Adaptive history of single copy genes highly expressed in the term human placenta

Specific expression and blood kinetics for relaxin 2, lipocalin 2, and tissue factor pathway inhibitor 2 at the canine placenta and pregnant bloods

In general, humoral factors released from the placenta influence pregnancy progression, but the involvement of the canine placenta is often unidentified. We investigated specific genes in canine placentas and analyzed the blood dynamics of the translated proteins. Furthermore, RNAs are known to be released from placentas embedding in exosomes, a type of extracellular vesicles. Here, the presence of cell-free RNAs in pregnant serums was also confirmed. RNA specimens were purified from the normal healthy dog placentas and applied to RNA-Seq analysis. Expressions of frequent genes were confirmed by RT-PCR using placentas from other individuals and breeds. Relaxin (RLN) 2, lipocalin (LCN) 2, and tissue factor pathway inhibitor (TFPI) 2 were selected as high-expressed and placenta-specific genes. By western blot, the three factors were clearly detected in the pregnant serums. Quantitative analysis revealed that the amount of RLN2 increased significantly from non-pregnancy to day 41 of pregnancy. Regarding LCN2 and TFPI2, the protein serum levels elevated during pregnancy, but the statistical differences were not detected. Exosomes were found in all pregnant serums; however, the percentage was less than 6% in total extracellular vesicles. The cell-free RNA related to RLN2 was detected, but no elevation was confirmed during pregnancy. We found specific genes in the canine placenta and the transition of their translated protein into the blood. These factors may become useful tools for research on canine pregnancy and monitoring of reproductive management. Exosomes and cell-free RNA could not be found to be valid in canine reproduction.

Repetitive DNA sequence detection and its role in the human genome

Repetitive DNA sequences playing critical roles in driving evolution, inducing variation, and regulating gene expression. In this review, we summarized the definition, arrangement, and structural characteristics of repeats. Besides, we introduced diverse biological functions of repeats and reviewed existing methods for automatic repeat detection, classification, and masking. Finally, we analyzed the type, structure, and regulation of repeats in the human genome and their role in the induction of complex diseases. We believe that this review will facilitate a comprehensive understanding of repeats and provide guidance for repeat annotation and in-depth exploration of its association with human diseases.

Evolutionary transcriptomics implicates new genes and pathways in human pregnancy and adverse pregnancy outcomes

Evolutionary changes in the anatomy and physiology of the female reproductive system underlie the origins and diversification of pregnancy in Eutherian ('placental') mammals. This developmental and evolutionary history constrains normal physiological functions and biases the ways in which dysfunction contributes to reproductive trait diseases and adverse pregnancy outcomes. Here, we show that gene expression changes in the human endometrium during pregnancy are associated with the evolution of human-specific traits and pathologies of pregnancy. We found that hundreds of genes gained or lost endometrial expression in the human lineage. Among these are genes that may contribute to human-specific maternal-fetal communication (HTR2B) and maternal-fetal immunotolerance (PDCD1LG2) systems, as well as vascular remodeling and deep placental invasion (CORIN). These data suggest that explicit evolutionary studies of anatomical systems complement traditional methods for characterizing the genetic architecture of disease. We also anticipate our results will advance the emerging synthesis of evolution and medicine ('evolutionary medicine') and be a starting point for more sophisticated studies of the maternal-fetal interface. Furthermore, the gene expression changes we identified may contribute to the development of diagnostics and interventions for adverse pregnancy outcomes.

New exon and accelerated evolution of placental gene Nrk occurred in the ancestral lineage of placental mammals

INTRODUCTION

The chorioallantoic placenta is a specific organ for placental mammals. However, the adaptive events during its emergence are still poorly investigated.

METHODS

We scanned the chromosome X to detect the accelerated evolution in the ancestral lineage of placental mammals, and constructed 3D protein structure models of a candidate by homology modeling.

