Genetic and epigenetic incompatibilities underlie hybrid dysgenesis in Peromyscus

Creation of true interspecies hybrids: Rescue of hybrid class with hybrid cytoplasm affecting growth and metabolism

Interspecies hybrids have nuclear contributions from two species but oocyte cytoplasm from only one. Species discordance may lead to altered nuclear reprogramming of the foreign paternal genome. We reasoned that initial reprogramming in same species cytoplasm plus creation of hybrids with zygote cytoplasm from both species, which we describe here, might enhance nuclear reprogramming and promote hybrid development. We report in Mus species that (i) mammalian nuclear/cytoplasmic hybrids can be created, (ii) they allow development and viability of a previously missing and uncharacterized hybrid class, (iii) different oocyte cytoplasm environments lead to different phenotypes of same nuclear hybrid genotype, and (iv) the novel hybrids exhibit sex ratio distortion with the absence of female progeny and represent a mammalian exception to Haldane's rule. Our results emphasize that interspecies hybrid phenotypes are not only the result of nuclear gene epistatic interactions but also cytonuclear interactions and that the latter have major impacts on fetal and placental growth and development.

United by conflict: Convergent signatures of parental conflict in angiosperms and placental mammals

Endosperm in angiosperms and placenta in eutherians are convergent innovations for efficient embryonic nutrient transfer. Despite advantages, this reproductive strategy incurs metabolic costs that maternal parents disproportionately shoulder, leading to potential inter-parental conflict over optimal offspring investment. Genomic imprinting-parent-of-origin-biased gene expression-is fundamental for endosperm and placenta development and has convergently evolved in angiosperms and mammals, in part, to resolve parental conflict. Here, we review the mechanisms of genomic imprinting in these taxa. Despite differences in the timing and spatial extent of imprinting, these taxa exhibit remarkable convergence in the molecular machinery and genes governing imprinting. We then assess the role of parental conflict in shaping evolution within angiosperms and eutherians using four criteria: 1) Do differences in the extent of sibling relatedness cause differences in the inferred strength of parental conflict? 2) Do reciprocal crosses between taxa with different inferred histories of parental conflict exhibit parent-of-origin growth effects? 3) Are these parent-of-origin growth effects caused by dosage-sensitive mechanisms and do these loci exhibit signals of positive selection? 4) Can normal development be restored by genomic perturbations that restore stoichiometric balance in the endosperm/placenta? Although we find evidence for all criteria in angiosperms and eutherians, suggesting that parental conflict may help shape their evolution, many questions remain. Additionally, myriad differences between the two taxa suggest that their respective biologies may shape how/when/where/to what extent parental conflict manifests. Lastly, we discuss outstanding questions, highlighting the power of comparative work in quantifying the role of parental conflict in evolution.

Imprinting as Basis for Complex Evolutionary Novelties in Eutherians

The epigenetic phenomenon of genomic imprinting is puzzling. While epigenetic modifications in general are widely known in most species, genomic imprinting in the animal kingdom is restricted to autosomes of therian mammals, mainly eutherians, and to a lesser extent in marsupials. Imprinting causes monoallelic gene expression. It represents functional haploidy of certain alleles while bearing the evolutionary cost of diploidization, which is the need of a complex cellular architecture and the danger of producing aneuploid cells by mitotic and meiotic errors. The parent-of-origin gene expression has stressed many theories. Most prominent theories, such as the kinship (parental conflict) hypothesis for maternally versus paternally derived alleles, explain only partial aspects of imprinting. The implementation of single-cell transcriptome analyses and epigenetic research allowed detailed study of monoallelic expression in a spatial and temporal manner and demonstrated a broader but much more complex and differentiated picture of imprinting. In this review, we summarize all these aspects but argue that imprinting is a functional haploidy that not only allows a better gene dosage control of critical genes but also increased cellular diversity and plasticity. Furthermore, we propose that only the occurrence of allele-specific gene regulation mechanisms allows the appearance of evolutionary novelties such as the placenta and the evolutionary expansion of the eutherian brain.

Regulatory and evolutionary impact of DNA methylation in two songbird species and their naturally occurring F1 hybrids

BACKGROUND

Regulation of transcription by DNA methylation in 5'-CpG-3' context is a widespread mechanism allowing differential expression of genetically identical cells to persist throughout development. Consequently, differences in DNA methylation can reinforce variation in gene expression among cells, tissues, populations, and species. Despite a surge in studies on DNA methylation, we know little about the importance of DNA methylation in population differentiation and speciation. Here we investigate the regulatory and evolutionary impact of DNA methylation in five tissues of two Ficedula flycatcher species and their naturally occurring F1 hybrids.

RESULTS

We show that the density of CpG in the promoters of genes determines the strength of the association between DNA methylation and gene expression. The impact of DNA methylation on gene expression varies among tissues with the brain showing unique patterns. Differentially expressed genes between parental species are predicted by genetic and methylation differentiation in CpG-rich promoters. However, both these factors fail to predict hybrid misexpression suggesting that promoter mismethylation is not a main determinant of hybrid misexpression in Ficedula flycatchers. Using allele-specific methylation estimates in hybrids, we also determine the genome-wide contribution of cis- and trans effects in DNA methylation differentiation. These distinct mechanisms are roughly balanced in all tissues except the brain, where trans differences predominate.

CONCLUSIONS

Overall, this study provides insight on the regulatory and evolutionary impact of DNA methylation in songbirds.

Evolution of gene expression across brain regions in behaviourally divergent deer mice

The evolution of innate behaviours is ultimately due to genetic variation likely acting in the nervous system. Gene regulation may be particularly important because it can evolve in a modular brain-region specific fashion through the concerted action of cis- and trans-regulatory changes. Here, to investigate transcriptional variation and its regulatory basis across the brain, we perform RNA sequencing (RNA-Seq) on ten brain subregions in two sister species of deer mice (Peromyscus maniculatus and P. polionotus)-which differ in a range of innate behaviours, including their social system-and their F1 hybrids. We find that most of the variation in gene expression distinguishes subregions, followed by species. Interspecific differential expression (DE) is pervasive (52-59% of expressed genes), whereas the number of DE genes between sexes is modest overall (~3%). Interestingly, the identity of DE genes varies considerably across brain regions. Much of this modularity is due to cis-regulatory divergence, and while 43% of genes were consistently assigned to the same gene regulatory class across subregions (e.g. conserved, cis- or trans-regulatory divergence), a similar number were assigned to two or more different gene regulatory classes. Together, these results highlight the modularity of gene expression differences and divergence in the brain, which may be key to explain how the evolution of brain gene expression can contribute to the astonishing diversity of animal behaviours.

