Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation

Sree Rohit Raj Kolora, Anne Weigert, Amin Saffari, Stephanie Kehr, Maria Beatriz Walter Costa, Cathrin Spröer, Henrike Indrischek, Manjusha Chintalapati, Konrad Lohse, Gero Doose, Jörg Overmann, Boyke Bunk, Christoph Bleidorn, Annegret Grimm-Seyfarth, Klaus Henle, Katja Nowick, Rui Faria, Peter F. Stadler, Martin Schlegel

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Number of pages15
JournalGigaScience
Volume8
Issue number2
DOIs
Publication statusPublished - 1 Feb 2019

Keywords

  • de novo hybrid assembly
  • gene flow
  • inversions
  • noncoding RNA
  • PacBio and Illumina
  • positive selection
  • sister species
  • transcripts
  • UV response
  • zinc fingers

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