Development Of Phenotype Research Articles

Dine and dash: how trophic ecology and migration shape functional locomotory traits in clupeiform fishes

Abstract Understanding how interactions between multiple selective forces influence traits at the macroevolutionary scale is key to understanding adaptive landscapes. Diadromy, an extreme form of migration between marine and freshwater environments, is thought to require locomotory traits conducive to long-distance migration. Yet, other selective forces, such as predator avoidance, habitat use, and prey acquisition, are also likely to shape locomotory adaptation in fishes. We examined how diadromy and trophic ecology together influenced locomotory trait diversity across Clupeiformes, a clade of fishes containing high trophic diversity and numerous transitions to diadromy. We found that both diadromy and trophic ecology influenced the pattern and pace of trait evolution. Diadromous taxa rapidly evolved traits characterized by high cruising efficiency, but the extent to which diadromous and non-diadromous taxa differed depended on their trophic ecology. Macropredators showed greater differences in locomotory traits between diadromous and non-diadromous taxa than phytodetritivores and micropredators, suggesting that traits conducive to migration might be most costly to consumers of evasive prey. This work shows that simultaneously characterizing the roles of multiple ecological or life-history factors in phenotypic evolution can bring the topography of adaptive landscapes into sharper focus and provide a more holistic view of the forces driving patterns of trait evolution.

Phenotypic Convergence Is Stronger and More Frequent in Herbivorous Fishes.

Constraints on phenotypic evolution can lead to patterns of convergent evolution, by limiting the "pool" of potential phenotypes in the face of endogenous (functional, developmental) or exogenous (competition, predation) selective pressures. Evaluation of convergence depends on integrating ecological and morphological data within a robust, comparative phylogenetic context. The staggering diversity of teleost fishes offers a multitude of lineages adapted for similar ecological roles and, therefore, offers numerous replicated evolutionary experiments for exploring phenotypic convergence. However, our understanding of fish feeding systems has been primarily shaped by marine species, with the monolithic exception of freshwater cichlids. Here we use piranhas and pacus (Serrasalmidae) to explore the evolution of different feeding ecologies and their morphological proxies in Neotropical freshwater environments. Specifically, we explore whether convergence is more widespread among plant-eating fishes, arising from strong constraints on phenotypic evolution in herbivores. Using osteological micro-computed tomographic imaging (μCT), we describe the major axes of morphological variation in pacus and piranhas, regarding their diet and feeding behaviors. Next, we evaluated whether herbivorous niches are less labile than other dietary guilds and whether herbivorous species' phenotypes evolve at a slower evolutionary rate than other taxa. We then assess how convergent herbivorous taxa are, using three different suites of morphological characters (dental, jaw, and abdominal morphometrics). Ecologically, herbivory is not a dead end, exhibiting similar observed transition rates as those between carnivores and omnivores. However, we documented widespread convergence in herbivores and that herbivores have slower rates of phenotypic evolution than carnivores. Most instances of convergence are found in herbivorous taxa, specifically in frugivores and folivores. Moreover, instances of "complete" convergence, indicated by positive convergence metrics observed in more than one morphometric dataset, were only found in herbivores. Herbivores do appear to evolve under constrained circumstances, but this has not limited their ecological ability.

Characterization of HIV variants from paired Cerebrospinal fluid and Plasma samples in primary microglia and CD4+ T-cells.

Despite antiretroviral therapy (ART), HIV persistence in the central nervous system (CNS) continues to cause a range of cognitive impairments in people living with HIV (PLWH). Upon disease progression, transmigrating CCR5-using T-cell tropic viruses are hypothesized to evolve into macrophage-tropic viruses in the CNS that can efficiently infect low CD4-expressing cells, such as microglia. We examined HIV-1 RNA concentration, co-receptor usage, and CSF compartmentalization in paired CSF and blood samples from 19 adults not on treatment. Full-length envelope CSF- and plasma-derived reporter viruses were generated from 3 subjects and phenotypically characterized in human primary CD4+ T-cells and primary microglia. Median HIV RNA levels were higher in plasma than in CSF (5.01 vs. 4.12 log10 cp/mL; p = 0.004), and coreceptor usage was mostly concordant for CCR5 across the paired samples (n = 17). Genetically compartmentalized CSF viral populations were detected in 2 subjects, one with and one without neurological symptoms. All viral clones could replicate in T-cells (R5 T cell-tropic). In addition, 3 CSF and 1 plasma patient-derived viral clones also had the capacity to replicate in microglia/macrophages and, therefore have an intermediate macrophage tropic phenotype. Overall, with this study, we demonstrate that in a subset of PLWH, plasma-derived viruses undergo genetic and phenotypic evolution within the CNS, indicating viral infection and replication in CNS cells. It remains to be studied whether the intermediate macrophage-tropic phenotype observed in primary microglia represents a midpoint in the evolution towards a macrophage-tropic phenotype that can efficiently replicate in microglial cells and propagate viral infection in the CNS.

