Defining the Molecular Targets of Evolution

With significant advances in next-generation sequencing technologies we now have the genomes of hundreds vertebrate species but understanding how the differences and similarities within these genomes control species diversity is largely unknown. The Tasmanian tiger or thylacine (Thylacinus cynocephalus) was the largest carnivorous Australian marsupial to exist into the modern era. Their phenotypic resemblance to the eutherian canids is considered the most striking example of convergent evolution in mammals. This convergence is even more astounding when you consider that they last shared a common ancestor over 160 million years ago. Sadly, the last known thylacine died in captivity in 1936.  We sequenced the thylacine genome from a preserved pouch young specimen and used it to examine the genetic basis of its convergence with canids. We performed comparative genomic analyses and demonstrated that in spite of their extraordinary phenotypic convergence, the genes and pathways targeted by positive selection differ markedly between the thylacine and canines. Despite not seeing any enrichment in protein coding homoplasy between the canids and the thylacine, some interesting genes were identified. We have extended these analyses to look at convergence within the noncoding portion of the genome and can identify convergent evolution in regions consistent with driving the craniofacial convergence observed between these species. Convergent evolution coupled with comparative genomics provides a powerful tool to examine how evolution works at the DNA level.