Conservation Genetics of Bycatch Albatross:

University of Washington Graduate Student Hollie Walsh and Scott Edwards recently published a paper in Conservation Genetics using mitochondrial DNA to infer the geographic origins of black-footed albatrosses caught in Pacific fisheries nets. For this we used the extensive collection of bycatch albatross specimens and tissues at the Burke Museum in conjunction with blood samples from the field in Hawaii and Japan. Hollie found that ~ 98% of the bycatch specimens were of Hawaiian origin and will soon finish her disseratation examining nuclear SNP variation in Laysan and Black-footed Albatross. Click here for further information.

Shotgun Sequencing:

Joe Gasper, a former technician in the laboratory at University of Washington, pioneered the application of shotgun sequencing of cosmid clones to natural populations of birds. His protocols and general approach have been published. Shotgun sequencing is a powerful method for obtaining detailed information on complex multigene families such as the major histocmpatibility complex, which we have done for House Finches, Red-winged blackbirds and other species. We are now using the method to obtain detailed information on regions of sex chromosomes and MHCs of birds and reptiles.

Ecological Genetics of Red-winged Blackbirds:

'Red-wings' have been a major focus of the lab due to the abundant data on mating system, sexual dimorphism, variation in parasites, female choice and geographic variation. Our most recent grant focuses on measuring levels and patterns of linkage disequilibrium (LD) in natural populations of red-wings and other avian species. We have recently published on naturally occuring rates of recombination in redwings and found unusually high rates for a vertebrate, resembling those found in some studies of Drosophila more so than rates in humans. We are now using pairs of loci sampled from the ends of plasmid and cosmid clones to measure levels of LD at several scales among sites whose physical distance in the genome is known. Click here for further information.

Comparative Genomics using BAC Libraries:

This image shows a Not I restriction analysis of BAC clones sampled randomly from a library constructed for the Tuatara (Sphenodon) by former postdoc Zhenshan Wang. Our NSF grant with Chris Amemiya and J. Robert Macey generated BAC libraries for several reptiles, including American Alligator, Painted Turtle, Tuatara, Emu, Garter Snake and Gila Monster. High-density nylon filters for these libraries as well as individual clones can be ordered through Symbio Corporation and their BAC clone program. Dan Janes, a postdoc in the lab, is currently using these libraries to study the molecular evolution of sex chromosomes in Reptilia. Research Associate Andrew Shedlock is examining retroposon evolution in alligators, turtles and birds. We plan to sequence the MHCs of a number of birds and reptiles in collaboration with Takashi Shiina and Jerzy Kulski and postdoctoral fellow Chris Balakrishnan.

Evolutionary Bioinformatics:

The image shows a genomic signature for 6 nucleotide DNA word frequencies found in a ~6 megabases of BAC-end sequence from the domestic chicken. Genomic signatures are a pictorial method for displaying the frequencies of n-letter DNA words in genomics signatures. They are organized such that all words ending in C are the top left quadrant, G in the top right, A in the lower left and T in the lower right. Dark pixels indicate common words and light pixels rare words. Collaborator Patrick Deschavanne has pioneered their recent use in bioinformatics. We have used them to study phylogenomics of birds and are now using them to understand genome evolution in reptiles.

Molecular ecology of Gene Expression:

The image shows a 'macroarray' of House Finch cDNA clones generated by former postdoc Zhenshan Wang. The probe used was cDNA from the spleen of a normal House Finch, and the strongly hybridizing clones indicate genes that are upregulated upon experimental infection with the parasitic bacterium Mycoplasma gallisepticum. In collaboration with Geoff Hill and Kristi Farmer of Auburn University, we have identified several hundred genes that show changes in expression between normal and experimentally infected birds. Such genes may represent candidates that have experienced natural selection during the recent epizootic in eastern US House Finches.

Comparative Phylogeography of Australian Birds:

Our recent NSF grant focuses on multilocus phylogeography of Australian birds. The project was spearheaded by postdoc Bryan Jennings and University of Washington graduate student Corey Welch, who conducted fieldwork in New South Wales in September-October 2002, and was also worked on by Research Technician Nancy Rotzel. The project utilizes a resequencing approach applied to anonymous loci from the nuclear genome to inform coalescent analyses of divergence time, ancestral population size and gene flow in east-west pairs of species divided at the Carpentarian divide in northern Queensland. This includes species such as treecreepers, wrens, finches, babblers, honeyeaters, orioles and many others. Over several collecting expeditions we have amassed many tissues that are now housed at the Burke Museum Genetic Resources Collection and Harvard's Museum of Comparative Zoology.

Phylogeography and population genetics of Australian Birds:

The image shows a Rainbow Bee-Eater (Merops ornatus). Our collections-based research in Australia will soon expand to widespread species such as Zebra Finches, which are a model for neurobiology and bird song. Postdoc Chris Balakrishnan will be examining phylogeography and population genetics of Mhc loci and ESTs from zebra finch brains in an effort to characterize the distribution of selection coefficients among loci in natural populations of birds. Such research can be compared to similar distributions characterized for humans and other mammals to understand how the forces acting on the genomes of birds may differ from those of mammals and how linkage and recombination rates vary throughout the genome.