Biology subjects

Lucky, A.

Publications and source records attributed to Lucky, A..

4 recordsLinked to original sources

bioRxiv2024

Evaluating UCE data adequacy and integrating uncertainty in a comprehensive phylogeny of ants

While some relationships in phylogenomic studies have remained stable since the era of Sanger sequencing, many challenging nodes elude resolution, even with genome-scale data. As early studies grappled with random error and insufficient information, incongruence or lack of resolution in phylogenomics is generally associated with inadequate modeling of biological phenomena combined with analytical issues leading to systematic biases. Few phylogenomic studies, however, explore the potential for random error or establish an expectation of what level of resolution should be expected from a given empirical dataset. In presenting incongruent results, phylogeneticists face a choice of providing a diverse array of results from different approaches or a single preferred tree, with few attempting to integrate uncertainties across methods. Recent phylogenetic work has uncovered many well-supported and often novel relationships, as well as more contentious findings, across the phylogeny of ants. Ants are the most species-rich lineage of social insects and among the most ecologically important terrestrial animals. As a result, they have attracted much research, including regarding systematics. To date, however, there has been no comprehensive genus-level phylogeny of the ants inferred using genomic data combined with an effort to evaluate signal and incongruence throughout. Here we provide deeper insight into and quantify uncertainty across the ant tree of life. We accomplish this with the most taxonomically comprehensive Ultraconserved Elements dataset to date, including 277 (81%) of recognized ant genera from all 16 extant subfamilies, representing over 98% of described species-level diversity. We use simulations to establish expectations for resolution, identify branches with less-than-expected concordance, and dissect the effects of data and model selection on recalcitrant nodes. We also construct a consensus tree integrating uncertainty from multiple analyses. Simulations show that hundreds of loci are needed to resolve recalcitrant nodes on our genus-level ant phylogeny, even under a best-case scenario of known model parameters and without systematic bias. This demonstrates that random error continues to play a role in phylogenomics. Our analyses provide a comprehensive picture of support and incongruence across the ant phylogeny, and our consensus topology is congruent with a recent phylogenomic study on the subfamily-level, while rendering a more realistic picture of uncertainty and significantly expanding generic sampling. We use this topology for divergence dating and find that assumptions about root age have significant impact on the dates inferred. Our results suggest that improved understanding of ant phylogeny will require both more data and better phylogenetic models. We also provide a workflow to identify under-supported nodes in concatenation analyses, outline a pragmatic way to reconcile conflicting results in phylogenomics, and introduce a user-friendly locus selection tool for divergence dating.

evolutionary biology↗

bioRxiv2022

The first fossil replete ant worker establishes living food storage in the Eocene

Worker specialization extends the behavioral and ecological repertoire of ant colonies. Specialization may relate to colony defense, brood care, foraging, and, in some taxa, storage. Replete workers swell the crop and gaster to store liquid food, which can be accessed by other colony members through trophallaxis. This storage ability, known as repletism, has independently evolved across several ant lineages, but the temporal history of this trait has not yet been investigated. Here, we describe the first fossil replete in the extinct species Leptomyrmex neotropicus Baroni Urbani, 1980 preserved in Miocene-age Dominican amber. Together with new evidence of repletism in L. neotropicus extant sister species, L. relictus Boudinot et al., 2016, we reconstruct the pattern of acquisition and descent in this storage-linked trait. Our ancestral state reconstruction suggests that Leptomyrmex acquired replete workers in the Eocene and may therefore represent the earliest instance of so-called "honeypot" ants among all known ants, both living and extinct.

evolutionary biology↗

bioRxiv2022

Delimiting the cryptic diversity and host preferences of Sycophila parasitoid wasps associated with oak galls using phylogenomic data

