Research

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


We are fortunate to have received funding for some of the research shown below from these organizations:


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.
  • Manthey JD, Boissinot S & Moyle RG. 2019. Biodiversity genomics of North American Dryobates woodpeckers reveals little gene flow across the D. nuttallii X D. scalaris contact zone. The Auk: Ornithological Advances doi.org/10.1093/auk/ukz015
  • Manthey JD, Moyle RG & Boissinot S. 2018. Multiple and independent phases of transposable element amplification in the genomes of Piciformes (woodpeckers and allies). Genome Biology and Evolution 10: 1445-1456.

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 were recently funded through Texas Parks and Wildlife to study Peromyscus truei comanche using conservation genomic methods. For this project, we will be assembling a high quality genome for this subspecies and resequencing multiple populations of the subspecies and closely-related subspecies to assess genomic distinctiveness, connectivity among populations, and levels of genetic diversity. This project will include morphometric analyses in concert with genomics.

This project is in collaboration with Caleb Phillips and Robert Bradley at TTU.

More to come as we obtain and analyze data!