RESULTS

Eight branch-specific accelerated regions were identified. Five of these regions (P=5.61×10^-11 ~ 9.03×10^-8) are located in the five exons of Nik-related kinase (Nrk), which is essential in placenta development and fetoplacental induction of labor. Nrk belongs to the germinal center kinase-IV subfamily with the overall similar protein structure; however, a new exon emerged in ancestors of placental mammals and its sequence has been conserved since then. Structure modelling of NRK suggests that the accelerated exons and the placental-mammal-specific exon (as a new loop) could change the enzymatic activity and the structure of placental mammal NRK.

DISCUSSION

Since the new loop is surrounded by the accelerated protein regions, it is likely that the new loop occurred and shifted the function of NRK, and then the accelerated evolution of Nrk occurred to adapt the structure change caused by the new loop in the ancestral lineage of placental mammals. Overall, this work suggests that the fundamental process of placental development and fetoplacental induction of labor has been targeted by positive Darwinian selection.

Organoids as Novel Models for Embryo Implantation Study

In the last decade, organoids have become emerging novel models for biomedical research. Organoids are small, self-organized three-dimensional (3D) tissue cultures derived from stem cells that mimic certain tissues or organs. In reproductive medicine, researchers have generated numerous organoids including blastoid (blastocyst organoid), endometrial organoid, and trophoblast organoid. These organdies provide useful models for studying the embryo implantation mechanism through observation of cell differentiation, gene expression, and epigenetic profiles at the implantation stage. As in vitro tissue models, organoids could be coupled with many other frontier technologies such as gene editing and genomic sequencing. However, the main drawback of organoids is that they do not fully mimic their counterparts in vivo tissues. Furthermore, there is a consensus of research ethics on organoids that may limit the types of studies that scientists perform with. Nevertheless, all discoveries and efforts surrounding organoids still greatly benefit therapy development for reproductive clinics.

The Genomes of the Livebearing Fish Species Poeciliopsis retropinna and Poeciliopsis turrubarensis Reflect Their Different Reproductive Strategies

The evolution of a placenta is predicted to be accompanied by rapid evolution of genes involved in processes that regulate mother-offspring interactions during pregnancy, such as placenta formation, embryonic development, and nutrient transfer to offspring. However, these predictions have only been tested in mammalian species, where only a single instance of placenta evolution has occurred. In this light, the genus Poeciliopsis is a particularly interesting model for placenta evolution, because in this genus a placenta has evolved independently from the mammalian placenta. Here, we present and compare genome assemblies of two species of the livebearing fish genus Poeciliopsis (family Poeciliidae) that differ in their reproductive strategy: Poeciliopsis retropinna which has a well-developed complex placenta and P. turrubarensis which lacks a placenta. We applied different assembly strategies for each species: PacBio sequencing for P. retropinna (622-Mb assembly, scaffold N50 of 21.6 Mb) and 10× Genomics Chromium technology for P. turrubarensis (597-Mb assembly, scaffold N50 of 4.2 Mb). Using the high contiguity of these genome assemblies and near-completeness of gene annotations to our advantage, we searched for gene duplications and performed a genome-wide scan for genes evolving under positive selection. We find rapid evolution in major parts of several molecular pathways involved in parent-offspring interaction in P. retropinna, both in the form of gene duplications as well as positive selection. We conclude that the evolution of the placenta in the genus Poeciliopsis is accompanied by rapid evolution of genes involved in similar genomic pathways as found in mammals.

The genome of the live-bearing fish Heterandria formosa implicates a role of conserved vertebrate genes in the evolution of placental fish

Background

The evolution of complex organs is thought to occur via a stepwise process, each subsequent step increasing the organ’s complexity by a tiny amount. This evolutionary process can be studied by comparing closely related species that vary in the presence or absence of their organs. This is the case for the placenta in the live-bearing fish family Poeciliidae, as members of this family vary markedly in their ability to supply nutrients to their offspring via a placenta. Here, we investigate the genomic basis underlying this phenotypic variation in Heterandria formosa, a poeciliid fish with a highly complex placenta. We compare this genome to three published reference genomes of non-placental poeciliid fish to gain insight in which genes may have played a role in the evolution of the placenta in the Poeciliidae.