Skin colour: A window into human phenotypic evolution and environmental adaptation.

As modern humans ventured out of Africa and dispersed around the world, they faced novel environmental challenges that led to geographic adaptations including skin colour. Over the long history of human evolution, skin colour has changed dramatically, showing tremendous diversity across different geographical regions, for example, the majority of individuals from the expansive lands of Africa have darker skin, whereas the majority of people from Eurasia exhibit lighter skin. What adaptations did lighter skin confer upon modern humans as they migrated from Africa to Eurasia? What genetic mechanisms underlie the diversity of skin colour observed in different populations? In recent years, scientists have gradually gained a deeper understanding of the interactions between pigmentation gene and skin colour through population-based genomic studies of different groups around the world, particularly in East Asia and Africa. In this review, we summarize our current understanding of 26 skin colour-related pigmentation genes and 48 SNPs that influence skin colour. Important pigmentation genes across three major populations are described in detail: MFSD12, SLC24A5, PDPK1 and DDB1/CYB561A3/TMEM138 influence skin colour in African populations; OCA2, KITLG, SLC24A2, GNPAT and PAH are key to the evolution of skin pigmentation in East Asian populations; and SLC24A5, SLC45A2, TYR, TYRP1, ASIP, MC1R and IRF4 significantly contribute to the lightening of skin colour in European populations. We summarized recent findings in genomic studies of skin colour in populations that implicate diverse geographic environments, local adaptation among populations, gene flow and multi-gene interactions as factors influencing skin colour diversity.

Social interactions generate complex selection patterns in virtual worlds.

Understanding the influence of social interactions on individual fitness is key to improving our predictions of phenotypic evolution. However, we often overlook the different components of selection regimes arising from interactions among organisms, including social, correlational, and indirect selection. This is due to the challenging sampling efforts required in natural populations to measure phenotypes expressed during interactions and individual fitness. Furthermore, behaviours are crucial in mediating social interactions, yet few studies have explicitly quantified these selection components on behavioural traits. In this study, we capitalize on an online multiplayer video game as a source of extensive data recording direct social interactions among prey, where prey collaborate to escape a predator in realistic ecological settings. We estimate natural and social selection and their contribution to total selection on behavioural traits mediating competition, cooperation, and predator-prey interactions. Behaviours of other prey in a group impact an individual's survival, and thus are under social selection. Depending on whether selection pressures on behaviours are synergistic or conflicting, social interactions enhance or mitigate the strength of natural selection, although natural selection remains the main driving force. Indirect selection through correlations among traits also contributed to the total selection. Thus, failing to account for the effects of social interactions and indirect selection would lead to a misestimation of the total selection acting on traits. Dissecting the contribution of each component to the total selection differential allowed us to investigate the causal mechanisms relating behaviour to fitness and quantify the importance of the behaviours of conspecifics as agents of selection. Our study emphasizes that social interactions generate complex selective regimes even in a relatively simple ecological environment.

Silencing Ditylenchus destructor cathepsin L-like cysteine protease has negative pleiotropic effect on nematode ontogenesis