Mechanisms of Intrinsic Postzygotic Isolation: From Traditional Genic and Chromosomal Views to Genomic and Epigenetic Perspectives

Intrinsic postzygotic isolation typically appears as reduced viability or fertility of interspecific hybrids caused by genetic incompatibilities between diverged parental genomes. Dobzhansky-Muller interactions among individual genes, and chromosomal rearrangements causing problems with chromosome synapsis and recombination in meiosis, have both long been considered as major mechanisms behind intrinsic postzygotic isolation. Recent research has, however, suggested that the genetic basis of intrinsic postzygotic isolation can be more complex and involves, for example, overall divergence of the DNA sequence or epigenetic changes. Here, we review the mechanisms of intrinsic postzygotic isolation from genic, chromosomal, genomic, and epigenetic perspectives across diverse taxa. We provide empirical evidence for these mechanisms, discuss their importance in the speciation process, and highlight questions that remain unanswered.

Evolution of parent-of-origin effects on placental gene expression in house mice

The mammalian placenta is a hotspot for the evolution of genomic imprinting, a form of gene regulation that involves the parent-specific epigenetic silencing of one allele. Imprinted genes are central to placental development and are thought to contribute to the evolution of reproductive barriers between species. However, it is unclear how rapidly imprinting evolves or how functional specialization among placental tissues influences the evolution of imprinted expression. We compared parent-of-origin expression bias across functionally distinct placental layers sampled from reciprocal crosses within three closely related lineages of mice ( Mus ). Using genome-wide gene expression and DNA methylation data from fetal and maternal tissues, we developed an analytical strategy to minimize pervasive bias introduced by maternal contamination of placenta samples. We corroborated imprinted expression at 42 known imprinted genes and identified five candidate imprinted genes showing parent-of-origin specific expression and DNA methylation. Paternally-biased expression was enriched in the labyrinth zone, a layer specialized in nutrient transfer, and maternally-biased genes were enriched in the junctional zone, which specializes in modulation of maternal physiology. Differentially methylated regions were predominantly determined through epigenetic modification of the maternal genome and were associated with both maternally- and paternally-biased gene expression. Lastly, comparisons between lineages revealed a small set of co-regulated genes showing rapid divergence in expression levels and imprinted status in the M. m. domesticus lineage. Together, our results reveal important links between core functional elements of placental biology and the evolution of imprinted gene expression among closely related rodent species.

Speciation and development

Understanding general principles about the origin of species remains one of the foundational challenges in evolutionary biology. The genomic divergence between groups of individuals can spawn hybrid inviability and hybrid sterility, which presents a tantalizing developmental problem. Divergent developmental programs may yield either conserved or divergent phenotypes relative to ancestral traits, both of which can be responsible for reproductive isolation during the speciation process. The genetic mechanisms of developmental evolution involve cis- and trans-acting gene regulatory change, protein-protein interactions, genetic network structures, dosage, and epigenetic regulation, all of which also have roots in population genetic and molecular evolutionary processes. Toward the goal of demystifying Darwin's "mystery of mysteries," this review integrates microevolutionary concepts of genetic change with principles of organismal development, establishing explicit links between population genetic process and developmental mechanisms in the production of macroevolutionary pattern. This integration aims to establish a more unified view of speciation that binds process and mechanism.

The kin selection theory of genomic imprinting and modes of reproduction in the eusocial Hymenoptera

Genomic imprinting is known from flowering plants and mammals but has not been confirmed for the Hymenoptera even though the eusocial Hymenoptera are prime candidates for this peculiar form of gene expression. Here, the kin selection theory of genomic imprinting is reviewed and applied to the eusocial Hymenoptera. The evidence for imprinting in eusocial Hymenoptera with the typical mode of reproduction, involving the sexual production of diploid female offspring, which develop into workers or gynes, and the arrhenotokous parthenogenesis of haploid males, is also reviewed briefly. However, the focus of this review is how atypical modes of reproduction, involving thelytokous parthenogenesis, hybridisation and androgenesis, may also select for imprinting. In particular, naturally occurring hybridisation in several genera of ants may provide useful tests of the role of kin selection in the evolution of imprinting. Hybridisation is expected to disrupt the coadaptation of antagonistically imprinted loci, and thus affect the phenotypes of hybrids. Some of the limited data available on hybrid worker reproduction and on colony sex ratios support predictions about patterns of imprinting derived from kin selection theory.

Genetic Analysis of the Stereotypic Phenotype in Peromyscus maniculatus (deer mice)

Peromyscus maniculatus, including the laboratory stock BW, have been used as a model organism for autism spectrum disorder and obsessive-compulsive disorder because of the high occurrence of stereotypy. Several studies have identified neurological and environmental components of the phenotype; however, the heritability of the phenotype has not been examined. This study characterizes the incidence and heritability of vertical jumping stereotypy (VS) and backflipping (BF) behavior in the BW stock of the Peromyscus Genetic Stock Center, which are indicative of autism spectrum disorders. In addition, interspecies crosses between P. maniculatus and P. polionotus were also performed to further dissect genetically stereotypic behavior. The inheritance pattern of VS suggests that multiple genes result in a quantitative trait with low VS being dominant over high VS. The inheritance pattern of BF suggests that fewer genes are involved, with one allele causing BF in a dominant fashion. An association analysis in BW could reveal the underlying genetic loci associated with stereotypy in P. maniculatus, especially for the BF behavior.

Indirect Effects of Parental Conflict on Conspecific Offspring Development

AbstractHybrid seed inviability is a common reproductive barrier in angiosperms. Recent work suggests that the rapid evolution of hybrid seed inviability may, in part, be due to conflict between maternal and paternal optima for resource allocation to developing offspring (i.e., parental conflict). However, parental conflict requires that paternally derived resource-acquiring alleles impose a maternal cost. I test this requirement using three closely related species in the Mimulus guttatus species complex that exhibit significant hybrid seed inviability and differ in their inferred histories of parental conflict. I show that the presence of hybrid seeds significantly affects conspecific seed size for almost all crosses, such that conspecific seeds are smaller after developing with hybrids sired by fathers with a stronger history of conflict and are larger after developing with hybrids sired by fathers with a weaker history of conflict. This work demonstrates a potential maternal cost of paternally derived alleles and also has implications for species fitness in secondary contact.

Comparative studies on speciation: 30 years since Coyne and Orr

Understanding the processes of population divergence and speciation remains a core question in evolutionary biology. For nearly a hundred years evolutionary geneticists have characterized reproductive isolation (RI) mechanisms and specific barriers to gene flow required for species formation. The seminal work of Coyne and Orr provided the first comprehensive comparative analysis of speciation. By combining phylogenetic hypotheses and species range data with estimates of genetic divergence and multiple mechanisms of RI across Drosophila, Coyne and Orr's influential meta-analyses answered fundamental questions and motivated new analyses that continue to push the field forward today. Now 30 years later, we revisit the five questions addressed by Coyne and Orr, identifying results that remain well supported and others that seem less robust with new data. We then consider the future of speciation research, with emphasis on areas where novel methods and data motivate potential progress. While the literature remains biased towards Drosophila and other model systems, we are enthusiastic about the future of the field.