Results

We sequenced the genome of H. formosa, providing the first whole genome sequence for a placental poeciliid. We looked for signatures of adaptive evolution by comparing its gene sequences to those of three non-placental live-bearing relatives. Using comparative evolutionary analyses, we found 17 genes that were positively selected exclusively in H. formosa, as well as five gene duplications exclusive to H. formosa. Eight of the genes evolving under positive selection in H. formosa have a placental function in mammals, most notably endometrial tissue remodelling or endometrial cell proliferation.

Conclusions

Our results show that a substantial portion of positively selected genes have a function that correlates well with the morphological changes that form the placenta of H. formosa, compared to the corresponding tissue in non-placental poeciliids. These functions are mainly endometrial tissue remodelling and endometrial cell proliferation. Therefore, we hypothesize that natural selection acting on genes involved in these functions plays a key role in the evolution of the placenta in H. formosa.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1484-2) contains supplementary material, which is available to authorized users.

Hemochorial placentation: development, function, and adaptations

Placentation is a reproductive adaptation that permits fetal growth and development within the protected confines of the female reproductive tract. Through this important role, the placenta also determines postnatal health and susceptibility to disease. The hemochorial placenta is a prominent feature in primate and rodent development. This manuscript provides an overview of the basics of hemochorial placental development and function, provides perspectives on major discoveries that have shaped placental research, and thoughts on strategies for future investigation.

Revisiting avian 'missing' genes from de novo assembled transcripts

Background

Argument remains as to whether birds have lost genes compared with mammals and non-avian vertebrates during speciation. High quality-reference gene sets are necessary for precisely evaluating gene gain and loss. It is essential to explore new reference transcripts from large-scale de novo assembled transcriptomes to recover the potential hidden genes in avian genomes.

Results

We explored 196 high quality transcriptomic datasets from five bird species to reconstruct transcripts for the purpose of discovering potential hidden genes in the avian genomes. We constructed a relatively complete and high-quality bird transcript database (1,623,045 transcripts after quality control in five birds) from a large amount of avian transcriptomic data, and found most of the presumed missing genes (83.2%) could be recovered in at least one bird species. Most of these genes have been identified for the first time in birds. Our results demonstrate that 67.94% genes have GC content over 50%, while 2.91% genes are AT-rich (AT% > 60%). In our results, 239 (53.59%) genes had a tissue-specific expression index of more than 0.9 in chicken. The missing genes also have lower Ka/Ks values than average (genome-wide: Ka/Ks = 0.99; missing gene: Ka/Ks = 0.90; t-test = 1.25E-14). Among all presumed missing genes, there were 135 for which we did not find any meaningful orthologues in any of the 5 species studied.

Conclusion

Insufficient reference genome quality is the major reason for wrongly inferring missing genes in birds. Those presumably missing genes often have a very strong tissue-specific expression pattern. We show multi-tissue transcriptomic data from various species are necessary for inferring gene family evolution for species with only draft reference genomes.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5407-1) contains supplementary material, which is available to authorized users.

Ancestral resurrection of anthropoid estrogen receptor β demonstrates functional consequences of positive selection

Anthropoid primates arose during the Eocene approximately 55 million years ago (mya), and extant anthropoids share a most recent common ancestor ∼40mya. Paleontology has been very successful at describing the morphological phenotypes of extinct anthropoids. Less well understood is the molecular biology of these extinct species as well as the phenotypic consequences of evolutionary variation in their genomes. Here we resurrect the most recent common ancestral anthropoid estrogen receptor β gene (ESR2) and demonstrate that the function of this ancestral estrogen receptor has been maintained during human descent but was altered during early New World monkey (NWM) evolution by becoming a more potent transcriptional activator. We tested hypotheses of adaptive evolution in the protein coding sequences of ESR2, and determined that ESR2 evolved via episodic positive selection on the NWM stem lineage. We separately co-transfected ESR2 constructs for human, NWM, and the anthropoid ancestor along with reporter gene vectors and performed hormone binding dose response experiments that measure transactivation activity. We found the transactivation potentials of the ancestral and human sequences to be significantly lower (p<0.0001 in each comparison) than that of the NWM when treated with estradiol, the most prevalent estrogen. We conclude the difference in fold activation is due to positive selection in the NWM ERβ ligand binding domain. Our study validates inferential methods for detecting adaptive evolution that predict functional consequences of nucleotide substitutions and points a way toward examining the functional consequences of positive Darwinian selection.

