Michael D. Shapiro

Widespread variation in EDNRB2 is associated with diverse melanin loss phenotypes across avian species

The paper identifies widespread coding variation in EDNRB2 and other pigmentation genes across avian species, linking EDNRB2 to melanin loss and bright plumage colors.

Genomics of experimental adaptive radiation in the cryptic coloration of feather lice

This study tracks genomic changes in feather lice adapting to different host color backgrounds over four years, finding distinct genetic responses to similar environmental pressures.

An allelic series at the EDNRB2 locus controls diverse piebalding patterns in the domestic pigeon

The paper identifies a locus, EDNRB2, associated with piebalding patterns in domestic pigeons, showing how genetic variation at this locus generates diverse pigment patterns.

Assembly and annotation of two high-quality columbid reference genomes from sequencing of a Columba livia x Columba guinea F1 hybrid

The paper presents high-quality genome assemblies and annotations for two pigeon species using long-read sequencing of an F1 hybrid, improving genomic resources for comparative genomics and functional studies.

Complex genetic architecture of three-dimensional craniofacial shape variation in domestic pigeons

The paper identifies genetic loci associated with craniofacial shape variation in domestic pigeons using quantitative trait locus scans and multi-locus modeling.

A ROR2 coding variant is associated with craniofacial variation in domestic pigeons

The paper identifies a ROR2 coding variant associated with short beak morphology in domestic pigeons, linking it to craniofacial variation through QTL mapping and genomic analysis.

Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia)

This study identifies two genomic loci associated with iris color variation in domestic pigeons, linking iris and plumage color traits and highlighting the role of gene duplicates in color evolution.

Trio-binned genomes of the woodrats Neotoma bryanti and N. lepida reveal novel gene islands and rapid copy number evolution of xenobiotic metabolizing cytochrome p450 genes

This study uses trio binning to assemble genomes of two woodrat species, revealing expanded and novel cytochrome p450 gene islands linked to dietary adaptation to toxic plants.

The assembled and annotated genome of the pigeon louse Columbicola columbae, a model ectoparasite

The paper presents a high-quality genome assembly and annotation for the pigeon louse Columbicola columbae, revealing genomic features shared with other lice and insights into its adaptation to host-parasite interactions.

The Almond plumage color pattern is associated with eye pigmentation defects in the domestic pigeon (Columba livia)

The paper examines eye pigmentation defects in Almond pigeons and finds reduced pigmentation in anterior eye structures with Almond alleles and severe reduction in homozygous birds.

A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia)

The paper identifies a copy number variant at the St locus associated with pigmentation patterns in rock pigeons, linking structural variation to gene expression and phenotypic diversity.

Pigeon foot feathering reveals conserved limb identity networks

The paper identifies gene expression changes downstream of PITX1 and TBX5 that drive partial forelimb identity in pigeon hindlimbs, revealing conserved limb identity networks across amniotes.

Improved genome assembly and annotation for the rock pigeon (Columba livia)

The paper updates the rock pigeon genome assembly and annotation, improving tools for evolutionary and functional genetic studies.