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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Systematic Entomology Laboratory » Research » Research Project #435486

Research Project: RUI: A Phylogenomic Approach to Understanding the Symbiosis between Acropyga Ants and Xenococcine Mealybugs

Location: Systematic Entomology Laboratory

Project Number: 8042-22000-290-61-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Mar 1, 2018
End Date: Mar 1, 2021

Objective:
This project will elucidate phylogenies for two groups engaged in a mutualistic symbiosis: Acropyga ants and xenococcine root mealybugs. These ants and root mealybugs engage in relationships that are analogous to human associations with domesticated livestock. The primary research question addressed is: have Acropyga and their associated xenococcine mealybugs undergone codiversification (aka cospeciation)? The production of robust phylogenies using a phylogenomic approach will provide data at multiple evolutionary timescales for both groups of organisms. These data will be used to reconstruct robust phylogenies that will provide the foundation for codiversification analyses. A vexing question in evolutionary biology is how mutualistic symbioses evolve and are consequently maintained over long periods of time. Ants practice two distinct types of farming that have the potential to serve as excellent models for studying the evolution of mutualistic symbioses: fungus-farming and herding of scale insects and aphids. Fossils and molecular dating indicate these ant-farming associations have been remarkably stable for tens of millions of years. While fungus-growing ants have been relatively well studied, rather few studies have addressed herder ants. The study of herder ants provides the opportunity to investigate the evolution and maintenance of an animal-to-animal mutualistic symbiosis (trophobiosis). The investigators will study trophobiosis between Acropyga ants and xenococcine mealybugs. In trophobiotic systems, ants provide trophobionts (typically phytophagous hemipterans) protection from predation and parasitism in return for nutritive rewards. Acropyga ants practice a unique form of herding where unmated alate Acropyga queens vertically transmit mealybugs by taking an individual with them on their mating flights (called trophophoresy). Trophophoresy is a method of trophobiont transmission that spans across generations and provides the strong possibility that codiversification has occurred between the partners. This study has the potential to become a new model in the study of ant farming systems and is the first one to address any group of herder ants from a phylogenomics perspective.

Approach:
Fieldwork: The cooperators from Towson University and the Smithsonian Institute's National Museum of Natural History (NMNH) already have 25 of 40 total Acropyga species known globally and their associated trophobionts. In order to obtain the remaining species, expand samples of associated ants and scales, and potentially discover new species, new targeted field studies will be conducted at the following field sites: Costa Rica (La Selva), Peru (Cocha Cashu), Guyana (western highlands), Borneo (Danum Valley), and Gabon (Lope N.P.). Data generation: The investigators will use a phylogenomic approach to capture and sequence ultraconserved elements (UCEs) using cost-efficient, multiplexed, next-generation sequencing methods already in standard deployment at NMNH. UCE probes have already been designed for Hymenoptera, yielding over 700 UCE loci from a variety of ant genera, including Acropyga and its close relatives. The investigators will design probes for root mealybugs in the same manner, using GenBank available genome assemblies of several mealybug taxa and a full genome assembly of the xenococcine, Eumyrmococcus scorpioides. Phylogenetic and cospeciation analyses: The investigators will collaboratively analyze data using implementations of maximum likelihood (RAxML v8) and Bayesian (ExaBayes v1.4.1) methods designed to handle large-scale datasets on computational clusters. Concatenated UCE data will be analyzed unpartitioned and partitioned by locus using PartitionFinder. The investigators will utilize a coalescent-based species tree approach, which can handle large UCE datasets. Using the best gene tree and bootstrap trees for each UCE locus, the program ASTRAL will be used to infer the species tree and conduct multilocus bootstrapping. In order to reduce noise from uninformative loci, the investigators will employ a statistical binning approach by inputting gene trees, generating a set of “supergenes” based on a support threshold, and using those to infer the species tree. UCE data will also be used to estimate time to most recent common ancestor under a coalescent model for tightly associated lineages in the program *BEAST, assessing convergence of time estimates for each associated lineage. Several approaches will be used to analyze cospeciation events between ants and root mealybugs, including both event-based and permutation methods. Responsibilities: Towson U PI will administer the project, provide taxonomic expertise on Acropyga, be responsible for organizing and executing field studies, and assist with cospeciation and phylogenetic analyses; NMNH Co-PI will be responsible for DNA sequencing and analysis, will participate in field studies, and will conduct cospeciation and phylogenetic analyses; ARS Co-PI will provide taxonomic expertise on root mealybugs, be responsible for DNA extractions and specimen vouchers, participate in field studies, and assist with phylogenetic analyses.