IFPA award in placentology lecture: Phylogenomic origins and evolution of the mammalian placenta

The placenta has had the most dynamic evolutionary history of all mammalian organs. It has undergone massive shifts in anatomy, physiology, and the way in which uterine and fetal tissue interact with one another during pregnancy. The human placenta is arguably the best studied amongst mammals, yet much about its function during pregnancy is not understood. The purpose of this paper is to outline the evolutionary history of the placenta, and to point out major gaps in the current state of knowledge. I also propose novel theoretical, experimental, and computational approaches that are likely to provide insight into the normal process of placentation and the role the placenta plays in the great obstetrical syndromes.

Placental origins of adverse pregnancy outcomes: potential molecular targets: an Executive Workshop Summary of the Eunice Kennedy Shriver National Institute of Child Health and Human Development

Although much progress is being made in understanding the molecular pathways in the placenta that are involved in the pathophysiology of pregnancy-related disorders, a significant gap exists in the utilization of this information for the development of new drug therapies to improve pregnancy outcome. On March 5-6, 2015, the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the National Institutes of Health sponsored a 2-day workshop titled Placental Origins of Adverse Pregnancy Outcomes: Potential Molecular Targets to begin to address this gap. Particular emphasis was given to the identification of important molecular pathways that could serve as drug targets and the advantages and disadvantages of targeting these particular pathways. This article is a summary of the proceedings of that workshop. A broad number of topics were covered that ranged from basic placental biology to clinical trials. This included research in the basic biology of placentation, such as trophoblast migration and spiral artery remodeling, and trophoblast sensing and response to infectious and noninfectious agents. Research findings in these areas will be critical for the formulation of the development of future treatments and the development of therapies for the prevention of a number of pregnancy disorders of placental origin that include preeclampsia, fetal growth restriction, and uterine inflammation. Research was also presented that summarized ongoing clinical efforts in the United States and in Europe that has tested novel interventions for preeclampsia and fetal growth restriction, including agents such as oral arginine supplementation, sildenafil, pravastatin, gene therapy with virally delivered vascular endothelial growth factor, and oxygen supplementation therapy. Strategies were also proposed to improve fetal growth by the enhancement of nutrient transport to the fetus by modulation of their placental transporters and the targeting of placental mitochondrial dysfunction and oxidative stress to improve placental health. The roles of microRNAs and placental-derived exosomes, as well as messenger RNAs, were also discussed in the context of their use for diagnostics and as drug targets. The workshop discussed the aspect of safety and pharmacokinetic profiles of potential existing and new therapeutics that will need to be determined, especially in the context of the unique pharmacokinetic properties of pregnancy and the hurdles and pitfalls of the translation of research findings into practice. The workshop also discussed novel methods of drug delivery and targeting during pregnancy with the use of macromolecular carriers, such as nanoparticles and biopolymers, to minimize placental drug transfer and hence fetal drug exposure. In closing, a major theme that developed from the workshop was that the scientific community must change their thinking of the pregnant woman and her fetus as a vulnerable patient population for which drug development should be avoided, but rather be thought of as a deprived population in need of more effective therapeutic interventions.

