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
We are studying the diversification of birds at the population, landscape, and continental levels using whole-genome sequencing methods.
- Population genomics and phylogeography in several avian taxa
- Landscape genomics of nuthatches
- Biodiversity genomics through time of Eastern African montane birds (currently NSF funded)
- Manthey JD, Bourgeois Y, Yonas M & Boissinot S. (Preprint) Demographic history and dispersal ability shape genomic diversity and differentiation in Ethiopian montane forest bird (Aves: Passeriformes) populations separated by the Great Rift Valley.
- Manthey JD, Oliveros CH, Andersen MJ, Filardi CE & Moyle RG. 2020. Gene flow and rapid differentiation characterize a rapid insular radiation in the southwest Pacific (Aves: Zosterops). Evolution doi: 10.1111/evo.14043
- 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. 2015. Isolation by environment in White-breasted Nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach. Molecular Ecology 24: 3628-3638.
We are studying the codiversification of Camponotus carpenter ants and their Blochmannia endosymbionts using whole genome sequencing methods and ecological data. We are currently focusing on North American taxa.
- Effects of host demography on endosymbiont genome evolution
- Landscape genomics of several North American Camponotus species
- Microbial community ecology in Camponotus hosts
- Manthey JD, Girón JC & Hruska JP. (Preprint) Impact of host evolutionary history on endosymbiont genome evolution: a test in Camponotus carpenter ants and their Blochmannia endosymbionts. DOI: 10.22541/au.160689628.80980759/v1
We recently learned we will be 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.
We are using multiple sequencing types, including whole-genome and transcriptome data, to understand how structural variants and more specifically transposable elements (TEs) are evolving in genomes, as well as how these changes impact diversification in multiple organisms.
- Effects of TEs on molecular evolution in woodpeckers
- Population genomics of TEs in multiple avian groups
- Landscape genomics of TEs in carpenter ants
- 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, 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.