@article{KoloraWeigertSaffarietal.2018,
  author    = {Kolora, Sree Rohit Raj and Weigert, Anne and Saffari, Amin and Kehr, Stephanie and Walter Costa, Maria Beatriz and Spr{\"o}er, Cathrin and Indrischek, Henrike and Chintalapati, Manjusha and Lohse, Konrad and Doose, Gero and Overmann, J{\"o}rg and Bunk, Boyke and Bleidorn, Christoph and Grimm-Seyfarth, Annegret and Henle, Klaus and Nowick, Katja and Faria, Rui and Stadler, Peter F. and Schlegel, Martin},
  title     = {Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation},
  series = {GigaScience},
  volume    = {8},
  journal   = {GigaScience},
  number    = {2},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {2047-217X},
  doi       = {10.1093/gigascience/giy160},
  pages     = {15},
  year      = {2018},
  abstract  = {Background Lacerta viridis and Lacerta bilineata are sister species of European green lizards (eastern and western clades, respectively) that, until recently, were grouped together as the L. viridis complex. Genetic incompatibilities were observed between lacertid populations through crossing experiments, which led to the delineation of two separate species within the L. viridis complex. The population history of these sister species and processes driving divergence are unknown. We constructed the first high-quality de novo genome assemblies for both L. viridis and L. bilineata through Illumina and PacBio sequencing, with annotation support provided from transcriptome sequencing of several tissues. To estimate gene flow between the two species and identify factors involved in reproductive isolation, we studied their evolutionary history, identified genomic rearrangements, detected signatures of selection on non-coding RNA, and on protein-coding genes. Findings Here we show that gene flow was primarily unidirectional from L. bilineata to L. viridis after their split at least 1.15 million years ago. We detected positive selection of the non-coding repertoire; mutations in transcription factors; accumulation of divergence through inversions; selection on genes involved in neural development, reproduction, and behavior, as well as in ultraviolet-response, possibly driven by sexual selection, whose contribution to reproductive isolation between these lacertid species needs to be further evaluated. Conclusion The combination of short and long sequence reads resulted in one of the most complete lizard genome assemblies. The characterization of a diverse array of genomic features provided valuable insights into the demographic history of divergence among European green lizards, as well as key species differences, some of which are candidates that could have played a role in speciation. In addition, our study generated valuable genomic resources that can be used to address conservation-related issues in lacertids.},
  language  = {en}
}
@article{LeDucRenaudKrishnanetal.2015,
  author    = {Le Duc, Diana and Renaud, Gabriel and Krishnan, Arunkumar and Almen, Markus Sallman and Huynen, Leon and Prohaska, Sonja J. and Ongyerth, Matthias and Bitarello, Barbara D. and Schioth, Helgi B. and Hofreiter, Michael and Stadler, Peter F. and Pr{\"u}fer, Kay and Lambert, David and Kelso, Janet and Sch{\"o}neberg, Torsten},
  title     = {Kiwi genome provides insights into evolution of a nocturnal lifestyle},
  series = {Genome biology : biology for the post-genomic era},
  volume    = {16},
  journal   = {Genome biology : biology for the post-genomic era},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1465-6906},
  doi       = {10.1186/s13059-015-0711-4},
  pages     = {15},
  year      = {2015},
  abstract  = {Background: Kiwi, comprising five species from the genus Apteryx, are endangered, ground-dwelling bird species endemic to New Zealand. They are the smallest and only nocturnal representatives of the ratites. The timing of kiwi adaptation to a nocturnal niche and the genomic innovations, which shaped sensory systems and morphology to allow this adaptation, are not yet fully understood. Results: We sequenced and assembled the brown kiwi genome to 150-fold coverage and annotated the genome using kiwi transcript data and non-redundant protein information from multiple bird species. We identified evolutionary sequence changes that underlie adaptation to nocturnality and estimated the onset time of these adaptations. Several opsin genes involved in color vision are inactivated in the kiwi. We date this inactivation to the Oligocene epoch, likely after the arrival of the ancestor of modern kiwi in New Zealand. Genome comparisons between kiwi and representatives of ratites, Galloanserae, and Neoaves, including nocturnal and song birds, show diversification of kiwi's odorant receptors repertoire, which may reflect an increased reliance on olfaction rather than sight during foraging. Further, there is an enrichment of genes influencing mitochondrial function and energy expenditure among genes that are rapidly evolving specifically on the kiwi branch, which may also be linked to its nocturnal lifestyle. Conclusions: The genomic changes in kiwi vision and olfaction are consistent with changes that are hypothesized to occur during adaptation to nocturnal lifestyle in mammals. The kiwi genome provides a valuable genomic resource for future genome-wide comparative analyses to other extinct and extant diurnal ratites.},
  language  = {en}
}