Genome skimming identifies polymorphism in tern populations and species

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.

Molecular phylogeny and systematics of Blue and Grey Noddies (Procelsterna)

“…For instance, the uncertainty in the position of Gygis in the trees recovered by Jackson et al . () was attributable to conflict between the different genes, but was also influenced by incomplete taxon sampling among Lari.…”

“…Our goal here was to decipher the phylogenetic relationships among noddies, rather than testing the position of Gygis and noddies among other members of the Laridae, which would have required much larger taxon sampling. For instance, the uncertainty in the position of Gygis in the trees recovered by Jackson et al (2012) was attributable to conflict between the different genes, but was also influenced by incomplete taxon sampling among Lari.…”

Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline

“…Whether genome skimming, which has been successfully applied using fresh plant and animal tissues (e.g. Jackson, Emslie & Tuinen, ; Bock et al ., ), will also be successful using a range of herbarium specimens (with regard to both phylogenetic diversity and specimen age) has not been rigorously tested so far, and is the subject of this study. We also explore the relationship between nuclear genome size ( C value) and assembled plastome coverage, which, when using genome skimming, can be hypothesized to affect read coverage of organelle genome sequences.…”

Species limits and English names in the genus Gygis (Laridae)

“…Nevertheless, molecular systematists (Thibault & Cibois 2017) and list-makers (Gill & Donsker 2019) have seized upon the Yeung et al (2009) study to make generalisations that dismiss other lines of evidence. However, the findings of Jackson et al (2012) suggest that fresh research, including both nuclear and mitochondrial genes, is sorely needed in this complex before genetic data can be seriously weighed against seemingly overwhelming non-molecular evidence. For now, the only meaningful taxonomy is to regard G. alba, G. candida and G. microrhyncha as biological species.…”

“…The eclectic study of Thomas et al (2004), with a different molecular dataset, considered microrhyncha a species. Subsequently, Jackson et al (2012) showed that molecular studies of Charadriiformes that depend entirely on mitochondrial DNA can be problematic and would profit from additional nuclear markers. No such study has yet been published.…”