Ditylenchus destructor is a migratory plant-parasitic nematode that severely harms many agriculturally important crops. The control of this pest is difficult, thus efficient strategies for its management in agricultural production are urgently required. Cathepsin L-like cysteine protease (CPL) is one important protease that has been shown to participate in various physiological and pathological processes. Here we decided to characterize the CPL gene (Dd-cpl-1) from D. destructor. Analysis of Dd-cpl-1 gene showed that Dd-cpl-1 gene contains a signal peptide, an I29 inhibitor domain with ERFNIN and GNFD motifs, and a peptidase C1 domain with four conserved active residues, showing evolutionary conservation with other nematode CPLs. RT-qPCR revealed that Dd-cpl-1 gene displayed high expression in third-stage juveniles (J3s) and female adults. In situ hybridization analysis demonstrated that Dd-cpl-1 was expressed in the digestive system and reproductive organs. Silencing Dd-cpl-1 in 1-cell stage eggs of D. destructor by RNAi resulted in a severely delay in development or even in abortive morphogenesis during embryogenesis. The RNAi-mediated silencing of Dd-cpl-1 in J2s and J3s resulted in a developmental arrest phenotype in J3 stage. In addition, silencing Dd-cpl-1 gene expression in female adults led to a 57.43% decrease in egg production. Finally, Dd-cpl-1 RNAi-treated nematodes showed a significant reduction in host colonization and infection. Overall, our results indicate that Dd-CPL-1 plays multiple roles in D. destructor ontogenesis and could serve as a new potential target for controlling D. destructor.

Proteomic profiling of Botryllus schlosseri, an emerging model organism

Botryllus schlosseri is a colonial chordate species that exhibits robust stem cell-mediated regeneration capacities throughout life. It grows through a process of colonial budding known as blastogenesis, in addition to its sexual reproduction mode, embryogenesis. In natural conditions, colony growth peaks in the summer and drastically decreases in the winter due to various seasonal factors. We have established and optimized a method to rear B. schlosseri animals in landlocked laboratories where the controlled conditions allow colonies to grow continuously and exponentially through asexual reproduction under constant temperature, salinity, light, and nutrient conditions. During the weekly blastogenic cycle, all asexually derived parental zooids synchronously regress within one day and are replaced by a new generation. To enable comprehensive molecular phenotyping of this species we established a quantitative proteomics workflow and spectral library for Liquid chromatography/Tandem mass spectrometry (LCMS) data-independent acquisition (DIA). In this study, we quantified the relative abundances of several thousand proteins representing molecular phenotypes of B. schlosseri. This workflow enables us to use proteomics to characterize zooid development during its regenerative cycle, including the short critical period of the takeover stage, during which degenerating zooids undergo massive apoptosis while succeeding buds quickly mature and migrate into place. From this data, protein networks associated with regeneration and degeneration can be created, offering insights into tissue developmental pathways in vivo and future cell immortalization strategies in vitro. Furthermore, the establishment of quantitative proteomics workflows for B. schlosseri coupled with its unique life cycle features promotes the use of this model organism for the study of phenotypic plasticity and evolution of aging, stem cells, and mechanisms of regeneration and cell differentiation. This project is funded by NSF Grant MCB — 2127516. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Automated profiling of gene function during embryonic development

Systematic functional profiling of the gene set that directs embryonic development is an important challenge. To tackle this challenge, we used 4D imaging of C.elegans embryogenesis to capture the effects of 500 gene knockdowns and developed an automated approach to compare developmental phenotypes. The automated approach quantifies features-including germ layer cell numbers, tissue position, and tissue shape-to generate temporal curves whose parameterization yields numerical phenotypic signatures. In conjunction with a new similarity metric that operates across phenotypic space, these signatures enabled the generation of ranked lists of genes predicted to have similar functions, accessible in the PhenoBank web portal, for ∼25% of essential development genes. The approach identified new gene and pathway relationships in cell fate specification and morphogenesis and highlighted the utilization of specialized energy generation pathways during embryogenesis. Collectively, the effort establishes the foundation for comprehensive analysis of the gene set that builds a multicellular organism.

Ocular features of NGLY1 deficiency from a prospective longitudinal cohort

BackgroundNGLY1 deficiency is a rare autosomal recessive disorder with core features of global developmental delay, liver enzyme abnormalities, movement disorder, polyneuropathy, and hypo- or alacrima. We characterized the full spectrum and evolution of the ocular phenotype in a prospective natural history of NGLY1 deficiency. MethodsWe collected ophthalmological data on 29 individuals with NGLY1 deficiency in a natural history study. Medical records were reviewed to confirm caregiver-reported symptoms. Of the 29, 15 participants appeared for at least one ophthalmological examination. ResultsCaregivers reported at least one ocular sign or symptom in 90% of participants (26/29), most commonly decreased tears, refractive error, and chronic infection. Daily eye medication, including artificial tears, ophthalmic ointment, and topical antibiotics were used by 62%. Ophthalmological examination confirmed refractive errors in 93% (14/15) and corneal abnormalities in 73% (11/15). ConclusionsGiven nearly universal hypolacrima and additional prominent ocular findings in NGLY1 deficiency, a targeted ocular history and ophthalmologic examination may facilitate prompt diagnosis and early initiation of preventive eye care, preserving vision and overall ocular health.

