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, Pachycephala, Setophaga, Sitta, Zosterops).
  2. Biodiversity genomics through time of Eastern African montane birds (animated video: https://www.youtube.com/watch?v=MfUO7oQc3zI).
  3. Population genomics of structural variants in multiple avian groups.
  4. Woodpecker genome evolution.

Recent Relevant Products:

  • Gyllenhaal EF, Boyane SS, Colmenares-Pinzón JE, Rice AA, Tocora MC, Bapeamoni F, Murhabale B, Kahindo C, Marks BD & Manthey JD (2024) Expansion From Lowland Pleistocene Refugia Followedby Cryptic Introgression in an African ElevationalGeneralist Bird. Molecular Ecology. https://onlinelibrary.wiley.com/doi/10.1111/mec.70488
  • Manthey JD, Settlecowski AE, Meheretu Y, Behrends GJ, Bourgeois Y, Campillo LC, Boissinot S & Marks BD (2025) Temporal genomics reveals a century of genomic diversity shifts in a biodiversity hotspot avian assemblage. Genome Biology and Evolution evaf163. https://doi.org/10.1093/gbe/evaf163
  • Gyllenhaal EF, Andersen MJ, Moyle RG & Manthey JD (2025) Island size shapes genomic diversity in a great speciator (Aves: Zosterops). Biology Letters. https://doi.org/10.1098/rsbl.2024.0692

Ant-Microbe Co-Evolution and Genome Evolution (currently NSF funded)

We are studying the codiversification and genome evolution of Camponotus carpenter ants and their Blochmanniella (formerly 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.
  6. Genome evolution in Blochmanniella endosymbionts of carpenter ants

Recent Relevant Products:

  • Boyane SS. Behrends GJ & Manthey JD. 2026. Quaternary Climatic Changes and Biogeographic Barriers Drove Codiversification in the Obligate Mutualism Between Camponotus laevigatus and Its Endosymbiont Blochmanniella. Ecology and Evolution 16, e74045.
  • Meadows BA, Emad M, Hruska JP, Silva J. Behrends GJ, Girón JC & Manthey JD. 2023. Relatedness within colonies of three North American species of carpenter ants (Subgenus: Camponotus) and a comparison with relatedness estimates across Formicinae. Insectes Sociaux 70, 191-202.
  • 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

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.