X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters

Embryonic development in mammals is highly sensitive to changes in gene expression within the placenta. The placenta is also highly enriched for genes showing parent-of-origin or imprinted expression, which is predicted to evolve rapidly in response to parental conflict. However, little is known about the evolution of placental gene expression, or if divergence of placental gene expression plays an important role in mammalian speciation. We used crosses between two species of dwarf hamsters (Phodopus sungorus and Phodopus campbelli) to examine the genetic and regulatory underpinnings of severe placental overgrowth in their hybrids. Using quantitative genetic mapping and mitochondrial substitution lines, we show that overgrowth of hybrid placentas was primarily caused by genetic differences on the maternally inherited P. sungorus X chromosome. Mitochondrial interactions did not contribute to abnormal hybrid placental development, and there was only weak correspondence between placental disruption and embryonic growth. Genome-wide analyses of placental transcriptomes from the parental species and first- and second-generation hybrids revealed a central group of co-expressed X-linked and autosomal genes that were highly enriched for maternally biased expression. Expression of this gene network was strongly correlated with placental size and showed widespread misexpression dependent on epistatic interactions with X-linked hybrid incompatibilities. Collectively, our results indicate that the X chromosome is likely to play a prominent role in the evolution of placental gene expression and the accumulation of hybrid developmental barriers between mammalian species.

Haldane's rule in the placenta: Sex-biased misregulation of the Kcnq1 imprinting cluster in hybrid mice

Hybrid phenotypes that contribute to postzygotic reproductive isolation often exhibit pronounced asymmetry, both between reciprocal crosses and between the sexes in accordance with Haldane's rule. Inviability in mammalian hybrids is associated with parent-of-origin placental growth abnormalities for which misregulation of imprinted gene (IGs) is the leading candidate mechanism. However, direct evidence for the involvement of IGs in hybrid growth dysplasia is limited. We used transcriptome and reduced representation bisulfite sequencing to conduct the first genome-scale assessment of the contribution of IGs to parent-of-origin placental growth dysplasia in the cross between the house mouse (Mus musculus domesticus) and the Algerian mouse (Mus spretus). IGs with transgressive expression and methylation were concentrated in the Kcnq1 cluster, which contains causal genes for prenatal growth abnormalities in mice and humans. Hypermethylation of the cluster's imprinting control region, and consequent misexpression of the genes Phlda2 and Ascl2, is a strong candidate mechanism for transgressive placental undergrowth. Transgressive placental and gene regulatory phenotypes, including expression and methylation in the Kcnq1 cluster, were more extreme in hybrid males. Although consistent with Haldane's rule, male-biased defects are unexpected in rodent placenta because the X-chromosome is effectively hemizygous in both sexes. In search of an explanation, we found evidence of leaky imprinted (paternal) X-chromosome inactivation in hybrid female placenta, an epigenetic disturbance that may buffer females from the effects of X-linked incompatibilities to which males are fully exposed. Sex differences in chromatin structure on the X and sex-biased maternal effects are nonmutually exclusive alternative explanations for adherence to Haldane's rule in hybrid placenta. The results of this study contribute to understanding the genetic basis of hybrid inviability in mammals, and the role of IGs in speciation.

Patterns of Hybrid Seed Inviability in the Mimulus guttatus sp. Complex Reveal a Potential Role of Parental Conflict in Reproductive Isolation

Genomic conflicts may play a central role in the evolution of reproductive barriers. Theory predicts that early-onset hybrid inviability may stem from conflict between parents for resource allocation to offspring. Here, we describe M. decorus: a group of cryptic species within the M. guttatus species complex that are largely reproductively isolated by hybrid seed inviability (HSI). HSI between M. guttatus and M. decorus is common and strong, but populations of M. decorus vary in the magnitude and directionality of HSI with M. guttatus. Patterns of HSI between M. guttatus and M. decorus, as well as within M. decorus, conform to the predictions of parental conflict: first, reciprocal F1s exhibit size differences and parent-of-origin-specific endosperm defects; second, the extent of asymmetry between reciprocal F1 seed size is correlated with asymmetry in HSI; and third, inferred differences in the extent of conflict predict the extent of HSI between populations. We also find that HSI is rapidly evolving, as populations that exhibit the most HSI are each others' closest relative. Lastly, although all populations appear largely outcrossing, we find that the differences in the inferred strength of conflict scale positively with π, suggesting that demographic or life history factors other than transitions to self-fertilization may influence the rate of parental-conflict-driven evolution. Overall, these patterns suggest the rapid evolution of parent-of-origin-specific resource allocation alleles coincident with HSI within and between M. guttatus and M. decorus. Parental conflict may therefore be an important evolutionary driver of reproductive isolation.

Blood transcriptome analysis in a buck-ewe hybrid and its parents

Examples of living sheep-goat hybrids are rare, mainly due to incorrect chromosome pairing, which is thought to be the main cause for species incompatibility. This case represents the first report of a buck-ewe hybrid and the first mammalian hybrid to be analyzed with next generation sequencing. The buck-ewe hybrid had an intermediate karyotype to the parental species, with 57 chromosomes. Analysis of the blood transcriptomes of the hybrid and both parents revealed that gene expression levels differed between the hybrid and its parents. This could be explained in part by age-dependent differences in gene expression. Contribution to the geep transcriptome was larger from the paternal, compared to the maternal, genome. Furthermore, imprinting patterns deviated considerably from what is known from other mammals. Potentially deleterious variants appeared to be compensated for by monoallelic expression of transcripts. Hence, the data imply that the buck-ewe hybrid compensated for the phylogenetic distance between the parental species by several mechanisms: adjustment of gene expression levels, adaptation to imprinting incompatibilities, and selective monoallelic expression of advantageous transcripts. This study offers a unique opportunity to gain insights into the transcriptome biology and regulation of a hybrid mammal.

How conflict shapes evolution in poeciliid fishes

In live-bearing animal lineages, the evolution of the placenta is predicted to create an arena for genomic conflict during pregnancy, drive patterns of male sexual selection, and increase the rate of speciation. Here we test these predictions of the viviparity driven conflict hypothesis (VDCH) in live-bearing poecilid fishes, a group showing multiple independent origins of placentation and extreme variation in male sexually selected traits. As predicted, male sexually selected traits are only gained in lineages that lack placentas; while there is little or no influence of male traits on the evolution of placentas. Both results are consistent with the mode of female provisioning governing the evolution of male attributes. Moreover, it is the presence of male sexually selected traits (pre-copulatory), rather than placentation (post-copulatory), that are associated with higher rates of speciation. These results highlight a causal interaction between female reproductive mode, male sexual selection and the rate of speciation, suggesting a role for conflict in shaping diverse aspects of organismal biology.