A discrete-time model of phenotypic evolution

A model is proposed for the phenotypic evolution of a very large population under sustained environmental change and non-overlapping generations, with a single trait considered. Due to an extension of the standard law of quantitative inheritance, each evolutionary mechanism corresponds to a function between random variables associated with distinct stages of the life cycle. Such an approach leads to a two-dimensional map where the dynamics of the phenotypic mean and variance are directly connected. Then, the declining population paradigm is explored in terms of the critical rate of environmental change and using the techniques of the dynamical systems theory. Our results first reveal the opposing pressures on the phenotypic variance due to the conflict between phenotypic load and the ability to pursue the optimum, translated into an optimal value for maximizing the critical rate. Secondly, the introduction of development, through the particular case of linear plasticity, leads to a decreasing degree of stability with the magnitude of plasticity, which means that the recovery time from disturbances is harmed as the plastic effect intensifies, even though no constitutive costs have been assumed, a feature almost as important as the mean fitness to the viability of populations subject to persistent changes. Notwithstanding, the system is stable, and the growth rate benefits from increased plasticity, as expected.

The First Defined Null Allele of the Notch Regulator, a Suppressor of Deltex: Uncovering Its Novel Roles in Drosophila melanogaster Oogenesis.

Suppressor of deltex (Su(dx)) is a Drosophila melanogaster member of the NEDD4 family of the HECT domain E3 ubiquitin ligases. Su(dx) acts as a regulator of Notch endocytic trafficking, promoting Notch lysosomal degradation and the down-regulation of both ligand-dependent and ligand-independent signalling, the latter involving trafficking through the endocytic pathway and activation of the endo/lysosomal membrane. Mutations of Su(dx) result in developmental phenotypes in the Drosophila wing that reflect increased Notch signalling, leading to gaps in the specification of the wing veins, and Su(dx) functions to provide the developmental robustness of Notch activity to environmental temperature shifts. The full developmental functions of Su(dx) are unclear; however, this is due to a lack of a clearly defined null allele. Here we report the first defined null mutation of Su(dx), generated by P-element excision, which removes the complete open reading frame. We show that the mutation is recessive-viable, with the Notch gain of function phenotypes affecting wing vein and leg development. We further uncover new roles for Su(dx) in Drosophila oogenesis, where it regulates interfollicular stalk formation, egg chamber separation and germline cyst enwrapment by the follicle stem cells. Interestingly, while the null allele exhibited a gain in Notch activity during oogenesis, the previously described Su(dx)SP allele, which carries a seven amino acid in-frame deletion, displayed a Notch loss of function phenotypes and an increase in follicle stem cell turnover. This is despite both alleles displaying similar Notch gain of function in wing development. We attribute this unexpected context-dependent outcome of Su(dx)sp being due to the partial retention of function by the intact C2 and WW domain regions of the protein. Our results extend our understanding of the developmental role of Su(dx) in the tissue renewal and homeostasis of the Drosophila ovary and illustrate the importance of examining an allelic series of mutations to fully understand developmental functions.

Pelagic zone is an evolutionary catalyst, but an ecological dead end, for North American minnows.

The colonization of a novel geographic area is a classic source of ecological opportunity. Likewise, complex microhabitats are thought to promote biodiversity. We sought to reconcile these two predictions when they are naturally opposing outcomes. We assess the macroevolutionary consequences of an ancestral shift from benthic to pelagic microhabitat zones on rates of speciation and phenotypic evolution in North American minnows. Pelagic species have more similar phenotypes and slower rates of phenotypic evolution, but faster speciation rates, than benthic species. These are likely two independent, opposing responses to specialization along the benthic-pelagic axis, as rates of phenotypic evolution and speciation are not directly correlated. The pelagic zone is more structurally homogenous and offers less ecological opportunity, acting as an ecological dead end for minnows. In contrast, pelagic species may be more mobile and prone to dispersal and subsequent geographic isolation and, consequently, experience elevated instances of allopatric speciation. Microhabitat shifts can have decoupled effects on different dimensions of biodiversity, highlighting the need for nuance when interpreting the macroevolutionary consequences of ecological opportunity.

The effect of global change on the expression and evolution of floral traits.

