Environmental and Comparative Genomics Research Projects
Common Loon

Genetic Diversity Using RAPD and mtDNA
We used random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphisms (RFLP) of mitochondrial cytochrome b (cyt b) gene to evaluate the genetic diversity in common loon Gavia immer populations from two regions in the United States: New England (NE) and Michigan (MI). RAPD analysis with 18 primers showed 74% polymorphism in NE and 50% in MI loons (similarity coefficient F = 0.92). Although no population-specific markers were found, the frequencies of some RAPD bands varied between the two populations suggesting geographical differences. RFLP analyses with BamHI enzyme and a 307-bp mitochondrial cyt b gene showed four haplotypes in the NE loon samples and two in the MI samples. The mtDNA haplotype diversity was 0.74 for NE and 0.51 for MI loons, supporting the RAPD data that NE loons have greater genetic diversity than MI loons.

Dhar, A., M. Pokras, D. K. Garcia, Z. Gordon, D. Evers, and A. Alcivar-Warren. 1997. Analysis of genetic diversity in common loon Gavia immer using RAPD and mitochondrial RFLP techniques. Molecular Ecology 6:581-586.

Microsatellites for Loons
We report here the first microsatellites from the common loon (Gavia immer) genome. A total of 224 recombinant clones were isolated from a genomic library of the common loon that were directly sequenced without probe hybridization. One hundred and five clones contained 192 short sequence repeats (SSRs), or microsatellites, with three or more repeats. The majority of motifs were quite short, with a maximum of eight repeats. Microsatellite motifs with three repeats represented 88.5% of all 192 sequences. Only 1.5% of motifs were longer than three repeats. Di-nucleotide motifs were by far the most common (87.5%), followed by tri- (10.9%), tetra- (1.0%), and hexa-nucleotides (0.52%). Eighteen primer sets were designed and tested for polymorphism at a single annealing temperature of 52ºC, 15 (83.3%) of which successfully amplified bands, but most need further optimization. Two (13.3%) of the 15 primers showed polymorphism when genotyped in twelve common loons presented at Tufts University School of Veterinary Medicine Wildlife Clinic. These 12 samples represent the species ranging from Maine, New Hampshire, Massachusetts and Connecticut. The results suggest that these microsatellites will be useful in population genetic studies. Additional markers are also being developed to construct a low-density genetic map for the common loon.

Murray, M., D. Meehan, M. Pokras and A. Alcivar-Warren. 2003. Low frequency of microsatellites in common loon (Gavia immer) genome. Book of Abstracts. Plant and Animal Genome XI, January 11-15, Town & Country Hotel, San Diego. Abstr. P677, p. 243. (View Abstract)