Craniofacial Evo‑Devo in Fast‑Evolving Fishes

Research

• 1. Craniofacial function of novel adaptive craniofacial genes

  We use in situ hybridization chain reaction to investigate differential expression of novel craniofacial genes during development in generalist and specialist pupfishes, revealing their contributions to phenotypic divergence. Our work on the regulatory region of galr2 in San Salvador Island pupfishes links sequence variation to spatial expression differences. Additional peptide inhibition experiments uncovered its novel role in jaw elongation

• 2. Integration of tissue-specific transcriptomics and genomics to study craniofacial divergence

  By integrating tissue-specific transcriptomics and speciation genomics, I identified fourteen novel candidate craniofacial genes in specialists that are exclusively expressed in craniofacial tissues at hatching —the earliest stage of morphological divergence— and carry differentiated regulatory mutations between species. We validated differential expression in the pharyngeal arches and craniofacial muscles of scale-eaters versus generalists for two novel genes, pycr3 and atp8a1. You can read the pre-print (now accepted at Genetics!) here.

• 3. Functional Genomics

  We are actively generating targeted mutants using CRISPR/Cas9 to dissect the functional roles of candidate genes, and creating Tol2 reporter lines to visualize their spatial and temporal expression in vivo. These resources will enable us direct testing of gene function and real-time tracking of developmental processes at cellular, tissue, and organismal level resolution.

• 4. Transcriptional regulation and Chromatin dynamics

  My lab will profile tissue-specific chromatin states across San Salvador Island and outgroup pupfishes using chromating profiling techniques such as ATAC- and MOA-seq to reveal genome-wide changes in chromatin accessibility and transcription factor occupancy linked to tissue- and species-specific gene expression. This work will shed light onto how regulatory variation drives divergent craniofacial developmental pathways.