Pollinators impose strong selection on floral traits. Indeed, pollinator syndromes are the result of these strong selective forces, but other abiotic and biotic agents also drive the evolution of floral traits and influence plant reproduction. Global change is expected to have widespread effects on biotic and abiotic systems resulting in novel selection on floral traits under future conditions. Global change has depressed pollinator abundance and altered abiotic conditions, thereby exposing flowering plant species to novel suites of selective pressures. Here we consider how biotic and abiotic factors interact to shape the expression and evolution of various floral characteristics (the targets of selection), including floral size, color, physiology, reward quantity and quality, and longevity amongst other traits. We examine cases in which selection imposed by climatic factors conflicts with pollinator-mediated selection. Additionally, we explore how floral traits respond to environmental changes through phenotypic plasticity and how that can alter plant fecundity. In this review, we evaluate how global change may shift the expression and evolution of floral phenotypes. Floral traits evolve in response to multiple interacting agents of selection. Different agents can sometimes exert conflicting selection. For example, pollinators often prefer large flowers, but drought stress can favor the evolution of smaller flowers, and the size of floral organs can evolve as a trade-off between selection mediated by these opposing actors. Nevertheless, few studies have factorially manipulated abiotic and biotic agents of selection to disentangle their relative strengths and directions of selection. The literature has more often evaluated plastic responses of floral traits to stressors than it has considered how abiotic factors alter selection on these traits. Furthermore, global change will likely alter the selective landscape through changes in the abundance and community compositions of mutualists and antagonists and novel abiotic conditions. We encourage future work to consider a more holistic model of floral evolution, which will enable more robust predictions about floral evolution and plant reproduction as global change progresses.

Characterization of genes related to the efflux pump and porin in multidrug-resistant Escherichia coli strains isolated from patients with COVID-19 after secondary infection

BackgroundEscherichia coli (E. coli) is a multidrug resistant opportunistic pathogen that can cause secondary bacterial infections in patients with COVID-19. This study aimed to determine the antimicrobial resistance profile of E. coli as a secondary bacterial infection in patients with COVID-19 and to assess the prevalence and characterization of genes related to efflux pumps and porin.MethodsA total of 50 nonduplicate E. coli isolates were collected as secondary bacterial infections in COVID-19 patients. The isolates were cultured from sputum samples. Confirmation and antibiotic susceptibility testing were conducted by Vitek 2. PCR was used to assess the prevalence of the efflux pump and porin-related genes in the isolates. The phenotypic and genotypic evolution of antibiotic resistance genes related to the efflux pump was evaluated.ResultsThe E. coli isolates demonstrated high resistance to ampicillin (100%), cefixime (62%), cefepime (62%), amoxicillin-clavulanic acid (60%), cefuroxime (60%), and ceftriaxone (58%). The susceptibility of E. coli to ertapenem was greatest (92%), followed by imipenem (88%), meropenem (86%), tigecycline (80%), and levofloxacin (76%). Regarding efflux pump gene combinations, there was a significant association between the acrA gene and increased resistance to levofloxacin, between the acrB gene and decreased resistance to meropenem and increased resistance to levofloxacin, and between the ompF and ompC genes and increased resistance to gentamicin.ConclusionsThe antibiotics ertapenem, imipenem, meropenem, tigecycline, and levofloxacin were effective against E. coli in patients with COVID-19. Genes encoding efflux pumps and porins, such as acrA, acrB, and outer membrane porins, were highly distributed among all the isolates. Efflux pump inhibitors could be alternative antibiotics for restoring tetracycline activity in E. coli isolates.

Genomic, transcriptomic, and metabolomic analyses provide insights into the evolution and development of a medicinal plant Saposhnikovia divaricata (Apiaceae).

Saposhnikovia divaricata, 2n = 2x = 16, as a perennial species, is widely distributed in China, Mongolia, Russia, etc. It is a traditional Chinese herb used to treat tetanus, rubella pruritus, rheumatic arthralgia, and other diseases. Here, we assembled a 2.07Gb and N50 scaffold length of 227.67Mb high-quality chromosome-level genome of S. divaricata based on the PacBio Sequel II sequencing platform. The total number of genes identified was 42 948, and 42 456 of them were functionally annotated. A total of 85.07% of the genome was composed of repeat sequences, comprised mainly of long terminal repeats (LTRs) which represented 73.7% of the genome sequence. The genome size may have been affected by a recent whole-genome duplication event. Transcriptional and metabolic analyses revealed bolting and non-bolting S. divaricata differed in flavonoids, plant hormones, and some pharmacologically active components. The analysis of its genome, transcriptome, and metabolome helped to provide insights into the evolution of bolting and non-bolting phenotypes in wild and cultivated S. divaricata and lays the basis for genetic improvement of the species.

