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(Above) Participants of the 2nd Manakin RCN meeting (2016) at SERC, MD.
(Below) Manakin RCN meeting, covid-style.
Manakin (Manacus spp.) population genomics
This work is done within the collaborative framework of the NSF-funded Manakin Genomics Research Coordination Network. In this group, researchers are interested in a wide variety of issues, such as female choice, the relationship between frugivory/social organization and environmental resources, physiological basis of behavior, and genome assembly and annotation. I am interested in the genomics of speciation, and is currently using genome resequencing and transcriptome sequencing to study a hybrid zone between two species of manakins (M. vitellinus and M. candei) where male secondary sexual traits of one species is introgressing asymmetrically.
Funding Received: Smithsonian Competitive Pell Grant. $100K
Genome scan between color variants of M. candei showing Fst peaks.
Bennett, K. F. P., H. C. Lim, and M. J. Braun. 2021. Sexual Selection and Introgression in Avian Hybrid Zones: Spotlight on Manacus. Integrative and Comparative Biology icab135.
Feng, S., J. Stiller, Y. Deng, J. Armstrong, et al. 2020. Dense sampling of bird diversity increases power of comparative genomics. Nature 587:252-257.
Nucleotide diversity (pi) and Fst value between two populations within 50kb window. Each color represent one scaffold
Red Siskin (Spinus cucullata) conservation genomics
Red siskin is a highly iconic but endangered bird found in South America. Domesticated birds have been for years mated with canary to introduce red coloration into the latter species. Along with other SI scientists, we are conducting conservation genomic study of the species using a PacBio/Illumina hybrid-assembled genome (N50=554kb) and whole-genome resequencing data. This study will tell us about their demographic and divergence histories, and inform local conservation efforts and breeding programs. In collaboration with other scientists, PhD student Karen Holm is studying genetic relationships of US captive Red siskin individuals.
Lim HC, Coyle B, Frandsen P, Dikow R, Johnson W and Braun M. Conservation genomics of the highly endangered red siskin. BioGenomics 2017 Conference (21-23 Feb, Washington, DC). Abstract
Population divergence between coastal and inland Song Sparrow (Melospiza melodia) populations
The coastal subspecies (atlantica) is adapted to the high-heat and freshwater limited environments of sand dunes and tidal marshes. It apparently uses its bill as a major thermoregulatory tool by shedding more dry heat (without evaporative water loss) with its larger bill. Using data from 100,000+ SNPs, master's student Jon Clark studied population genetics of coastal and inland populations.
Greenberg et al (2012)
(Left) Sampling sites of Song Sparrows. (Right) Plot showing gradual decrease in the level of coastal ancestry as distance from the coast increases.
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