Research

We utilize a combination of fieldwork, ecological data, genomics, and bioinformatics to study how organisms evolve across both geographic and genomic landscapes.


Avian Population Genomics and Genome Evolution

We are studying the population genomics and genome evolution of birds at multiple taxonomic scales (within populations, between populations, between closely related species) using multiple sequencing types, including long-read data, whole-genome resequencing Illumina data, and transcriptome data. Our goals are to better understand the evolutionary dynamics of diversification and to understand how structural variants (including indels, inversions, transposable elements, etc.) are evolving in genomes. Lastly, we want to better understand how structural variants impact genome evolution, molecular evolution, population genomics processes, and diversification.

Current Projects:

  1. Population genomics, landscape genomics, hybrid zone genomics, and phylogeography in several avian taxa (including species in the genera: Certhia, Contopus, Leiothlypis, Setophaga, Sitta, Zosterops)
  2. Biodiversity genomics through time of Eastern African montane birds (currently NSF funded)
  3. Effects of structural variants on molecular evolution and transcription variation in woodpeckers
  4. Population genomics of structural variants in multiple avian groups

Recent Relevant Products:

  • Manthey JD, Bourgeois Y, Meheretu Y & Boissinot S. 2022. Varied diversification patterns and distinct demographic trajectories in Ethiopian montane forest bird (Aves: Passeriformes) populations separated by the Great Rift Valley. Molecular Ecology. doi: 10.1111/mec.16417
  • Manthey JD, Klicka J & Spellman GM. 2021. The genomic signature of allopatric speciation in a songbird is shaped by genome architecture (Aves: Certhia americana). Genome Biology and Evolution.
  • Hruska JP & Manthey JD. 2021. De Novo Assembly of a chromosome-scale reference genome for the Northern Flicker Colaptes auratus. G3: Genes, Genomes, Genetics 11 (1): 1-7.

Ant-Microbe Co-Evolution and Genome Evolution

We are studying the codiversification and genome evolution of Camponotus carpenter ants and their Blochmannia endosymbionts using whole genome sequencing methods and ecological data. We are currently focusing on North American taxa.

Current Projects:

  1. Effects of host demography on endosymbiont genome evolution
  2. Landscape genomics of several North American Camponotus species
  3. Hybridization between Camponotus species
  4. Microbial community ecology in Camponotus hosts
  5. Population genomics of structural variants in carpenter ants (and some other invertebrates).
  6. Genome evolution in Blochmannia endosymbionts of carpenter ants

Relevant Products:

  • Manthey JD, Girón JC & Hruska JP. 2022. Impact of host demography and evolutionary history on endosymbiont molecular evolution: A test in carpenter ants (genus Camponotus) and their Blochmannia endosymbionts. Ecology and Evolution doi: 10.1002/ece3.9026

Conservation Genomics

We are always pursuing funding for conservation genomics projects relevant to local and regional stakeholders. Currently, we are working on conservation genomics of a couple species in Texas, including the Palo Duro Mouse (Peromyscus truei comanche) and American Black Bear (Ursus americanus). In addition to our research group, these projects are in collaboration with Caleb Phillips and Robert Bradley at TTU.

These projects generally consist of using whole-genome sequencing to address population and conservation genomics questions of interest, including assessment of regional genomic distinctiveness, connectivity among populations, and regional levels of genetic diversity.