Genome skimming identifies polymorphism in tern populations and species.

BMC Research Notes
David George JacksonMarcel van Tuinen

Abstract

Terns (Charadriiformes: Sterninae) are a lineage of cosmopolitan shorebirds with a disputed evolutionary history that comprises several species of conservation concern. As a non-model system in genetics, previous study has left most of the nuclear genome unexplored, and population-level studies are limited to only 15% of the world's species of terns and noddies. Screening of polymorphic nuclear sequence markers is needed to enhance genetic resolution because of supposed low mitochondrial mutation rate, documentation of nuclear insertion of hypervariable mitochondrial regions, and limited success of microsatellite enrichment in terns. Here, we investigated the phylogenetic and population genetic utility for terns and relatives of a variety of nuclear markers previously developed for other birds and spanning the nuclear genome. Markers displaying a variety of mutation rates from both the nuclear and mitochondrial genome were tested and prioritized according to optimal cross-species amplification and extent of genetic polymorphism between (1) the main tern clades and (2) individual Royal Terns (Thalasseus maxima) breeding on the US East Coast. Results from this genome skimming effort yielded four new nuclear sequence-based markers...Continue Reading

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Datasets Mentioned

BETA
X001-Y100

Methods Mentioned

BETA
PCR
electrophoresis

Software Mentioned

Tracer
Sequencher
BEAST
FigTree
TreeAnnotator
MEGA

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