Extensive load of somatic CNVs in the human placenta

Placenta is a temporary, but indispensable organ in mammalian pregnancy. From its basic nature, it exhibits highly invasive tumour-like properties facilitating effective implantation through trophoblast cell proliferation and migration, and a critical role in pregnancy success. We hypothesized that similarly to cancer, somatic genomic rearrangements are promoted in the support of placental function. Here we present the first profiling of copy number variations (CNVs) in human placental genomes, showing an extensive load of somatic CNVs, especially duplications and suggesting that this phenomenon may be critical for normal gestation. Placental somatic CNVs were significantly enriched in genes involved in cell adhesion, immunity, embryonic development and cell cycle. Overrepresentation of imprinted genes in somatic duplications suggests that amplified gene copies may represent an alternative mechanism to support parent-of-origin specific gene expression. Placentas from pregnancy complications exhibited significantly altered CNV profile compared to normal gestations, indicative to the clinical implications of the study.

Integrating de novo transcriptome assembly and cloning to obtain chicken Ovocleidin-17 full-length cDNA

Efficiently obtaining full-length cDNA for a target gene is the key step for functional studies and probing genetic variations. However, almost all sequenced domestic animal genomes are not ‘finished’. Many functionally important genes are located in these gapped regions. It can be difficult to obtain full-length cDNA for which only partial amino acid/EST sequences exist. In this study we report a general pipeline to obtain full-length cDNA, and illustrate this approach for one important gene (Ovocleidin-17, OC-17) that is associated with chicken eggshell biomineralization. Chicken OC-17 is one of the best candidates to control and regulate the deposition of calcium carbonate in the calcified eggshell layer. OC-17 protein has been purified, sequenced, and has had its three-dimensional structure solved. However, researchers still cannot conduct OC-17 mRNA related studies because the mRNA sequence is unknown and the gene is absent from the current chicken genome. We used RNA-Seq to obtain the entire transcriptome of the adult hen uterus, and then conducted de novo transcriptome assembling with bioinformatics analysis to obtain candidate OC-17 transcripts. Based on this sequence, we used RACE and PCR cloning methods to successfully obtain the full-length OC-17 cDNA. Temporal and spatial OC-17 mRNA expression analyses were also performed to demonstrate that OC-17 is predominantly expressed in the adult hen uterus during the laying cycle and barely at immature developmental stages. Differential uterine expression of OC-17 was observed in hens laying eggs with weak versus strong eggshell, confirming its important role in the regulation of eggshell mineralization and providing a new tool for genetic selection for eggshell quality parameters. This study is the first one to report the full-length OC-17 cDNA sequence, and builds a foundation for OC-17 mRNA related studies. We provide a general method for biologists experiencing difficulty in obtaining candidate gene full-length cDNA sequences.

The evolution of embryo implantation

Embryo implantation varies widely in placental mammals. We review this variation in mammals with a special focus on two features: the depth of implantation and embryonic diapause. We discuss the two major types of implantation depth, superficial and interstitial, and map this character on a well-resolved molecular phylogenetic tree of placental mammals. We infer that relatively deep interstitial implantation has independently evolved at least eight times within placental mammals. Moreover, the superficial type of implantation represents the ancestral state for placental mammals. In addition, we review the genes involved in various phases of implantation, and suggest a future direction in investigating the molecular evolution of implantation-related genes.

Retroviruses facilitate the rapid evolution of the mammalian placenta

The mammalian placenta exhibits elevated expression of endogenous retroviruses (ERVs), but the evolutionary significance of this feature remains unclear. I propose that ERV-mediated regulatory evolution was, and continues to be, an important mechanism underlying the evolution of placental development. Many recent studies have focused on the co-option of ERV-derived genes for specific functional adaptations in the placenta. However, the co-option of ERV-derived regulatory elements could potentially lead to the incorporation of entire gene regulatory networks, which, I argue, would facilitate relatively rapid developmental evolution of the placenta. I suggest a model in which an ancient retroviral infection led to the establishment of the ancestral placental developmental gene network through the co-option of ERV-derived regulatory elements. Consequently, placental development would require elevated tolerance to ERV activity. This in turn would expose a continuous stream of novel ERV mutations that may have catalyzed the developmental diversification of the mammalian placenta.