The viviparity driven conflict hypothesis predicts the evolution of the placenta will suppress the evolution of traits associated with pre-copulatory mate choice and accelerate speciation rate. Furness et al. support the former and disprove the latter predictions with comparative analyses of the poecilid fishes.

Maternal and paternal origin differentially affect prosocial behavior and neural mechanisms in prairie voles

This study tested the hypotheses that maternal and paternal effects differentially influence expression of their offspring's adult behavior and underlying neural mechanisms. We predicted that maternal influences would be greater than paternal influences on male offspring. We tested these hypotheses by cross-breeding two phenotypically-, behaviorally- and neuroanatomically-distinct populations of prairie voles (Microtus ochrogaster) from Illinois, which are highly prosocial, and Kansas, which are significantly less prosocial. Females from each population were crossed with males from the other population. F₁ crosses were tested as adults to determine the effect of parentage on the expression of prosocial behavior and aggression, using a same-sex dyadic encounter and a heterosexual partner preference test, and for the expression of oxytocin (OT) and arginine vasopressin (AVP) in the paraventricular nucleus of the hypothalamus (PVN). As predicted, all significant differences in males, behavioral, OT and AVP immunoreactivity, were associated exclusively with maternal influences. There was a significant effect of treatment in the OT immunoreactivity of females. The effect of treatment in females' OT was associated with an interaction of population and sex, while same-sex social interactions differences were associated with population. Finally, in females, paternity influenced heterosexual bonds, with females with Illinois sires forming a partner preference. The results indicate that maternal influences dominate in male offspring, suggesting a parent-of-origin effect, while paternal effects are limited to selected prosocial behavioral expression in daughters.

Ultrasonographic measurements in first trimester concepti identify predictors of birth weight and postnatal development in cattle

The placenta is a major driver of prenatal growth and involved in programming of postnatal performance. We therefore determined placental and embryo-fetal ultrasonographic parameters in early pregnancy and their relationships with birth weight and postnatal weights in a Bos indicus-Bos taurus composite beef cattle population. Pregnancies were generated in 2-yr-old Droughtmaster heifers by artificial insemination after estrus synchronization in 2 consecutive years (2009, n = 36 and 2010, n = 57), with a subset of 2010 heifers used again as lactating 3-yr-old cows in 2011 (n = 24). Each cohort was managed as 1 contemporary group for measurements of Corpus luteum diameter, amnion length and width, placentome width and thickness, and embryo-fetal crown-rump length, at 7 and 8 wk of gestation. This was followed by recordings of birth weight, branding weight at 5 to 6 mo of age and weaning weight 2 mo later. At a significance threshold of P < 0.05, placentome thickness at week 7 was negatively correlated with weights at birth (r = -0.23), branding (r = -0.25), and weaning (r = -0.35), whereas placentome width at week 7 (r = 0.24) and thickness at week 8 (r = 0.29) were positively correlated with birth weight. Thicker placentomes in males at week 7 (7%) difference mirrored sex differences in weights at birth (7%), branding (10%), and weaning (6%). The sex difference trend for birth weight was not consistent across sire-year combinations, ranging from -3.2 to +4.7 kg (birth weight of males - females per sire). These results support the hypothesis that placental parameters at the transition from embryo to fetal stage are major predictors of fetal and postnatal growth, albeit with significant environmentally induced plasticity, in stabilized B. indicus-B. taurus composite populations, and suggest that elements of B. indicus-B. taurus reciprocal differences in birth weight persist in composite populations.

Reciprocal F1 Hybrids of Two Inbred Mouse Strains Reveal Parent-of-Origin and Perinatal Diet Effects on Behavior and Expression

Parent-of-origin effects (POE) in mammals typically arise from maternal effects or imprinting. In some instances, such POE have been associated with psychiatric disorders, as well as with changes in a handful of animal behaviors. However, POE on complex traits such as behavior remain largely uncharacterized. Moreover, although both behavior and epigenetic effects are known to be modified by perinatal environmental exposures such as nutrient deficiency, the architecture of such environment-by-POE is mostly unexplored. To study POE and environment-by-POE, we employ a relatively neglected but especially powerful experimental system for POE-detection: reciprocal F1 hybrids (RF1s). We exposed female NOD/ShiLtJ×C57Bl/6J and C57Bl/6J×NOD/ShiLtJ mice, perinatally, to one of four different diets, then after weaning recorded a set of behaviors that model psychiatric disease. Whole-brain microarray expression data revealed an imprinting-enriched set of 15 genes subject to POE. The most-significant expression POE, on the non-imprinted gene Carmil1 (a.k.a. Lrrc16a), was validated using qPCR in the same and in a new set of mice. Several behaviors, especially locomotor behaviors, also showed POE. Bayesian mediation analysis suggested Carmil1 expression suppresses behavioral POE, and that the imprinted gene Airn suppresses POE on Carmil1 expression. A suggestive diet-by-POE was observed on percent center time in the open field test, and a significant diet-by-POE was observed on one imprinted gene, Mir341, and on 16 non-imprinted genes. The relatively small, tractable set of POE and diet-by-POE detected on behavior and expression here motivates further studies examining such effects across RF1s on multiple genetic backgrounds.

An updated genetic map of Peromyscus with chromosomal assignment of linkage groups

Species across the rodent genus Peromyscus have become prominent models for studying diverse mechanistic and evolutionary processes, including chromosome evolution, infectious disease transmission and human health, ecological adaptation, coat color variation, and parental care. Supporting such diverse research programs has been the development of genetic and genomic resources for species within this genus, including genome data, interspecific chromosome homologies, and a recently developed genetic map. Based on interspecific hybrids between the deer mouse (Peromyscus maniculatus bairdii) and the old-field, or beach, mouse (Peromyscus polionotus) and backcross progeny to Peromyscus maniculatus, a linkage map was developed based on 190 genes and 141 microsatellite loci. However, resolution of several linkage groups with respect to chromosome assignment was lacking and four chromosomes (8, 16, 20, and 21) were not clearly delineated with linkage data alone. The recent development of a high-density map for Peromyscus proved ineffective in resolving chromosome linkage for these four chromosomes. Herein we present an updated linkage map for Peromyscus maniculatus, including linkage group-chromosome assignments, using fluorescence in situ hybridization mapping of BACs and whole chromosome paints. We resolve the previously conflicting chromosome assignment of linkage groups to Chromosomes 8, 16, 20, and 21, and confirm the assignment of linkage groups to Chromosomes 18 and 22. This updated linkage map with validated chromosome assignment provides a solid foundation for chromosome nomenclature for this species.

