive radiations demonstrate the remarkable power of natural selection as a driver of biological diversity and provide excellent systems for studying evolutionary processes involved in diversification and speciation (13).Adaptive radiations on remote oceanic islands are especially interesting, as colonization of remote islands is expected to involve population bottlenecks that restrict genetic variation (14). Adaptive radiations in such settings are especially impressive and even paradoxical, given the generation of high species richness from an initially limited gene pool (15). Several classic examples of adaptive radiation occur on oceanic islands, such as Darwin’s finches from the Galapagos islands (16), anole lizards from the Caribbean islands (9), Hawaiian Drosophilids (17), and Hawaiian silverswords (18), to name a few.Recent advances in genome sequencing and analyses have greatly improved our ability to examine the genetics of speciation and adaptive radiation. By examining sequences of multiple individuals from their natural environment, it has become possible to “catch in the act” the speciation processes between incipient lineages (19). Genomic studies of early stage speciation show that differentiation accumulates in genomic regions that restrict the homogenizing effects of gene flow between incipient species (20). The number, size, and distribution of these genomic regions can shed light on evolutionary factors involved in speciation (19). Regions of high genomic differentiation can also form from evolutionary factors unrelated to speciation, such as linkage associated with recurrent background selection or selective sweeps on shared genomic features (21, 22).Genomic studies of lineages undergoing rapid ecological diversification have begun to reveal the evolutionary mechanisms underlying adaptive radiations. Importantly, these studies highlight the pivotal role of hybridization between populations and the consequent exchange of adaptive alleles that facilitates rapid speciation and the colonization of diverse niches (23–25). Most genomic studies of adaptive radiation involve animal systems, however, in particular, birds and fishes. In plants, genomic studies of adaptive radiation are sparse (26–28), and all examine continent-wide radiations. There are no genomics studies of plant adaptive radiations in geographically restricted systems such as remote islands. Because the eco-evolutionary scenarios associated with adaptive radiations are diverse (5, 29), whether commonalities identified in adaptive radiations in animals (23, 30) are applicable to plants is an open question. For example, the genetic architecture of animal adaptive radiations typically involves differentiation at a small number of genomic regions (31–33). In contrast, the limited insights available for plants suggest a more complex genetic architecture (26).We investigated the evolutionary genomics of adaptive radiation in Metrosideros Banks ex Gaertn. (Myrtaceae) across the Hawaiian Islands. Hawaiian Metrosideros is a landscape-dominant, hypervariable, and highly dispersible group of long-lived (possibly >650 y) (34) woody taxa that are nonrandomly distributed across Hawaii’s heterogeneous landscape, including cooled lava flows, wet forests and bogs, subalpine zones, and riparian zones (35, 36). About 25 taxa or morphotypes are distinguished by vegetative characters ranging from prostate plants that flower a few centimeters above ground to 30-m-tall trees, and leaves range dramatically in size, shape, pubescence, color, and rugosity (35, 37, 38); a majority of these forms are intraspecific varieties or races (provisional varieties) of the abundant species, Metrosideros polymorpha (35, 36, 38). Variation in leaf mass per area within the four Metrosideros taxa on Hawaii Island alone matches that observed for woody species globally (39). Common garden experiments (38, 40–44) and parent–offspring analysis (45) demonstrate heritability of taxon-diagnostic vegetative traits, indicating that taxa are distinct genetic groups and not the result of phenotypic plasticity. Metrosideros taxa display evidence of local adaptation to contrasting environments (46, 47), suggesting ecological divergent selection is responsible for diversification within the group (48). This diversification, which spans the past ∼3.1 to 3.9 million years (49, 50), has occurred despite the group’s high capacity for gene flow by way of showy bird-pollinated flowers and tiny wind-dispersed seeds (36, 51). Lastly, the presence of partial reproductive isolating barriers between taxa is consistent with the early stages of speciation (52). Here, we generated several genomic resources for Hawaiian Metrosideros and used these in population genomics analyses to gain deeper insights into the genomic architecture and evolutionary processes underlying this island adaptive radiation.     

Ecological and evolutionary determinants for the adaptive radiation of the Madagascan vangas

Adaptive radiation is the rapid diversification of a single lineage into many species that inhabit a variety of environments or use a variety of resources and differ in traits required to exploit these. Why some lineages undergo adaptive radiation is not well-understood, but filling unoccupied ecological space appears to be a common feature. We construct a complete, dated, species-level phylogeny of the endemic Vangidae of Madagascar. This passerine bird radiation represents a classic, but poorly known, avian adaptive radiation. Our results reveal an initial rapid increase in evolutionary lineages and diversification in morphospace after colonizing Madagascar in the late Oligocene some 25 Mya. A subsequent key innovation involving unique bill morphology was associated with a second increase in diversification rates about 10 Mya. The volume of morphospace occupied by contemporary Madagascan vangas is in many aspects as large (shape variation)--or even larger (size variation)--as that of other better-known avian adaptive radiations, including the much younger Galapagos Darwin's finches and Hawaiian honeycreepers. Morphological space bears a close relationship to diet, substrate use, and foraging movements, and thus our results demonstrate the great extent of the evolutionary diversification of the Madagascan vangas.     

Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries

Specific sets of brain-expressed genes, such as aerobic energy metabolism genes, evolved adaptively in the ancestry of humans and may have evolved adaptively in the ancestry of other large-brained mammals. The recent addition of genomes from two afrotherians (elephant and tenrec) to the expanding set of publically available sequenced mammalian genomes provided an opportunity to test this hypothesis. Elephants resemble humans by having large brains and long life spans; tenrecs, in contrast, have small brains and short life spans. Thus, we investigated whether the phylogenomic patterns of adaptive evolution are more similar between elephant and human than between either elephant and tenrec lineages or human and mouse lineages, and whether aerobic energy metabolism genes are especially well represented in the elephant and human patterns. Our analyses encompassed ≈6,000 genes in each of these lineages with each gene yielding extensive coding sequence matches in interordinal comparisons. Each gene''s nonsynonymous and synonymous nucleotide substitution rates and dN/dS ratios were determined. Then, from gene ontology information on genes with the higher dN/dS ratios, we identified the more prevalent sets of genes that belong to specific functional categories and that evolved adaptively. Elephant and human lineages showed much slower nucleotide substitution rates than tenrec and mouse lineages but more adaptively evolved genes. In correlation with absolute brain size and brain oxygen consumption being largest in elephants and next largest in humans, adaptively evolved aerobic energy metabolism genes were most evident in the elephant lineage and next most evident in the human lineage.     

Systematic changes in gene expression patterns following adaptive evolution in yeast.

Culturing a population of Saccharomyces cerevisiae for many generations under conditions to which it is not optimally adapted selects for fitter genetic variants. This simple experimental design provides a tractable model of adaptive evolution under natural selection. Beginning with a clonal, founding population, independently evolved strains were obtained from three independent cultures after continuous aerobic growth in glucose-limited chemostats for more than 250 generations. DNA microarrays were used to compare genome-wide patterns of gene expression in the evolved strains and the parental strain. Several hundred genes were found to have significantly altered expression in the evolved strains. Many of these genes showed similar alterations in their expression in all three evolved strains. Genes with altered expression in the three evolved strains included genes involved in glycolysis, the tricarboxylic acid cycle, oxidative phosphorylation, and metabolite transport. These results are consistent with physiological observations and indicate that increased fitness is acquired by altering regulation of central metabolism such that less glucose is fermented and more glucose is completely oxidized.     

Global patterns of antigen receptor repertoire disruption across adaptive immune compartments in COVID-19

Whereas pathogen-specific T and B cells are a primary focus of interest during infectious disease, we have used COVID-19 to ask whether their emergence comes at a cost of broader B cell and T cell repertoire disruption. We applied a genomic DNA-based approach to concurrently study the immunoglobulin-heavy (IGH) and T cell receptor (TCR) β and δ chain loci of 95 individuals. Our approach detected anticipated repertoire focusing for the IGH repertoire, including expansions of clusters of related sequences temporally aligned with SARS-CoV-2–specific seroconversion, and enrichment of some shared SARS-CoV-2–associated sequences. No significant age-related or disease severity–related deficiencies were noted for the IGH repertoire. By contrast, whereas focusing occurred at the TCRβ and TCRδ loci, including some TCRβ sequence–sharing, disruptive repertoire narrowing was almost entirely limited to many patients aged older than 50 y. By temporarily reducing T cell diversity and by risking expansions of nonbeneficial T cells, these traits may constitute an age-related risk factor for COVID-19, including a vulnerability to new variants for which T cells may provide key protection.