Cryptic species diversity is a major challenge for the species-rich community of parasitoids attacking oak gall wasps due to a high degree of sexual dimorphism, morphological plasticity, small size, and poorly known biology. As such, we know very little about the number of species present, nor the evolutionary forces responsible for generating this diversity. One hypothesis is that trait diversity in the gall wasps, including the morphology of the galls they induce, has evolved in response to selection imposed by the parasitoid community, with reciprocal selection driving diversification of the parasitoids. Using a rare, continental-scale data set of Sycophila parasitoid wasps reared from 44 species of cynipid galls from 18 species of oak across the US, we combined mitochondrial DNA barcodes, Ultraconserved Elements (UCEs), morphological, and natural history data to delimit putative species. Using these results, we generate the first large-scale assessment of ecological specialization and host association in this species-rich group, with implications for evolutionary ecology and biocontrol. We find most Sycophila target specific subsets of available cynipid host galls with similar morphologies, and generally attack larger galls. Our results suggest that parasitoid wasps such as Sycophila have adaptations allowing them to exploit particular host trait combinations, while hosts with contrasting traits are resistant to attack. These findings support the tritrophic niche concept for the structuring of plant-herbivore-parasitoid communities.

evolutionary biology↗

bioRxiv2021

A unique GCN5 histone acetyltransferase complex controls erythrocyte invasion and virulence in the malaria parasite Plasmodium falciparum

The histone acetyltransferase GCN5-associated SAGA complex is evolutionarily conserved from yeast to human and functions as a general transcription co-activator in global gene regulation. In this study, we identified a divergent GCN5 complex in Plasmodium falciparum, which contains two plant homeodomain (PHD) proteins (PfPHD1 and PfPHD2) and a plant apetela2 (AP2)-domain transcription factor (PfAP2-LT). To dissect the functions of the PfGCN5 complex, we generated parasites with the bromodomain deletion in PfGCN5 and the PHD domain deletion in PfPHD1. The two deletion mutants closely phenocopied each other, exhibiting significantly reduced merozoite invasion of erythrocytes and elevated sexual conversion. These domain deletions caused dramatic decreases not only in histone H3K9 acetylation but also in H3K4 trimethylation, indicating synergistic crosstalk between the two euchromatin marks. Domain deletion in either PfGCN5 or PfPHD1 profoundly disturbed the global transcription pattern, causing altered expression of more than 60% of the genes. At the schizont stage, these domain deletions were linked to specific downregulation of merozoite genes involved in erythrocyte invasion, many of which harbor the DNA-binding motifs for AP2-LT and/or AP2-I, suggesting targeted recruitment of the PfGCN5 complex to the invasion genes by these specific transcription factors. Conversely, at the ring stage, PfGCN5 or PfPHD1 domain deletions disrupted the mutually exclusive expression pattern of the entire var gene family, which encodes the virulent factor PfEMP1. Correlation analysis between the chromatin state and alteration of gene expression demonstrated that up- and down-regulated genes in these mutants are highly correlated with the silenct and active chromatin states in the wild-type parasite, respectively. Collectively, the PfGCN5 complex represents a novel HAT complex with a unique subunit composition including the AP2 transcription factor, which signifies a new paradigm for targeting the co-activator complex to regulate general and parasite-specific cellular processes in this low-branching parasitic protist. Author SummaryEpigenetic regulation of gene expression plays essential roles in orchestrating the general and parasite-specific cellular pathways in the malaria parasite Plasmodium falciparum. Using tandem affinity purification and proteomic characterization, we identified a divergent transcription co-activator - the histone acetyltransferase GCN5-associated complex in P. falciparum, which contains nine core components, including two PHD domain proteins (PfPHD1 and PfPHD2) and a plant apetela2-domain transcription factor. To understand the functions of the PfGCN5 complex, we performed gene disruption in two subunits of this complex, PfGCN5 and PfPHD1. We found that the two deletion mutants displayed very similar growth phenotypes, including significantly reduced merozoite invasion rates and elevated sexual conversion. These two mutants were associated with dramatic decreases in histone H3K9 acetylation and H3K4 trimethylation, which led to global changes in chromatin states and gene expression. Genes significantly affected by the PfGCN5 and PfPHD1 gene disruption include those participating in parasite-specific pathways such as invasion, virulence, and sexual development. In conclusion, this study presents a new model of the PfGCN5 complex for targeting the co-activator complex to regulate general and parasite-specific cellular processes in this low-branching parasitic protist.

microbiology↗