title: Determining the Position of Storks on the Phylogenetic Tree of Waterbirds by Retroposon Insertion Analysis.
abstract: Despite many studies on avian phylogenetics in recent decades that used morphology, mitochondrial genomes, and/or nuclear genes, the phylogenetic positions of several birds (e.g., storks) remain unsettled. In addition to the aforementioned approaches, analysis of retroposon insertions, which are nearly homoplasy-free phylogenetic markers, has also been used in avian phylogenetics. However, the first step in the analysis of retroposon insertions, that is, isolation of retroposons from genomic libraries, is a costly and time-consuming procedure. Therefore, we developed a high-throughput and cost-effective protocol to collect retroposon insertion information based on next-generation sequencing technology, which we call here the STRONG (Screening of Transposons Obtained by Next Generation Sequencing) method, and applied it to 3 waterbird species, for which we identified 35,470 loci containing chicken repeat 1 retroposons (CR1). Our analysis of the presence/absence of 30 CR1 insertions demonstrated the intra- and interordinal phylogenetic relationships in the waterbird assemblage, namely 1) Loons diverged first among the waterbirds, 2) penguins (Sphenisciformes) and petrels (Procellariiformes) diverged next, and 3) among the remaining families of waterbirds traditionally classified in Ciconiiformes/Pelecaniformes, storks (Ciconiidae) diverged first. Furthermore, our genome-scale, in silico retroposon analysis based on published genome data uncovered a complex divergence history among pelican, heron, and ibis lineages, presumably involving ancient interspecies hybridization between the heron and ibis lineages. Thus, our retroposon-based waterbird phylogeny and the established phylogenetic position of storks will help to understand the evolutionary processes of aquatic adaptation and related morphological convergent evolution.
authors.affiliation: Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan.
authors.forename: Tae
authors.initials: T
authors.lastname: Kuramoto
authors.affiliation: Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan.
authors.forename: Hidenori
authors.initials: H
authors.lastname: Nishihara
authors.affiliation: Division of Microbiology, National Institute of Health Sciences, Setagaya, Tokyo, Japan.
authors.forename: Maiko
authors.initials: M
authors.lastname: Watanabe
authors.affiliation: Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan Foundation for Advancement of International Science, Tsukuba, Ibaraki, Japan Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan nokada@fais.or.jp.
authors.forename: Norihiro
authors.initials: N
authors.lastname: Okada
mesh_terms: D000818:Animals; D001717:Birds / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D010802:Phylogeny; D018626:Retroelements; D017422:Sequence Analysis, DNA
chemical_list: D018626:Retroelements
keywords: Aves; Ciconiiformes; chicken repeat 1; incomplete lineage sorting; next-generation sequencing