Severe disease and death caused by SARS-CoV-2 infection appear to be largely due to failures and/or dysregulation of the immune response in vulnerable populations (1). Thus, most SARS-CoV-2 infections are asymptomatic or pauci-symptomatic, particularly among younger people, who, by measures of diversity and functional responses, have greater adaptive immunocompetence than do the elderly (2, 3).In addition to providing host protection, adaptive immune functions may contribute pathologic mediators, including B cell autoreactivities associated with specific disease-related characteristics in many patients with COVID-19 (4, 5). Additionally, early B cell responses after SARS-CoV-2 infection in some donors are enriched in cross-reactive memory B cells, including those against seasonal coronaviruses, which are of uncertain protective benefit (6). Collectively, these examples illustrate the importance of considering the dynamics of immune responses beyond those that are pathogen specific.Over 2 y since the start of the pandemic, age remains the most evident predisposing factor for COVID-19 severity (7), evoking the increased susceptibility of older persons to other newly emerged viruses, including West Nile virus and SARS-CoV-1 (8, 9). The sequence richness of the CD4⁺ and CD8⁺ T cell receptor (TCR) repertoires is reduced in older persons relative to younger persons (10) and may underlie such vulnerabilities. This raises the question of how age might affect the mobilization of antigen-receptor repertoires in response to SARS-CoV-2 infection.The COVID-19 pandemic has provided a unique opportunity to interrogate naïve responses to a novel human pathogen. To examine this at scale, we describe here the application of immunoPETE, a newly developed, genomic DNA (gDNA)-based technique permitting simultaneous characterization of antigen-receptor repertoires for the major adaptive lymphocyte subsets: B cells (immunoglobulin heavy chain [IGH] sequences); αβ T cells (TCRβ chain and TRB sequences), which comprise two distinct subsets; CD4⁺ and CD8⁺ cells; and γδ T cells (TCRδ chain and TRD sequences), which comprise Vδ1⁺ and Vδ2⁺ T cells.Whereas many studies have offered important insights into antigen-receptor repertoires in active COVID-19 (11–15), our study builds on those by uniquely harnessing an array of technical and methodological approaches. Thus, immunoPETE combines gDNA-based sequencing, used in other COVID-19 repertoire studies (15), with unique molecular identifier (UMI)-based deduplication of clonal expansions and correction of PCR sequencing errors; cell sorting to segregate functionally distinct CD4⁺ and CD8⁺ populations; human leukocyte antigen (HLA) typing to enhance clustering and determination of shared specificities within CD4⁺ and CD8⁺ T cell populations; and TRD sequencing permitting a real-time comparison of the responses of qualitatively distinct Vδ1 and Vδ2 subsets to a defined human virus infection.Studying 95 individuals comprising hospital-treated patients with COVID-19 and seropositive [sero(+)] and seronegative [sero(−)] individuals, we found clear adaptive response patterns in each lymphocyte subset studied. Repertoire focusing at the IGH locus was generalizable, with the expansion of related sequence clusters temporally aligned with seroconversion. Whereas TRB repertoires also showed similar shared sequence expansions, these were conspicuously buffered by the scale and diversity of the T lymphocyte compartments in most individuals aged <50 y, whereas they exerted much more disruptive effects in many individuals aged ≥50 y, who likewise displayed major disruptions in TRD repertoire diversity. Such impacts may limit the capacity to recognize diverse challenges (e.g., coinfections and emerging new variants) and may afford undue prominence to expanding nonneutralizing and/or self-reactive clones. Thus, they should be considered an additional age-related disease risk, monitoring of which may help inform the management of COVID-19 and of other infections.     

Dynamic patterns of avian and human influenza in east and southeast Asia

The seasonal patterns of human influenza in temperate regions have been well documented; however, much less attention has been paid to patterns of infection in the tropical and subtropical areas of east and southeast Asia. During the period 1997-2006, this region experienced several outbreaks of highly pathogenic avian influenza A (H5N1) in hosts including wild and domestic poultry, human beings, and other mammals. H5N1 is thought to be a likely source of a pandemic strain of human influenza. Incidence of both human influenza and avian influenza in human beings shows evidence of seasonality throughout east and southeast Asia, although the seasonal patterns in tropical and subtropical areas are not as simple or as pronounced as those in temperate regions around the world. The possibility of a human being becoming co-infected with both human and avian strains of influenza is not restricted to a short season, although the risks do appear to be greatest during the winter months.     

Dynamic patterns of medial preoptic mu-opiate receptor regulation by gonadal steroid hormones.

The density of mu-opiate receptors located in the medial preoptic area (MPOA) of the rat hypothalamus is cyclical and sexually dimorphic. The hormonal regulation of MPOA mu-receptors was examined in ovariectomized rats treated with a variety of hormone regimens. In experiment 1, animals received acute estradiol (E2), progesterone (P), or prolactin (PRL), or E2 followed in 48 h by either P or vehicle by subcutaneous injection. Brains were removed 3 h after the final injection. In experiment 2, animals were implanted with empty or E2-filled Silastic capsules, and received either P or vehicle by injection 48 h later, at which time E2 capsules were removed. One group received E2 implants which remained in place following sham removal surgery. Brains and trunk blood for radioimmunoassay of E2 and P were collected 3, 27 or 51 h after the final injection. Frozen brain sections were prepared, incubated in [3H]D-Ala2,MePhe4,Gly-ol5-enkephalin, which selectively labels mu-receptors, and analyzed using quantitative receptor autoradiography. P treatment significantly increased MPOA mu-receptors, but only 27 h after E2 priming. Neither shorter P exposure, nor E2, P or PRL alone affected MPOA mu-receptor density. Following this delayed E2,P-induced increase, mu-receptor density subsequently decreased in the presence of absence of E2. The results suggest that E2,P treatment produces a gradual and transient increase of MPOA mu-receptor density. The subsequent decrease of receptor density is independent of the presence of E2 and may be related to receptor turnover. The time course of this effect is consistent with that of the estrus cycle. Such hormone-induced regulation of MPOA mu-receptor density could influence the physiologic effects of opiates on gonadotropin secretion and reproductive behavior in cycling females.