Bio

The Tiley lab is broadly interested in the evolutionary consequences of polyploidy, from local adaptation among populations of the same species with variable ploidy to how new species arise through hybridization with genome duplication or allopolyploidy. The organismal focus of the lab is on grasses and grassy ecosystems in Madagascar and the Southeastern United States, but there are also projects in the lab that address large-scale questions of plant molecular evolution across angiosperms. Computational and statistical development is focused on coalescent models in population genomics and phylogenomics, especially for reconstructing demographic histories and estimating phylogenetic networks, respectively.

Research goals are rooted in fundamental evolutionary biology, but there are explicit connections to understanding the resilience of grasslands for land management, the genetic basis of agricultural traits, and the biodiversity and conservation of vulnerable ecosystems that provide crucial services. Polyploid plants remain challenging in evolutionary biology while also being deeply consequential for human livelihoods. The lab is committed to bridging these themes while also raising the appreciation of plant diversity globally and locally.

The lab currently has four research priorities:

1. Understanding the genetic basis of environmental niche expansion into hotter and drier conditions in  Tropical East African and Malagasy grasses with ploidy variation.
2. Improving the inference of evolutionary histories for allopolyploid complexes with phylogenetic networks, and making it easier to connect evolutionary inference with functional genomics when using haplotype-phased chromosome-level assemblies.
3. Improving population genomics inference in polyploids by addressing statistical biases when genotyping with whole-genome resequencing data and inferring selection across the genome.
4. Reconstructing the evolutionary history of Southeastern grasslands, especially the Piedmont, and using historical inferences to make future predictions about changes in grassy ecosystems.

Area(s) of Expertise

Phylogenomics, Population Genomics, Polyploidy, Geome Evolution, Poaceae, Madagascar

Publications

• A simple and accurate method for inferring missing ploidy information from sequence data , bioRxiv (Cold Spring Harbor Laboratory) (2026)
• Beyond tree-like evolution in ostariophysan fishes , bioRxiv (Cold Spring Harbor Laboratory) (2026)
• Branching out: Resolving plant evolution through phylogenetic networks , Applications in Plant Sciences (2026)
• Advancing transdisciplinary research on Madagascar's grassy biomes to support resilience in ecosystems and livelihoods , Ecological Monographs (2025)
• Extracting diamonds: identifiability of 4-node cycles in level-1 phylogenetic networks , Evolutionary Journal of the Linnean Society (2025)
• Madagascar's grassy biomes, from Holocene to Anthropocene , Plants People Planet (2025)
• Phylogenetic networks empower biodiversity research , Proceedings of the National Academy of Sciences (2025)
• Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes , Systematic Biology (2024)
• Integrative taxonomy clarifies the evolution of a cryptic primate clade , Nature Ecology & Evolution (2024)
• SLEDGe: Inference of ancient whole genome duplications using machine learning , bioRxiv (Cold Spring Harbor Laboratory) (2024)

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