Jones, Beryl

Group Research Activities

Research in the Jones Lab integrates behavior and ecology with modern approaches in computational biology and genomics to understand the evolution and development of phenotypic complexity. We focus on social insects as models, as they represent a major evolutionary transition and epitomize phenotypic plasticity within and across developmental and evolutionary timescales.

Projects

Gene regulatory changes in social behavior

Social bees evolved from solitary ancestors, in which females raised offspring alone. In contrast, social bees raise offspring as a unit, with a reproductively active queen and one or more non-reproductive workers. These queens and workers are excellent examples of phenotypic plasticity, developing from a totipotent genome through differential utilization of the gene regulatory network (e.g., the regulatory connections between transcription factors (TFs) and their target genes). Theory predicts that – much like changes in body plans or cell types – the evolution of social phenotypes from solitary ancestors involved changes in this GRN. We seek to identify key changes in regulatory relationships associated with evolutionary transitions in social phenotypes. In sweat bees, the multiple gains and losses of sociality enable us to ask whether convergent GRN changes underlie these independent evolutionary transitions in social behavior.

Personnel:

Dr. Beryl Jones, Savanna Ploessl

Mechanisms of intraspecific plasticity

In addition to variation across species, many species of sweat bees exhibit extensive behavioral plasticity within and across nests. The sources of this variation include both genetics and the environment, which acts upon the gene regulatory network (GRN) to result in a given phenotype. We are interested in understanding how differential utilization of GRNs leads to different phenotypes. In addition, we seek to manipulate the activity of GRNs to influence the phenotypes of lab-reared bees. We use a combination of genomics, transcriptomics, cell culture, RNAi, and other techniques to understand the mechanisms of plasticity within behaviorally plastic species of bees.

Personnel: Dr. Beryl Jones, Savanna Ploessl, Elijah Cruz Cardona

Characterizing behavioral plasticity of sweat bees

Halictid bees are incredibly diverse, and we've only just scratched the surface in understanding the natural history and behavior of a small number of species in this group. We are interested in better characterizing behavior within and across local species of halictids using standardized phenotyping assays. Understanding the natural history of this group will not only aid in our goal of understanding mechanisms of behavioral plasticity, but may also aid in conservation efforts for these important wild pollinators. We will use Raspberry Pis and opensource software to record and analyze behavior within and across species.

Personnel: Dr. Beryl Jones, Savanna Ploessl, Elijah Cruz Cardona

Using eDNA and pollen metagenetics to build a plant-pollinator network

Differences in host plant preferences, body size, lipid content, and other characteristics suggest there are likely distinct optimal nutrients for growth across native bees, but what these are for different species is unknown. We will sample native bees and pollen across local landscapes to build a plant-pollinator network. In addition to live collecting, eDNA collected from flowers will be used to identify visitors of different plant species, and collection of pollen on bees and from bee provisions will be used to identify which plant species these bees visit.

Personnel: Dr. Beryl Jones, Elijah Cruz Cardona

Computational Methods

Read processing, transcriptome assembly, read alignment, genome and transcriptome annotation, orthology detection, differential expression analysis, gene ontology, transcription factor binding analysis, metabarcoding for species identification, chromatin analyses, peak calling, linear mixed models. All methods are available.

List of Software

FASTQC, multiQC, fastp, deML, trimmomatic, cutadapt, picardtools, BLAST, BWA, STAR, subread, conda, samtools, bedtools, GATK, VCFtools, MACS2, Genrich, HOMER, OrthoFinder, deepTools, snakemake, Stubb, python, snparcher, WGCNA, R, FIMO, DiffBind, tmux, singularity

Collaborators

Dr. Sarah Kocher, Princeton University
Dr. Brendan Hunt, University of Georgia

Group Members

Savanna Ploessl
Elijah Cruz Cardona