DNA from feces and museum specimens confirms a first state record bird

In October 2005, a vagrant kingbird (Aves: Tyrannus sp.) appeared in Michigan’s Upper Peninsula, nearly 2000 km from the northern limit of its usual range. Using mitochondrial DNA obtained from a fecal sample deposited by the bird and mitochondrial DNA isolated from museum reference specimens, the species iden- tity of this bird was definitively confirmed as a Tropical Kingbird (T. melancholicus) rather than a Couch’s Kingbird (T. couchii). This is the first time DNA evidence has been used to establish a state bird record, and one of the few studies of any type to successfully use avian feces for DNA analysis. Circumstantial evidence indicates that this bird was possibly displaced from its original range by Hurricane Wilma in October, 2005. Identification of vagrant birds is important for studying avian populations, and non-invasive genetic sampling techniques should be considered when traditional means of identification fail to provide definitive evidence of identity

Winter Microhabitat Foraging Preferences of Sympatric Boreal and Black-capped chickadees in Michigan\u27s Upper Peninsula

We examined differences in microhab- itat use between Boreal (Poecile hudsonicus) and Black- capped chickadees (P. atricapillus) where they co-occur near Marquette, Michigan, USA. Twenty-four Boreal and 37 Black-capped chickadees were followed during 60 hrs of field observation. Boreal Chickadees foraged only in three conifer species, 76% of which were black spruce (Picea mariana), while Black-capped Chickadees foraged widely across six coniferous and three deciduous tree species. Analysis of foraging data categorized by zones within conifer trees indicated high niche overlap (0.676) between Boreal and Black-capped chickadees across all foraging zones. Individual comparisons on a zone-by-zone basis revealed a significant difference in foraging occupancy in the medial portion of the crowns of conifer trees (P 5 0.0002). Our results indicate exclusive use by Boreal Chickadees of dense medial foliage within the top 3 m of conifer crowns

A simple and improved PCR-based technique for white-tailed deer (Odocoileus virginianus) sex identification

We describe a simple single-reaction technique for identifying the sex of white-tailed deer (Odocoileus virginianus) based on the PCR amplification of a zinc-finger intron using one pair of primers. Although Sry-coamplification confirmed sex identities, use of the Sry marker was unnecessary due to dimorphic alleles on the X and Y chromosomes at the zinc-finger locus. Insertions in intron 7 of the Y-linked allele (417 bp) make it nearly twice as long as the X-linked allele (236 bp) and thus the amplification products are easily discernable by simple agarose gel electrophoresis. The relatively short size of these products makes them useful for DNA-based sex identification from potentially low-yield tissue samples (e.g., hair, feces). This technique will provide ecologists, conservation geneticists and wildlife managers with a mechanism to readily and reliably identify the sex of un- known white-tailed deer tissue samples, and likely similar samples from other cervid species

Cues used by the black fly, Simulium annulus, for attraction to the common loon (Gavia immer)

The parasitic relationship between a black fly, Simulium annulus, and the common loon (Gavia immer) has been considered one of the most exclusive relationships between any host species and a black fly species. To test the host specificity of this blood-feeding insect, we made a series of bird decoy presentations to black flies on loon-inhabited lakes in northern Wisconsin, U.S.A. To examine the importance of chemical and visual cues for black fly detection of and attraction to hosts, we made decoy presentations with and without chemical cues. Flies attracted to the decoys were collected, identified to species, and quantified. Results showed that S. annulus had a strong preference for common loon visual and chemical cues, although visual cues from Canada geese (Branta canadensis) and mallards (Anas platyrynchos) did attract some flies in significantly smaller numbers

It\u27s not too Late for the Harpy Eagle (Harpia harpyja): High Levels Of Genetic Diversity and Differentiation Can Fuel Conservation Programs

Background: The harpy eagle (Harpia harpyja) is the largest Neotropical bird of prey and is threatened by human persecution and habitat loss and fragmentation. Current conservation strategies include local education, captive rearing and reintroduction, and protection or creation of trans-national habitat blocks and corridors. Baseline genetic data prior to reintroduction of captive-bred stock is essential for guiding such efforts but has not been gathered previously. Methodology/Findings: We assessed levels of genetic diversity, population structure and demographic history for harpy eagles using samples collected throughout a large portion of their geographic distribution in Central America (n = 32) and South America (n = 31). Based on 417 bp of mitochondrial control region sequence data, relatively high levels of haplotype and nucleotide diversity were estimated for both Central and South America, although haplotype diversity was significantly higher for South America. Historical restriction of gene flow across the Andes (i.e. between our Central and South American subgroups) is supported by coalescent analyses, the haplotype network and significant FST values, however reciprocally monophyletic lineages do not correspond to geographical locations in maximum likelihood analyses. A sudden population expansion for South America is indicated by a mismatch distribution analysis, and further supported by significant (p,0.05) negative values of Fu and Li’s DF and F, and Fu’s FS. This expansion, estimated at approximately 60 000 years BP (99 000–36 000 years BP 95% CI), encompasses a transition from a warm and dry time period prior to 50 000 years BP to an interval of maximum precipitation (50 000–36 000 years BP). Notably, this time period precedes the climatic and habitat changes associated with the last glacial maximum. In contrast, a multimodal distribution of haplotypes was observed for Central America suggesting either population equilibrium or a recent decline. Significance: High levels of mitochondrial genetic diversity in combination with genetic differentiation among subgroups within regions and between regions highlight the importance of local population conservation in order to preserve maximal levels of genetic diversity in this species. Evidence of historically restricted female-mediated gene flow is an important consideration for captive-breeding programs

Genomic Insights Into Natural Selection in the Common Loon (Gavia immer): Evidence for Aquatic Adaptation

Background: The common loon (Gavia immer) is one of five species that comprise the avian order Gaviiformes. Loons are specialized divers, reaching depths up to 60 m while staying submerged for intervals up to three minutes. In this study we used comparative genomics to investigate the genetic basis of the common loon adaptations to its ecological niche. We used Illumina short read DNA sequence data from a female bird to produce a draft assembly of the common loon (Gavia immer) genome. Results: We identified 14,169 common loon genes, which based on well-resolved avian genomes, represent approximately 80.7% of common loon genes. Evolutionary analyses between common loon and Adelie penguin (Pygoscelis adeliae), red-throated loon (Gavia stellata), chicken (Gallus gallus), northern fulmar (Fulmarus glacialis), and rock pigeon (Columba livia) show 164 positively selected genes in common and red-throated loons. These genes were enriched for a number of protein classes, including those involved in muscle tissue development, immunoglobulin function, hemoglobin iron binding, G-protein coupled receptors, and ATP metabolism. Conclusions: Signatures of positive selection in these areas suggest the genus Gavia may have adapted for underwater diving by modulating their oxidative and metabolic pathways. While more research is required, these adaptations likely result in (1) compensations in oxygen respiration and energetic metabolism, (2) low-light visual acuity, and (3) elevated solute exchange. This work represents the first effort to understand the genomic adaptations of the common loon as well as other Gavia and may have implications for subsequent studies that target particular genes for loon population genetic, ecological or conservation studies