Genomes of historical specimens reveal multiple invasions of LTR retrotransposons in Drosophila melanogaster during the 19th century

Transposable element invasions have a profound impact on the evolution of genomes and phenotypes. It is thus an important open question how often such TE invasions occur. To address this question, we utilize the genomes of historical specimens, sampled about 200 y ago. We found that the LTR retrotransposons Blood, Opus, and 412 spread in Drosophila melanogaster in the 19th century. These invasions constitute second waves, as degraded fragments were found for all three TEs. The composition of Opus and 412, but not of Blood, shows a pronounced geographic heterogeneity, likely due to founder effects during the invasions. Finally, we identified species from the Drosophila simulans complex as the likely origin of the TEs. We show that in total, seven TE families invaded D. melanogaster during the last 200y, thereby increasing the genome size by up to 1.2Mbp. We suggest that this high rate of TE invasions was likely triggered by human activity. Based on the analysis of strains and specimens sampled at different times, we provide a detailed timeline of TE invasions, making D. melanogaster the first organism where the invasion history of TEs during the last two centuries could be inferred.

Different selection regimes explain morphological evolution in fossorial lizards

Abstract Independent origins of similar phenotypes are ubiquitous to the evolutionary process and evoke strong and recurrent environmental associations. Snakelike lizards evolved multiple times and are often portrayed as limb‐reduced and body‐elongated outcomes from shared selection associated with fossoriality. However, a refined evaluation including specific head traits and subtle differences in subterranean microhabitats unveils some degree of uniqueness even among lineages traditionally interpreted as phenotypically similar. Here, we address regimes of selection in fossorial lizards accounting for differences in the burrowing substrate and emphasizing head shape in addition to body and limbs. We assembled an ecomorphological database comprising 213 species from all major lizard clades, and then characterized contemporary morphological diversity and modelled phenotypic evolution to test the hypothesis that fossoriality encompasses at least two distinct selection regimes. We identified two ecomorphological groups within the fossorial lizards: moist‐soil fossorial and dry‐soil fossorial. Both groups evolved towards distinct adaptive optima concerning head shape and limb size. Despite some degree of uniqueness, these groups also share similar patterns in specific traits. Dry‐soil fossorial lizards present less morphological variation than moist‐soil fossorial, possibly due to the combination of distinct sets of selective pressures with shared ancestry. Our study provides evidence that an often‐interpreted general adaptive regime (e.g. fossoriality) may in fact comprise enough ecological and functional diversity to elicit several distinct ecomorphological associations despite overall convergence among phenotypic traits. Read the free Plain Language Summary for this article on the Journal blog.

Integrating ecological niche modeling and rates of evolution to model geographic regions of mimetic color pattern selection

Geographic variation in natural selection derived from biotic sources is an important driver of trait evolution. The evolution of Müllerian mimicry is governed by dual biotic forces of frequency-dependent predator selection and densities of prey populations consisting of conspecifics or congeners. Difficulties in quantifying these biotic forces can lead to difficulties in delimiting and studying phenomena such as mimicry evolution. We explore the spatial distribution of morphotypes and identify areas of high mimetic selection using a novel combination of methods to generate maps of mimetic phenotype prevalence in Ranitomeya poison frogs, a group of frogs characterized by great phenotypic variation and multiple putative Müllerian mimic pairs. We categorized representative populations of all species into four major recurring color patterns observed in Ranitomeya: striped, spotted, redhead, and banded morphs. We calculated rates of phenotypic evolution for each of the 4 morphs separately and generated ecological niche models (ENMs) for all species. We then split our species-level ENMs on the basis of intraspecific variation in color pattern categorization, and weighted ENM layers by relative evolutionary rate to produce mimicry maps. Our phenotypic evolutionary rate analyses identified multiple significant shifts in rates of evolution for the spotted, redhead, and banded phenotypes. Our mimicry maps successfully identify all suspected and known areas of Müllerian mimicry selection in Ranitomeya from the literature and show geographic areas with a gradient of suitability for Müllerian mimicry surrounding mimic hotspots. This approach offers an effective hypothesis generation method for studying traits that are tied to geography by explicitly connecting evolutionary patterns of traits to trends in their geographic distribution, particularly in situations where there are unknowns about drivers of trait evolution.

