The placenta is the first organ to be differentiated during development in eutherian mammals, and during its life it performs functions analogous to those of lung, intestine, kidney, liver, ovary, pituitary, and hypothalamus [1
]. Failures in placentation and pathology of the placenta often result in human reproductive disorders and pregnancy complications including spontaneous abortion [4
], pre-eclampsia [5
], and intrauterine growth restriction [6
]. Because placental anatomy is so variable, much research has focused on the evolution, development, and pathology of the placenta within eutherian mammals. Here we ask what genes may have been involved in the emergence of the chorioallantoic placenta and their subsequent evolutionary modifications during human descent.
Studies of gene expression in the placenta are one of the key sources for discovering the genes controlling placental development [7
]. One of the significant differences between the choriovitelline marsupial placenta and the chorioallantoic eutherian placenta is extravillous trophoblast invasion of the placenta into the eutherian uterus [8
]. Recently [9
], we suggested that many key features of the human placenta (e.g. hemochorial interface, discoid shape) represent the ancestral character state among placental mammals, and these features have been maintained throughout human descent since the time of the last common ancestor (LCA) of placental mammals. Furthermore, there is evidence that many genes expressed in the placenta originated well before the emergence of the organ [10
]. In addition to these ancient genes, subsequent gene duplication and divergence have likely contributed to changes in placental morphology during mammalian evolution [10
]. For example, adaptive evolution has been detected in pregnancy-associated glycoproteins (PAG) [12
], and many placenta-specific genes are uniquely found in specific mammalian clades [11
Considerable variation in traits involved in placentation exists among placental mammals. During the evolution of extant placental mammals four major clades have emerged, although the relationship among them remains controversial [13
]. Because of the placenta’s importance in reproductive success, it is likely that intense selective pressure has shaped changes in placental anatomy and function during mammalian cladogenesis. Investigations of genes involved in the biology of the placenta are crucially important for understanding both placenta-related diseases and the evolutionary history of variation in the anatomy and physiology of the mammalian placenta. While much genomic research has examined human placental expression data to identify placenta related genes (e.g. [7
]), this approach is limited by the fact that > 15,000 genes are expressed in the human term placenta [15
]. Mouse mid-gestation placenta and embryo expression profiles have also identified thousands of expressed genes [16
]. Thus, the sheer number of expressed genes makes it a challenge to identify the genes most important in placental biology based on expression data alone.
In the present study, we integrated DNA sequence and gene expression data using evolutionary analysis methods to implicate single copy genes involved in placental evolution. Specifically, we tested whether adaptations in single copy genes highly expressed in the term human placenta occurred predominantly in earlier periods of human evolution, defined here as prior to the divergence of the human and chimpanzee lineages [7
]. Single copy genes were chosen because techniques for their analysis are exceptionally robust (see Materials and Methods). Highly expressed genes were chosen based on the assumption that genes expressed at high levels in a given tissue likely contribute to the development and function of that tissue [17
]. Our expectation was that a proportionally greater number of genes highly expressed in the human placenta would show evidence of adaptive evolution during the emergence of the chorioallantoic placenta on the eutherian stem lineage (i.e., after the divergence from marsupials but before the last common ancestor of extant placental mammals; ) than would be found in subsequent descendant lineages leading to humans. Our rationale for this prediction is that many anatomical features of the human placenta are phylogenetically ancient. Nevertheless, in subsequent human evolutionary history, different genes might then have undergone adaptations associated with the modifications of placental functions and/or phenotypes that distinguish the human placenta from placentae of other mammals.
Phylogenetic relationships among study species
While this scenario has an intuitive appeal and genes important in placental development and function have been shown to evolve adaptively in mammalian lineages [19
], no statistical evidence on a genome-wide scale has yet been offered in support of the idea that positive selection on genes highly expressed in the human placenta occurred during the emergence of this vital organ. Our findings provide statistical support for the proposal that single copy genes important in human placentation underwent a burst of adaptive change in the more ancient lineages within the mammalian clade, in particular the eutherian stem lineage. This study illustrates the power that evolutionary and comparative genomics methods have to categorize the genes initially involved in the emergence of novel organs. In addition, it demonstrates the utility of an evolutionary approach in identifying candidate genes involved in organ-specific disorders.