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amazonmatt1 committed Jan 7, 2016
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Matthew Miller (Smithsonian Tropical Research Institute & Villanova University), Daniel Buitrago-Rosas (Smithsonian Tropical Research Institute), Justin Bernstein (Villanova University), Eldredge Bermingham ( Smithsonian Tropical Research Institute & the Patricia and Phillip Frost Museum of Science)

## overview
Our goal was to sequence a 652 basepair fragment of the COI mitocondrial gene from as many Panamanian breeding bird species across their national range as possible, given existing vouchered tissue samples, in order to provide baseline taxonomic, biogeographic, and phyogeographic data on Panamanian bird diversity.
Our goal was to sequence a 652 basepair fragment of the COI mitochondrial gene from as many Panamanian breeding bird species across their national range as possible, given existing vouchered tissue samples, in order to provide baseline taxonomic, biogeographic, and phylogeographic data on Panamanian bird diversity.

##results
We sequenced a total of 2272 specimens representing 476 species of resident and migratory birds. However, we recovered 501 Barcode clusters (BINS), suggesting that as many as 25 avian lineages in Panama may represent cryptic species. Taking a closer look at our data we find that all cryptic cases involve Panamanian breeding landbirds, of which we only surveyed 100 species comprehensively across the country. Furthermore, 24 of the 25 cases involve lowland, rather than highland, species, that geographically replace each other between eastern and western Panama . Our results suggest that Panamanian bird biodiversity may be under represented by 20%. Because there are no major geographic barriers separating the eastern and western lowlands in Panama, our study demonstrates the utility of this fauna for fundamental comparative studies in the dynamics of avian secondary contact and speciation.
We sequenced a total of 2272 specimens representing 476 species of resident and migratory birds. However, we recovered 501 Barcode clusters (BINS), suggesting that as many as 25 avian lineages in Panama may represent cryptic species. Taking a closer look at our data we find that all cryptic cases involve Panamanian breeding land birds, of which we only surveyed 100 species comprehensively across the country. Furthermore, 24 of the 25 cases involve lowland, rather than highland, species, that geographically replace each other between eastern and western Panama . Our results suggest that Panamanian bird biodiversity may be under represented by 20%. Because there are no major geographic barriers separating the eastern and western lowlands in Panama, our study demonstrates the utility of this fauna for fundamental comparative studies in the dynamics of avian secondary contact and speciation.

We are working on the final manuscript for publication.

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