Developmental and behavioral phenotypes of pediatric patients with PTEN hamartoma tumor syndrome.

Our study characterized the neurodevelopmental spectrum of individuals with PTEN Hamartoma Tumor Syndrome (PHTS), a syndrome that predisposes to both neurodevelopmental phenotypes and cancer risk. We aim to better understand life-impacting neurodevelopmental features of PHTS. Our study recruited 20 children/adolescents with PHTS, who were then administered assessments for autism spectrum disorder (ASD) and other neurocognitive measures, including assessment of IQ, executive and adaptive functioning, and health-related quality of life. Thirteen individuals (65%) were identified as having ASD, of which five were newly diagnosed during the study. Of those, ASD symptom severity was in the mild-moderate range for 77%. Overall, IQ was in the average range, with a mean of 92.61 (SD 24.45, p = 0.5), though there was a non-statistically significant trend toward individuals without ASD having a higher mean IQ (102.7 vs 82.3; p = 0.1). Subjects had significant impairment in processing speed (mean 75.38, SD 24.75, p < 0.05), decreased adaptive functioning skills across all domains, and a trend toward having more executive functioning problems. Individuals with PHTS are at increased risk of neurodevelopmental disorders, including ASD and impaired executive and adaptive functioning. Although clear guidelines exist for cancer surveillance for individuals with PHTS, additional guidelines and screening for neurodevelopmental disorders are warranted.

Abstract 1226: Genomically encoded lineage plasticity drives resistance to EGFR targeted therapy in lung adenocarcinoma

Abstract EGFR-mutant lung adenocarcinoma (LUAD) represents 20% of all non-small cell lung carcinomas, with most patients presenting with incurable metastatic disease. Treatment with mutant-selective EGFR tyrosine kinase inhibitor (TKI) therapies such as osimertinib, the current standard of care for metastatic EGFR-mutant LUAD, results in greater overall and progression-free survival. However, all patients eventually relapse. Uncovering the mechanisms driving primary and acquired resistance to osimertinib is therefore critical to improving disease management. Here, we use clinical genomic sequencing (n=47) and single-nucleus RNA (snRNA) sequencing (n=62) to profile a cohort of unmatched treatment-naïve (n=26), on-treatment (n=6), and post-treatment relapsed (n=30) EGFR-mutant LUADs treated with osimertinib. Relapsed tumors are marked by increased tumor mutation burden, along with elevated rates of genome doubling and loss-of-heterozygosity. We derived expression-based signatures of LUAD, lung squamous cell carcinoma (LUSC), and small cell lung carcinoma (SCLC) and applied them to tumor cells across our cohort. Relapsed tumors had a marked decrease in LUAD gene signature expression compared to untreated tumors and accompanying increases in epithelial-mesenchymal transition (EMT) and stemness markers, consistent with dedifferentiation. Notably, tumors harboring secondary mutations to EGFR, MET, or other MAPK pathway genes and showing sustained MAPK signaling retained a more differentiated state. Patients lacking these secondary on-target or bypass mutations were more likely to experience relapse with histological transdifferentiation, marked by complete loss of LUAD signatures, and accompanying increases in LUSC or SCLC signatures. Phenotype matching of tumor cells to normal cells from the developing fetal lung revealed enrichment of airway progenitor populations in non-histologically transformed treatment-resistant patients, in contrast to a proportion of late bud-tip and club-like epithelial cells which predominated in treatment-naïve samples. In rare cases, we observed subpopulations of basal stem-like progenitors in otherwise well-differentiated pre-treatment tumors. In summary, single-cell mapping of histological and developmental phenotypes has revealed divergent evolutionary trajectories during the acquisition of resistance to osimertinib, defined by MAPK signaling reactivation or by loss of LUAD identity and histological transformation respectively. Citation Format: Matthew Zatzman, Alvaro Quintanal-Villalonga, Sohrab Salehi, Christina Falcon, Nicholas Ceglia, Sohrab P. Shah, Charles M. Rudin, Helena A. Yu. Genomically encoded lineage plasticity drives resistance to EGFR targeted therapy in lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1226.