Emslie, Steven D

Jackson, David George

van Tuinen, Marcel

BMC Research Notes

English

PubMed

David Jackson

Steven D Emslie

Marcel van Tuinen

Springer - Publisher Connector

Genome skimming identifies polymorphism in tern populations and species

Abstract
          
            Background
            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
            Results 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.
          
          
            Conclusions
            These 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.
          </jats:sec

David George Jackson

Crossref

A smorgasbord of markers for avian ecology and evolution. Mol Ecol

A: Evaluation of the genetic structure of the breeding common tern (Sterna hirundo) population by means of microsatellite markers. Biologija

Ahlquist JA: Phylogeny and Classification of Birds New Haven:

AJ: A phylogenetic framework for the terns (Sternini) inferred from mtDNA sequences: implications for taxonomy and plumage evolution. Mol Phyl Evol

Allström P: Evolution of ultraviolet vision in shorebirds (Charadriiformes). Biol Lett

American Ornithologist’s Union: Check-List of North American Birds Lawrence: American Ornithologists’

Barrowclough GF: RAG-1 sequences resolve phylogenetic relationships within Charadriiform birds. Mol Phyl Evol

Bonatto SL: Multigene phylogeny and DNA barcoding indicate that the Sandwich tern complex (Thalasseus sandvicensis, Laridae, Sternini) comprises two species. Mol Phyl Evol

CM: Identification of birds through DNA barcodes. PLoS Biol

Congdon BC: Reconciling historical processes and population structure in the sooty tern Sterna fuscata.

Desmarais E: Slow rate of evolution in the mitochondrial control region of gulls (Aves: Laridae). Mol Biol Evol

Development of new nuclear markers and characterization of single nucleotide polymorphisms in kelp gull (Larus dominicanus). Mol Ecol Res

DP: Primers for a PCRbased approach to mitochondrial genome sequencing in birds and other vertebrates. Mol Phyl Evol

Edwards SV: Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica

Effects of varied electrophoretic conditions on detection of evolutionary patterns in the Laridae. Condor

Ellegren H: Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Mol Ecol

Ellegren H: Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome. Mol Ecol

Emslie SD: An analysis of possible genotoxic exposure in adult and juvenile Royal Terns in North Carolina,

Ericson PGP: Systematic relationships and biogeography of the tracheophone suboscines (Aves: Passeriformes). Mol Phyl Evol

Family Sternidae (Terns).

FG: Royal Tern (Sterna maxima).

Genetic variation among subspecies of Least Tern (Sterna antillarum): implications for conservation. Waterbirds

Genome-enabled development of DNA markers for ecology, evolution and conservation. Mol Ecol

GJ: Avian molecular systematics on the rebound: a fresh look at modern shorebird phylogenetic relationships.

Hadly EA: Tempo and mode of modern bird evolution observed with large-scale taxonomic sampling. Hist Bio

JA: Inter-familial relationships of the shorebirds (Aves: Charadriiformes) based on nuclear DNA sequence data.

KC: Waterbird Conservation for the Americas: the North American Waterbird Conservation Plan Version 1 Washington: Waterbird Conservation for the Americas;

Kesseli RV: Novel microsatellite markers used to determine the population genetic structure of the endangered Roseate Tern, Sterna dougallii, in Northwest Atlantic and Western Australia. Cons Gen

L: A multi-locus analysis of honeyeaters (Aves: Meliphagidae) highlights spatio-temporal heterogeneity in the influence of biogeographic barriers in the Australian monsoonal zone. Mol Ecol

Multilocus perspectives on the monophyly and phylogeny of the order Charadriiformes (Aves).

MW: Challenges and prospects of population genetic studies in terns (Charadriiformes,

MW: Population structure in the South American tern Sterna hirundinacea in the South Atlantic: two populations with distinct breeding phenologies.

Novel intron phylogeny supports plumage convergence in orioles (Icterus). Auk

Phylogenetic reanalysis of Strauch’s osteological data set for the Charadriiformes. Condor

Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds. Biol Lett

Phylogenetic relationships within the Laridae (Charadriiformes: Aves) inferred from mitochondrial markers. Mol Phyl Evol

Phylogenetics of modern shorebirds (Charadriiformes) based on phenotypic evidence: analysis and discussion.

Phylogeny of “core Gruiformes” (Aves: Grues) and resolution of the Limpkin-Sungrebe problem. Mol Phyl Evol

Population genetic relationships in the roseate tern: globally, regionally and locally.

Population genetics and gene flow of the common tern. Condor

RC: Mitochondrial and nuclear DNA sequences reveal recent divergence in morphologically indistinguishable petrels. Mol Ecol

S: MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol

Saetre G-P: Contrasting patterns of polymorphisms and divergence on the Z chromosome and autosomes in two Ficedula flycatcher species. Genetics

SB: Convergence and divergence in the evolution of aquatic birds. Proc Roy Soc London B

SB: Phylogeny and biogeography of the ratite birds inferred from DNA sequences of the mitochondrial ribosomal genes. Mol Biol Evol

Sidlauskas B: Genetic applications in avian conservation. Auk

SL: Shorebirds (Charadriiformes).

SM: Subspecific status and population genetic structure of least terns (Sternula antillarum inferred by mitochondrial DNA control-region sequences and microsatellite DNA. Auk

Székely T: A supertree approach to shorebird phylogeny.

T: A phylogenomic study of birds reveals their evolutionary history. Science

Testing subspecies hypothesis with molecular markers and morphometrics in the Pacific white tern complex.

The phylogeny of charadriiform birds (shorebirds and allies) -reassessing the conflict between morphology and molecules. Zool J Linn Soc

TP: Intron variation in marbled murrelets detected using analyses of single-stranded conformational polymorphisms. Mol Ecol

Väli Ü: Sex- and species-biased gene flow in a spotted eagle hybrid zone.

W: Population trends in royal and sandwich terns along the MidAtlantic Seaboard,

WS: The utility of DNA sequences of an intron from the b-fibrinogen gene in phylogenetic analysis of woodpeckers (Aves: Picidae). Mol Phyl Evol

https://bmcresnotes.biomedcentral.com/track/pdf/10.1186/1756-0500-5-94?site=bmcresnotes.biomedcentral.com

Genome skimming identifies polymorphism in tern populations and species

Abstract

Similar works

Full text

Available Versions

Springer - Publisher Connector

Crossref

Springer - Publisher Connector