Also, low cloning efficiency and low overall number make microsatellites an unfavorable choice. The value of mitochondrial DNA for population genetic study is limited in this lineage due to slow rate of evolution in the mitochondrial control region and presence of nuclear copies. Previous study has left most of the nuclear genome unexplored, and population-level studies are limited to only 15% of the world's terns. Terns are a lineage of cosmopolitan shorebirds with an unresolved evolutionary history that comprises several species of conservation concern. One lineage of non-model birds for which novel genetic markers are especially needed is the subfamily Sterninae, family Laridae, consisting of terns and noddies. Secondly, because bird orders may differ in genomic mutation rate and species vary in effective population size, polymorphic loci in one species may not be useful for other species. Despite the apparent universal nature of these primers, amplification success varied across avian taxa (93% in Gallus 79-85% in Passeridan songbirds 78% in Falco 34% in Aegolius 26% in Aquila. The applicability of these markers in population studies of non-model avian species is promising, but remains untested for the majority of birds. 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.Ī new avenue was recently provided by publication of a large number of autosomal, intronic (exon-priming and intron crossing) markers that were shown to amplify across Neognathous birds, many of which also displayed extensive intraspecific variation in a representative songbird. Thus, for many biologists that study non-model species with a minimal budget for DNA analysis, mitochondrial or microsatellite loci are still the preferred choice. However, these markers are not widely used yet in population studies due to apparent low level of divergence or lack of access. For phylogeographic investigations, nuclear sequence-based markers (exonic, intronic or anonymous loci) are becoming increasingly popular especially with access to reference genomes and next-generation sequencing that allows sampling many loci. Mitochondrial and nuclear microsatellite markers are most often used in population studies. The choice of genomic marker is frequently guided by published and previously tested loci, but also dependent on the mutation rate appropriate for the temporal depth of the study and the quality of the sampled DNA. To investigate the role of physical boundaries to evolutionary divergence and ecological isolation, specific genomic markers are often targeted. 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. These data document the value of intronic markers to the study of terns and allies. 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. 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). Results from this genome skimming effort yielded four new nuclear sequence-based markers for tern phylogenetics and 11 intra-specific polymorphic markers. 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. 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. 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. 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. Terns (Charadriiformes: Sterninae) are a lineage of cosmopolitan shorebirds with a disputed evolutionary history that comprises several species of conservation concern.
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