Evolutionary perspectives into placental biology and disease

In all mammals including humans, development takes place within the protective environment of the maternal womb. Throughout gestation, nutrients and waste products are continuously exchanged between mother and fetus through the placenta. Despite the clear importance of the placenta to successful pregnancy and the health of both mother and offspring, relatively little is understood about the biology of the placenta and its role in pregnancy-related diseases. Given that pre- and peri-natal diseases involving the placenta affect millions of women and their newborns worldwide, there is an urgent need to understand placenta biology and development. Here, we suggest that the placenta is an organ under unique selective pressures that have driven its rapid diversification throughout mammalian evolution. The high divergence of the placenta complicates the use of non-human animal models and necessitates an evolutionary perspective when studying its biology and role in disease. We suggest that diversifying evolution of the placenta is primarily driven by intraspecies evolutionary conflict between mother and fetus, and that many pregnancy diseases are a consequence of this evolutionary force. Understanding how maternal-fetal conflict shapes both basic placental and reproductive biology - in all species - will provide key insights into diseases of pregnancy.

From PPROM to caul: The evolution of membrane rupture in mammals

Rupture of the extraembryonic membranes that form the gestational sac in humans is a typical feature of human parturition. However, preterm premature rupture of membranes (PPROM) occurs in approximately 1% of pregnancies, and is a leading cause of preterm birth. Conversely, retention of an intact gestational sac during parturition in the form of a caul is a rare occurrence. Understanding the molecular and evolutionary underpinnings of these disparate phenotypes can provide insight into both normal pregnancy and PPROM. Using phylogenetic techniques we reconstructed the evolution of the gestational sac phenotype at parturition in 55 mammal species representing all major viviparous mammal groups. We infer the ancestral state in therians, eutherians, and primates, as in humans, is a ruptured gestational sac at parturition. We present evidence that intact membranes at parturition have evolved convergently in diverse mammals including horses, elephants, and bats. In order to gain insight into the molecular underpinnings of the evolution of enhanced membrane integrity we also used comparative genomics techniques to reconstruct the evolution of a subset of genes implicated in PPROM, and find that four genes (ADAMTS2, COL1A1, COL5A1, LEPRE1) show significant evidence of increased nonsynonymous rates of substitution on lineages with intact membranes as compared to those with ruptured membranes. Among these genes, we also discovered that 17 human SNPs are associated with or near amino acid replacement sites in those mammals with intact membranes. These SNPs are candidate functional variants within humans, which may play roles in both PPROM and/or the retention of the gestational sac at birth.

Endogenous retroviruses function as species-specific enhancer elements in the placenta

The mammalian placenta is remarkably distinct between species, suggesting a history of rapid evolutionary diversification¹. To gain insight into the molecular drivers of placental evolution, we compared biochemically predicted enhancers between mouse and rat trophoblast stem cells (TSCs) and find that species-specific enhancers are highly enriched for endogenous retroviruses (ERVs) on a genome-wide level. One of these ERV families, RLTR13D5, contributes hundreds of mouse-specific H3K4me1/H3K27ac-defined enhancers that functionally bind Cdx2, Eomes, and Elf5 - core factors that define the TSC regulatory network. Furthermore, we demonstrate that RLTR13D5 is capable of driving gene expression in rat placental cells. Comparison with other tissues revealed that species-specific ERV enhancer activity is generally restricted to hypomethylated tissues, suggesting that tissues permissive to ERV activity gain access to an otherwise silenced source of regulatory variation. Overall, our results implicate ERV enhancer cooption as a mechanism underlying the striking evolutionary diversification of placental development.

Regulatory pathways controlling the endovascular invasive trophoblast cell lineage

Hemochorial placentation is characterized by trophoblast-directed uterine spiral artery remodeling. The rat and human both possess hemochorial placentation and exhibit remarkable similarities regarding the depth of trophoblast invasion and the extent of uterine vascular modification. In vitro and in vivo research methodologies have been established using the rat as an animal model to investigate the extravillous/invasive trophoblast lineage. With these research approaches, two signaling pathways controlling the differentiation and invasion of the trophoblast cell lineage have been identified: i) hypoxia/hypoxia inducible factor and ii) phosphatidylinositol 3-kinase/AKT/Fos like antigen 1. Dissection of these pathways has facilitated identification of fundamental regulators of the invasive trophoblast cell lineage.