Selfish X chromosomes and speciation

In two papers published at about the same time almost thirty years ago, Frank (Evolution, 45, 1991a, 262) and Hurst and Pomiankowski (Genetics, 128, 1991, 841) independently suggested that divergence of meiotic drive systems-comprising genes that cheat meiosis and genes that suppress this cheating-might provide a general explanation for Haldane's rule and the large X-effect in interspecific hybrids. Although at the time, the idea was met with skepticism and a conspicuous absence of empirical support, the tide has since turned. Some of the clearest mechanistic explanations we have for hybrid male sterility involve meiotic drive systems, and several other cases of hybrid sterility are suggestive of a role for meiotic drive. In this article, I review these ideas and their descendants and catalog the current evidence for the meiotic drive model of speciation. In addition, I suggest that meiotic drive is not the only intragenomic conflict to involve the X chromosome and contribute to hybrid incompatibility. Sexually and parentally antagonistic selection pressures can also pit the X chromosome and autosomes against each other. The resulting intragenomic conflicts should lead to co-evolution within populations and divergence between them, thus increasing the likelihood of incompatibilities in hybrids. I provide a sketch of these ideas and interpret some empirical patterns in the light of these additional X-autosome conflicts.

Evolution and Genetics of Precocious Burrowing Behavior in Peromyscus Mice

A central challenge in biology is to understand how innate behaviors evolve between closely related species. One way to elucidate how differences arise is to compare the development of behavior in species with distinct adult traits [1]. Here, we report that Peromyscus polionotus is strikingly precocious with regard to burrowing behavior, but not other behaviors, compared to its sister species P. maniculatus. In P. polionotus, burrows were excavated as early as 17 days of age, whereas P. maniculatus did not build burrows until 10 days later. Moreover, the well-known differences in burrow architecture between adults of these species-P. polionotus adults excavate long burrows with an escape tunnel, whereas P. maniculatus dig short, single-tunnel burrows [2-4]-were intact in juvenile burrowers. To test whether this juvenile behavior is influenced by early-life environment, we reciprocally cross-fostered pups of both species. Fostering did not alter the characteristic burrowing behavior of either species, suggesting that these differences are genetic. In backcross hybrids, we show that precocious burrowing and adult tunnel length are genetically correlated and that a P. polionotus allele linked to tunnel length variation in adults is also associated with precocious onset of burrowing in juveniles, suggesting that the same genetic region-either a single gene with pleiotropic effects or linked genes-influences distinct aspects of the same behavior at these two life stages. These results raise the possibility that genetic variants affect behavioral drive (i.e., motivation) to burrow and thereby affect both the developmental timing and adult expression of burrowing behavior.

Ancestry-Specific Methylation Patterns in Admixed Offspring from an Experimental Coyote and Gray Wolf Cross

Reduced fitness of admixed individuals is typically attributed to genetic incompatibilities. Although mismatched genomes can lead to fitness changes, in some cases the reduction in hybrid fitness is subtle. The potential role of transcriptional regulation in admixed genomes could provide a mechanistic explanation for these discrepancies, but evidence is lacking for nonmodel organisms. Here, we explored the intersection of genetics and gene regulation in admixed genomes derived from an experimental cross between a western gray wolf and western coyote. We found a significant positive association between methylation and wolf ancestry, and identified outlier genes that have been previously implicated in inbreeding-related, or otherwise deleterious, phenotypes. We describe a pattern of site-specific, rather than genome-wide, methylation driven by inter-specific hybridization. Epigenetic variation is thus suggested to play a nontrivial role in both maintaining and combating mismatched genotypes through putative transcriptional mechanisms. We conclude that the regulation of gene expression is an underappreciated key component of hybrid genome functioning, but could also act as a potential source of novel and beneficial adaptive variation in hybrid offspring.

Prenatal exposure to valproic acid increases miR-132 levels in the mouse embryonic brain

Background

MicroRNAs, small non-coding RNAs, are highly expressed in the mammalian brain, and the dysregulation of microRNA levels may be involved in neurodevelopmental disorders such as autism spectrum disorder (ASD). In the present study, we examined whether prenatal valproic acid (VPA) exposure affects levels of microRNAs, especially the brain specific and enriched microRNAs, in the mouse embryonic brain.

Results

Prenatal exposure to VPA at E12.5 immediately increased miR-132 levels, but not miR-9 or miR-124 levels, in the male embryonic brain. Prenatal exposure to VPA at E12.5 also increased miR-132 levels in the female embryonic brain. We further found that the prenatal exposure to VPA at E12.5 increased mRNA levels of Arc, c-Fos and brain-derived neurotrophic factor in both male and female embryonic brains, prior to miR-132 expression. In contrast, prenatal exposure to VPA at E14.5 did not affect miR-132 levels in either male or female embryonic brain. The prenatal VPA exposure at E12.5 also decreased mRNA levels of methyl-CpG-binding protein 2 and Rho GTPase-activating protein p250GAP, both of which are molecular targets of miR-132. Furthermore, RNA sequence analysis revealed that prenatal VPA exposure caused changes in several microRNA levels other than miR-132 in the embryonic whole brain.

Conclusions

These findings suggest that the alterations in neuronal activity-dependent microRNAs levels, including an increased level of miR-132, in the embryonic period, at least in part, underlie the ASD-like behaviors and cortical pathology produced by prenatal VPA exposure.

Determination of dosage compensation and comparison of gene expression in a triploid hybrid fish

Background

Polyploidy and hybridization are both recognized as major forces in evolution. Most of our current knowledge about differences in gene regulation in polyploid hybrids comes from plant studies. The gene expression of diverged genomes and regulatory interactions are still unclear in lower vertebrates.

Results

We generated 229 million cleaned reads (42.23 Gbp) from triploid of maternal grass carp (Ctenopharyngodon idellus, Cyprininae, 2n = 48) × paternal blunt snout bream (Megalobrama amblycephala, Cultrinae, 2n = 48) and their diploid parents using next-generation sequencing. In total, 157,878 contigs were assembled and 15,444 genes were annotated. We examined gene expression level changes among the parents and their triploid offspring. The mechanisms of dosage compensation that reduced triploid expression levels to the diploid state were determined in triploid fish. In this situation, novel gene expression and gene silencing were observed. Then, we established a model to determine the extent and direction of expression level dominance (ELD) and homoeolog expression bias (HEB) based on the relative expression level among the parents and their triploid offspring.

Conclusions

Our results showed that the genome-wide ELD was biased toward maternal genome in triploid. Extensive alterations in homoeolog expression suggested a combination of regulatory and epigenetic interactions through the transcriptome network. Additionally, the expression patterns of growth genes provided insights into the relationship between the characteristics of growth and underlying mechanisms in triploids. Regulation patterns of triploid state suggest that various expression levels from the initial genomic merger have important roles in adaptation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3424-5) contains supplementary material, which is available to authorized users.

