Abstract
BackgroundTerns (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.ResultsResults from this genome skimming effort yielded four new nuclear sequence-based markers for tern phylogenetics and 11 intra-specific polymorphic markers. Further, comparison between the two genomes indicated a phylogenetic conflict at the base of terns, involving the inclusion (mitochondrial) or exclusion (nuclear) of the Angel Tern (Gygis alba). Although limited mitochondrial variation was confirmed, both nuclear markers and a short tandem repeat in the mitochondrial control region indicated the presence of considerable genetic variation in Royal Terns at a regional scale.ConclusionsThese data document the value of intronic markers to the study of terns and allies. We expect that these and additional markers attained through next-generation sequencing methods will accurately map the genetic origin and species history of this group of birds.
Highlights
Terns (Charadriiformes: Sterninae) are a lineage of cosmopolitan shorebirds with a disputed evolutionary history that comprises several species of conservation concern
16 loci were used for further analyses, including two mitochondrial markers and 14 intronic loci that vary in length from 236-844 bp
The 11th intron of GAPDH showed significant length variation (270-428 bp) across several neognathous orders with terns displaying above average length: 380 bp, with an average of 340 bp per order
Summary
Terns (Charadriiformes: Sterninae) are a lineage of cosmopolitan shorebirds with a disputed evolutionary history that comprises several species of conservation concern. Nuclear sequence-based markers (exonic, intronic or anonymous loci) are becoming increasingly popular [1] especially with access to reference genomes and next-generation sequencing that allows sampling many loci [2] These markers are not widely used yet in population studies due to apparent low level of divergence or lack of access [3]. For many biologists that study non-model species with a minimal budget for DNA analysis, mitochondrial or microsatellite loci are still the preferred choice When such researchers work with lineages for which published microsatellite loci have not been developed, the single choice is to focus on mitochondrial markers, where number of appropriate loci, and statistical power, is limited
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