@article{CornettiValenteDunningetal.2015,
  author    = {Cornetti, Luca and Valente, Luis M. and Dunning, Luke T. and Quan, Xueping and Black, Richard A. and Hebert, Olivier and Savolainen, Vincent},
  title     = {The Genome of the "Great Speciator" Provides Insights into Bird Diversification},
  series = {Genome biology and evolution},
  volume    = {7},
  journal   = {Genome biology and evolution},
  number    = {9},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1759-6653},
  doi       = {10.1093/gbe/evv168},
  pages     = {2680 -- 2691},
  year      = {2015},
  abstract  = {Among birds, white-eyes (genusZosterops) have diversified so extensively that Jared Diamond and Ernst Mayr referred to them as the 'great speciator." The Zosterops lineage exhibits some of the fastest rates of species diversification among vertebrates, and its members are the most prolific passerine island colonizers. We present a high-quality genome assembly for the silvereye (Zosterops lateralis), a white-eye species consisting of several subspecies distributed across multiple islands. We investigate the genetic basis of rapid diversification in white-eyes by conducting genomic analyses at varying taxonomic levels. First, we compare the silvereye genome with those of birds from different families and searched for genomic features that may be unique to Zosterops. Second, we compare the genomes of different species of white-eyes from Lifou island (South Pacific), using whole genome resequencing and restriction site associated DNA. Third, we contrast the genomes of two subspecies of silvereye that differ in plumage color. In accordance with theory, we show that white-eyes have high rates of substitutions, gene duplication, and positive selection relative to other birds. Below genus level, we find that genomic differentiation accumulates rapidly and reveals contrasting demographic histories between sympatric species on Lifou, indicative of past interspecific interactions. Finally, we highlight genes possibly involved in color polymorphism between the subspecies of silvereye. By providing the first whole-genome sequence resources for white-eyes and by conducting analyses at different taxonomic levels, we provide genomic evidence underpinning this extraordinary bird radiation.},
  language  = {en}
}
@article{BurleighBansalEulensteinetal.2011,
  author    = {Burleigh, J. Gordon and Bansal, Mukul S. and Eulenstein, Oliver and Hartmann, Stefanie and Wehe, Andre and Vision, Todd J.},
  title     = {Genome-Scale Phylogenetics inferring the plant tree of life from 18,896 gene trees},
  series = {Systematic biology},
  volume    = {60},
  journal   = {Systematic biology},
  number    = {2},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1063-5157},
  doi       = {10.1093/sysbio/syq072},
  pages     = {117 -- 125},
  year      = {2011},
  abstract  = {Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.},
  language  = {en}
}