Peromyscus transcriptomics: Understanding adaptation and gene expression plasticity within and between species of deer mice

Deer mice in the genus Peromyscus occupy nearly every terrestrial habitat in North America, and have a long history as subjects of behavioral, ecological, evolutionary, and physiological study. Recent advances in transcriptomics, the study of the complete set of RNA transcripts produced by certain cell types or under certain conditions, have contributed to the development of Peromyscus as a model system. We review the recent use of transcriptomics to investigate how natural selection and gene expression plasticity contribute to the existence of deer mice in challenging environments such as highlands, deserts, and cities across North America. Transcriptomics also holds great promise for elucidating the genetic basis of mating systems and other behaviors in Peromyscus, but has to date been underutilized for developmental biology and disease studies. Future Peromyscus studies should apply robust comparative frameworks to analyze the transcriptomics of multiple populations of the same species across varying environmental conditions, as well as multiple species that vary in traits of interest.

Genomic imprinting, disrupted placental expression, and speciation

The importance of regulatory incompatibilities to the early stages of speciation remains unclear. Hybrid mammals often show extreme parent-of-origin growth effects that are thought to be a consequence of disrupted genetic imprinting (parent-specific epigenetic gene silencing) during early development. Here, we test the long-standing hypothesis that abnormal hybrid growth reflects disrupted gene expression due to loss of imprinting (LOI) in hybrid placentas, resulting in dosage imbalances between paternal growth factors and maternal growth repressors. We analyzed placental gene expression in reciprocal dwarf hamster hybrids that show extreme parent-of-origin growth effects relative to their parental species. In massively enlarged hybrid placentas, we observed both extensive transgressive expression of growth-related genes and biallelic expression of many genes that were paternally silenced in normal sized hybrids. However, the apparent widespread disruption of paternal silencing was coupled with reduced gene expression levels overall. These patterns are contrary to the predictions of the LOI model and indicate that hybrid misexpression of dosage-sensitive genes is caused by other regulatory mechanisms in this system. Collectively, our results support a central role for disrupted gene expression and imprinting in the evolution of mammalian hybrid inviability, but call into question the generality of the widely invoked LOI model.

Genetic loci with parent-of-origin effects cause hybrid seed lethality in crosses between Mimulus species

In flowering plants, F1 hybrid seed lethality is a common outcome of crosses between closely related diploid species, but the genetic basis of this early-acting and potentially widespread form of postzygotic reproductive isolation is largely unknown. We intercrossed two closely related species of monkeyflower, Mimulus guttatus and Mimulus tilingii, to characterize the mechanisms and strength of postzygotic reproductive isolation. Then, using a reciprocal backcross design, we performed high-resolution genetic mapping to determine the genetic architecture of hybrid seed lethality and directly test for loci with parent-of-origin effects. We found that F1 hybrid seed lethality is an exceptionally strong isolating barrier between Mimulus species, with reciprocal crosses producing < 1% viable seeds. This form of postzygotic reproductive isolation appears to be highly polygenic, indicating that multiple incompatibility loci have accumulated rapidly between these closely related Mimulus species. It is also primarily caused by genetic loci with parent-of-origin effects, suggesting a possible role for imprinted genes in the evolution of Mimulus hybrid seed lethality. Our findings suggest that divergence in loci with parent-of-origin effects, which is probably driven by genomic coevolution within lineages, might be an important source of hybrid incompatibilities between flowering plant species.

Speciation and reduced hybrid female fertility in house mice

In mammals, intrinsic postzygotic isolation has been well studied in males but has been less studied in females, despite the fact that female gametogenesis and pregnancy provide arenas for hybrid sterility or inviability that are absent in males. Here, we asked whether inviability or sterility is observed in female hybrids of Mus musculus domesticus and M. m. musculus, taxa which hybridize in nature and for which male sterility has been well characterized. We looked for parent-of-origin growth phenotypes by measuring adult body weights in F1 hybrids. We evaluated hybrid female fertility by crossing F1 females to a tester male and comparing multiple reproductive parameters between intrasubspecific controls and intersubspecific hybrids. Hybrid females showed no evidence of parent-of-origin overgrowth or undergrowth, providing no evidence for reduced viability. However, hybrid females had smaller litter sizes, reduced embryo survival, fewer ovulations, and fewer small follicles relative to controls. Significant variation in reproductive parameters was seen among different hybrid genotypes, suggesting that hybrid incompatibilities are polymorphic within subspecies. Differences in reproductive phenotypes in reciprocal genotypes were observed and are consistent with cyto-nuclear incompatibilities or incompatibilities involving genomic imprinting. These findings highlight the potential importance of reduced hybrid female fertility in the early stages of speciation.

Tracing reinforcement through asymmetrical partner preference in the European common vole Microtus arvalis

Background

The mechanistic basis of speciation and in particular the contribution of behaviour to the completion of the speciation process is often contentious. Contact zones between related taxa provide a situation where selection against hybridization might reinforce separation by behavioural mechanisms, which could ultimately fully isolate the taxa. One of the most abundant European mammals, the common vole Microtus arvalis, forms multiple natural hybrid zones where rapidly diverging evolutionary lineages meet in secondary contact. Very narrow zones of hybridization spanning only a few kilometres and sex-specific gene flow patterns indicate reduced fitness of natural hybrids and incipient speciation between some of the evolutionary lineages. In this study, we examined the contribution of behavioural mechanisms to the speciation process in these rodents by fine-mapping allopatric and parapatric populations in the hybrid zone between the Western and Central lineages and experimental testing of the partner preferences of wild, pure-bred and hybrid female common voles.

Results

Genetic analysis based on microsatellite markers revealed the presence of multiple parapatric and largely non-admixed populations at distances of about 10 km at the edge of the area of natural hybridization between the Western and Central lineages. Wild females from Western parapatric populations and lab-born F1 hybrids preferred males from the Western lineage whereas wild females of Central parapatric origin showed no measurable preference. Furthermore, wild and lab-born females from allopatric populations of the Western or Central lineages showed no detectable preference for males from either lineage.

Conclusions

The detected partner preferences are consistent with asymmetrical reinforcement of pre-mating reproductive isolation mechanisms in the European common vole and with earlier results suggesting that hybridization is more detrimental to the Western lineage. As a consequence, these differences in behaviour might contribute to a further geographical stabilization of this moving hybrid zone. Such behavioural processes could also provide a mechanistic perspective for frequently-detected asymmetrical introgression patterns in the largely allopatrically diversifying Microtus genus and other rapidly speciating rodents.

