Baby Genomics: Tracing the Evolutionary Changes That Gave Rise to Placentation

It has long been a challenge to determine the genetic origin of new characters in the evolution. The molecular mechanisms behind many morphological innovations are still unknown, including such striking evolutionary transitions as the appearance of the placenta. Our approach is based on using orthology to link genotype to phenotype. Orthology describes a relation between homologous genes (or chromosomal segments) that last diverged by a speciation event. Orthologous genes are often used to study evolutionary history because they tend to be conservative in molecular and biological functions. Using our orthology assignment pipeline, we have inferred orthologs in 38, primarily mammalian, genomes with reference to the human genome. Our pipeline differs from the common orthology inference tools in the use of both robust, distance-based measures of gene relationships and in the use of synteny to clarify relationships that are ambiguous when using sequence data alone. A character matrix for these >20,000 ortholog pairs for each genome has been constructed. We then mapped these orthologs to a phylogenetic tree, reconstructed ancestral character states using Mesquite, and pinpointed genes that appeared on interesting evolutionary branches. These genes will be mined using functional analysis approaches, including ones using the GeneOntology framework. We plan to identify molecular functions or biological processes that are enriched in set of genes that appeared in evolutionarily important moments (especially, the appearance of placental mammals) relative to the rest of the genome.