Fetal programming by maternal stress: Insights from a conflict perspective

Maternal stress during pregnancy has pervasive effects on the offspring's physiology and behavior, including the development of anxious, reactive temperament and increased stress responsivity. These outcomes can be seen as the result of adaptive developmental plasticity: maternal stress hormones carry useful information about the state of the external world, which can be used by the developing fetus to match its phenotype to the predicted environment. This account, however, neglects the inherent conflict of interest between mother and fetus about the outcomes of fetal programming. The aim of this paper is to extend the adaptive model of prenatal stress by framing mother-fetus interactions in an evolutionary conflict perspective. In the paper, I show how a conflict perspective provides many new insights in the functions and mechanisms of fetal programming, with particular emphasis on human pregnancy. I then take advantage of those insights to make sense of some puzzling features of maternal and fetal physiology and generate novel empirical predictions.

Rat placentation: an experimental model for investigating the hemochorial maternal-fetal interface

The rat possesses hemochorial placentation with deep intrauterine trophoblast cell invasion and trophoblast-directed uterine spiral artery remodeling; features shared with human placentation. Recognition of these similarities spurred the establishment of in vitro and in vivo research methods using the rat as an animal model to address mechanistic questions regarding development of the hemochorial placenta. The purpose of this review is to provide the requisite background to help move the rat to the forefront in placentation research.

Review: Toward an integrated evolutionary understanding of the mammalian placenta

The placenta is fundamentally important for the success of pregnancy. Disruptions outside the normal range for placental function can result in pregnancy failure and other complications. The anatomy of the placenta varies greatly across mammals, as do key parameters in pregnancy such as neonatal body mass, length of gestation and number of offspring per pregnancy. An accurate understanding of the evolution of the mammalian placenta will require at minimum the integration of anatomical, developmental, physiological, genetic, and epigenetic data. Currently available data suggest that the placenta is a dynamic organ that has evolved rapidly in a lineage specific manner. Examination of the placenta from the perspective of human evolution shows that many anatomical features of the human placenta are relatively conserved. Despite the anatomical conservation of the human placenta there are many recently evolved placenta-specific genes (e.g. CGB, LGALS13, GH2) that are important in the development and function of the human placenta. Other mammalian genomes have also evolved specific suites of placenta-expressed genes. For example, rodents have undergone expansions of the cathepsin and prolactin families, and artiodactyls have expanded their suite of pregnancy-associated glycoproteins. In addition to lineage specific birth and death of gene family members, the pattern of imprinted loci varies greatly among species. Taken together, these studies suggest that a strategy reliant upon the sampling of placentally expressed and imprinted genes from a phylogenetically diverse range of species is appropriate for unraveling the conserved and derived aspects of placental biology.

Maternal-fetal conflict: rapidly evolving proteins in the rodent placenta

Conflicting evolutionary interests between mother and offspring are hypothesized to drive an evolutionary arms race during mammalian pregnancy, and thus, positive selection may cause the rapid divergence of placental proteins that affect maternal or fetal fitness. We investigated the genomic consequences of placental expression in rodents and report that a substantial proportion (20.5%) of genes specifically expressed in the mature placenta are rapidly evolving. Moreover, we found that most rapidly evolving genes belong to just three pregnancy-related gene families: placental cathepsins, prolactins, and placental carcinoembryonic antigens. We then sequenced the most rapidly evolving gene, trophoblast-specific protein alpha (Tpbpa), in nine different Mus species/subspecies and found evidence of positive selection within the Mus lineage, with an excess of nonsynonymous changes clustering near a functionally important interaction site. Together, these results suggest that placental proteins, which mediate interactions between mother and offspring, often may be the targets of evolutionary conflict.