Peromyscus mice as a model for studying natural variation

The deer mouse (genus Peromyscus) is the most abundant mammal in North America, and it occupies almost every type of terrestrial habitat. It is not surprising therefore that the natural history of Peromyscus is among the best studied of any small mammal. For decades, the deer mouse has contributed to our understanding of population genetics, disease ecology, longevity, endocrinology and behavior. Over a century's worth of detailed descriptive studies of Peromyscus in the wild, coupled with emerging genetic and genomic techniques, have now positioned these mice as model organisms for the study of natural variation and adaptation. Recent work, combining field observations and laboratory experiments, has lead to exciting advances in a number of fields—from evolution and genetics, to physiology and neurobiology.

DOI:http://dx.doi.org/10.7554/eLife.06813.001

Maternal-foetal genomic conflict and speciation: no evidence for hybrid placental dysplasia in crosses between two house mouse subspecies

Interspecific hybridization between closely related mammalian species, including various species of the genus Mus, is commonly associated with abnormal growth of the placenta and hybrid foetuses, a phenomenon known as hybrid placental dysplasia (HPD). The role of HPD in speciation is anticipated but still poorly understood. Here, we studied placental and foetal growth in F1 crosses between four inbred mouse strains derived from two house mouse subspecies, Mus musculus musculus and Mus musculus domesticus. These subspecies are in the early stage of speciation and still hybridize in nature. In accordance with the maternal-foetal genomic conflict hypothesis, we found different parental influences on placental and foetal development, with placental weight most affected by the father's body weight and foetal weight by the mother's body weight. After removing the effects of parents' body weight, we did not find any significant differences in foetal or placental weights between intra-subspecific and inter-subspecific F1 crosses. Nevertheless, we found that the variability in placental weight in inter-subspecific crosses is linked to the X chromosome, similarly as for HPD in interspecific mouse crosses. Our results suggest that maternal-foetal genomic conflict occurs in the house mouse system, but has not yet diverged sufficiently to cause abnormalities in placental and foetal growth in inter-subspecific crosses. HPD is thus unlikely to contribute to speciation in the house mouse system. However, we cannot rule out that it might have contributed to other speciation events in the genus Mus, where differences in the levels of polyandry exist between the species.

Parent-of-origin growth effects and the evolution of hybrid inviability in dwarf hamsters

Mammalian hybrids often show abnormal growth, indicating that developmental inviability may play an important role in mammalian speciation. Yet, it is unclear if this recurrent phenotype reflects a common genetic basis. Here, we describe extreme parent-of-origin-dependent growth in hybrids from crosses between two species of dwarf hamsters, Phodopus campbelli and Phodopus sungorus. One cross type resulted in massive placental and embryonic overgrowth, severe developmental defects, and maternal death. Embryos from the reciprocal cross were viable and normal sized, but adult hybrid males were relatively small. These effects are strikingly similar to patterns from several other mammalian hybrids. Using comparative sequence data from dwarf hamsters and several other hybridizing mammals, we argue that extreme hybrid growth can contribute to reproductive isolation during the early stages of species divergence. Next, we tested if abnormal growth in hybrid hamsters was associated with disrupted genomic imprinting. We found no association between imprinting status at several candidate genes and hybrid growth, though two interacting genes involved in embryonic growth did show reduced expression in overgrown hybrids. Collectively, our study indicates that growth-related hybrid inviability may play an important role in mammalian speciation but that the genetic underpinnings of these phenotypes remain unresolved.

Twists and turns: a scientific journey

In this perspective I look back on the twists and turns that influenced the direction of my scientific career over the past 40 years. From my early ambition to be a chemist to my training in Philadelphia and Bethesda as a molecular biologist, I benefited enormously from generous and valuable mentoring. In my independent career in Philadelphia and Princeton, I was motivated by a keen interest in the changes in gene expression that direct the development of the mammalian embryo and inspired by the creativity and energy of my students, fellows, and research staff. After twelve years as President of Princeton University, I have happily returned to the faculty of the Department of Molecular Biology.

The genomic architecture of population divergence between subspecies of the European rabbit

The analysis of introgression of genomic regions between divergent populations provides an excellent opportunity to determine the genetic basis of reproductive isolation during the early stages of speciation. However, hybridization and subsequent gene flow must be relatively common in order to localize individual loci that resist introgression. In this study, we used next-generation sequencing to study genome-wide patterns of genetic differentiation between two hybridizing subspecies of rabbits (Oryctolagus cuniculus algirus and O. c. cuniculus) that are known to undergo high rates of gene exchange. Our primary objective was to identify specific genes or genomic regions that have resisted introgression and are likely to confer reproductive barriers in natural conditions. On the basis of 326,000 polymorphisms, we found low to moderate overall levels of differentiation between subspecies, and fewer than 200 genomic regions dispersed throughout the genome showing high differentiation consistent with a signature of reduced gene flow. Most differentiated regions were smaller than 200 Kb and contained very few genes. Remarkably, 30 regions were each found to contain a single gene, facilitating the identification of candidate genes underlying reproductive isolation. This gene-level resolution yielded several insights into the genetic basis and architecture of reproductive isolation in rabbits. Regions of high differentiation were enriched on the X-chromosome and near centromeres. Genes lying within differentiated regions were often associated with transcription and epigenetic activities, including chromatin organization, regulation of transcription, and DNA binding. Overall, our results from a naturally hybridizing system share important commonalities with hybrid incompatibility genes identified using laboratory crosses in mice and flies, highlighting general mechanisms underlying the maintenance of reproductive barriers.

Imprinted gene expression in hybrids: perturbed mechanisms and evolutionary implications

Diverse mechanisms contribute to the evolution of reproductive barriers, a process that is critical in speciation. Amongst these are alterations in gene products and in gene dosage that affect development and reproductive success in hybrid offspring. Because of its strict parent-of-origin dependence, genomic imprinting is thought to contribute to the aberrant phenotypes observed in interspecies hybrids in mammals and flowering plants, when the abnormalities depend on the directionality of the cross. In different groups of mammals, hybrid incompatibility has indeed been linked to loss of imprinting. Aberrant expression levels have been reported as well, including imprinted genes involved in development and growth. Recent studies in humans emphasize that genetic diversity within a species can readily perturb imprinted gene expression and phenotype as well. Despite novel insights into the underlying mechanisms, the full extent of imprinted gene perturbation still remains to be determined in the different hybrid systems. Here we review imprinted gene expression in intra- and interspecies hybrids and examine the evolutionary scenarios under which imprinting could contribute to hybrid incompatibilities. We discuss effects on development and reproduction and possible evolutionary implications.

A genetic map of Peromyscus with chromosomal assignment of linkage groups (a Peromyscus genetic map)

The rodent genus Peromyscus is the most numerous and species-rich mammalian group in North America. The naturally occurring diversity within this genus allows opportunities to investigate the genetic basis of adaptation, monogamy, behavioral and physiological phenotypes, growth control, genomic imprinting, and disease processes. Increased genomic resources including a high quality genetic map are needed to capitalize on these opportunities. We produced interspecific hybrids between the prairie deer mouse (P. maniculatus bairdii) and the oldfield mouse (P. polionotus) and scored meiotic recombination events in backcross progeny. A genetic map was constructed by genotyping of backcross progeny at 185 gene-based and 155 microsatellite markers representing all autosomes and the X-chromosome. Comparison of the constructed genetic map with the molecular maps of Mus and Rattus and consideration of previous results from interspecific reciprocal whole chromosome painting allowed most linkage groups to be unambiguously assigned to specific Peromyscus chromosomes. Based on genomic comparisons, this Peromyscus genetic map covers ~83% of the Rattus genome and 79% of the Mus genome. This map supports previous results that the Peromyscus genome is more similar to Rattus than Mus. For example, coverage of the 20 Rattus autosomes and the X-chromosome is accomplished with only 28 segments of the Peromyscus map, but coverage of the 19 Mus autosomes and the X-chromosome requires 40 chromosomal segments of the Peromyscus map. Furthermore, a single Peromyscus linkage group corresponds to about 91% of the rat and only 76% of the mouse X-chromosomes.

Peromyscus (deer mice) as developmental models

Deer mice (Peromyscus) are the most common native North American mammals, and exhibit great natural genetic variation. Wild-derived stocks from a number of populations are available from the Peromyscus Genetic Stock Center (PGSC). The PGSC also houses a number of natural variants and mutants (many of which appear to differ from Mus). These include metabolic, coat-color/pattern, neurological, and other morphological variants/mutants. Nearly all these mutants are on a common genetic background, the Peromyscus maniculatus BW stock. Peromyscus are also superior behavior models in areas such as repetitive behavior and pair-bonding effects, as multiple species are monogamous. While Peromyscus development generally resembles that of Mus and Rattus, prenatal stages have not been as thoroughly studied, and there appear to be intriguing differences (e.g., longer time spent at the two-cell stage). Development is greatly perturbed in crosses between P. maniculatus (BW) and Peromyscus polionotus (PO). BW females crossed to PO males produce growth-restricted, but otherwise healthy, fertile offspring which allows for genetic analyses of the many traits that differ between these two species. PO females crossed to BW males produce overgrown but severely dysmorphic conceptuses that rarely survive to late gestation. There are likely many more uses for these animals as developmental models than we have described here. Peromyscus models can now be more fully exploited due to the emerging genetic (full linkage map), genomic (genomes of four stocks have been sequenced) and reproductive resources.

Understanding the chromatin remodeling code

Remodeling a chromatin structure enables the genetic elements stored in a genome to function in a condition-specific manner and predisposes the interactions between cis-regulatory elements and trans-acting factors. A chromatin signature can be an indicator of the activity of the underlying genetic elements. This paper reviews recent studies showing that the combination and arrangements of chromatin remodeling marks play roles as chromatin code affecting the activity of genetic elements. This paper also reviews recent studies inferring the primary DNA sequence contexts associated with chromatin remodeling that suggest interactions between genetic and epigenetic factors. We conclude that chromatin remodeling, which provides accurate models of gene expression and morphological variations, may help to find the biological marks that cannot be detected by genome-wide association study or genetic study.

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.

An imprinted gene underlies postzygotic reproductive isolation in Arabidopsis thaliana

Postzygotic reproductive isolation in response to interploidy hybridizations is a well-known phenomenon in plants that forms a major path for sympatric speciation. A main determinant for the failure of interploidy hybridizations is the endosperm, a nutritious tissue supporting embryo growth, similar to the functional role of the placenta in mammals. Although it has been suggested that deregulated imprinted genes underpin dosage sensitivity of the endosperm, the molecular basis for this phenomenon remained unknown. In a genetic screen for suppressors of triploid seed abortion, we have identified the paternally expressed imprinted gene ADMETOS (ADM). Here, we present evidence that increased dosage of ADM causes triploid seed arrest. A large body of theoretical work predicted that deregulated imprinted genes establish the barrier to interploidy hybridization. Our study thus provides evidence strongly supporting this hypothesis and generates the molecular basis for our understanding of postzygotic hybridization barriers in plants.

Senescence is accelerated through donor cell specificity in cloned pigs

Animals cloned by somatic cell nuclear transfer (SCNT) sometimes have abnormalities that result in large offspring syndrome or early death during gestation due to respiratory and metabolic defects. We cloned pigs using two sources of donor cells and observed phenotypic anomalies in three pigs cloned from one type of cell, s-pig fetal fibroblasts. These animals had many wrinkles on their faces and bodies and looked older than age-matched normal pigs. We performed the present study to examine whether the wrinkled phenotype in the cloned pigs was due to senescence, a genetic problem with donor specificity, or epigenetic problems with reprogramming. To address this issue, we investigated biomarkers of senescence, including telomere length and the expression of senescence-associated β-galactosidase (SA-β-gal), glyceraldehyde phosphate dehydrogenase (GAPDH) and β-actin. We also assessed the methylation status of euchromatic PRE-1 repetitive sequences and centromeric satellite DNA, and measured the mRNA levels of six imprinted genes, Copg2, Mest, Igf2R, GNAS, SNRPN and Ube3a. The telomeres of the wrinkled cloned pigs were much shorter than those of the normal cloned pigs and age-matched normal pigs. In the wrinkled cloned pigs, SA-β-gal activity was detected and GAPDH and β-actin were repressed. The mRNA levels of Mest, GNAS and Ube3a were reduced in the wrinkled cloned pigs, although there was no difference between the normal cloned pigs and normal controls. This gene expression analysis indicates that the wrinkled abnormality of our pigs originates from genetic abnormalities in the donor cells used for SCNT.

Somatic reactivation of expression of the silent maternal Mest allele and acquisition of normal reproductive behaviour in a colony of Peg1/Mest mutant mice

Genomic imprinting confers allele-specific expression in less than 1% of genes, in a parent-of-origin specific fashion. In humans and mice the Peg1/Mest gene (Mest) is maternally repressed, and paternally expressed. Mest is expressed in embryogenic mesoderm-derived tissues and in adult brain, and paternal mutations in Mest lead to growth retardation and defective maternal behaviour. Despite our current understanding of mechanisms associated with the establishment of imprinting of Mest and other imprinted genes, it is unclear to what extent Mest imprinting needs to be maintained in adult tissues. Aberrations of imprinting are known to occur in certain rare syndromes, and involve either inherited mutations, or constitutive epigenetic alterations occurring soon after fertilization. Imprinting abnormalities may also occur in the aging somatic tissues of adult individuals. Here we report an occurrence of post-embryonic somatic variability of Mest allelic expression in a colony of mice where heterozygotes at the imprinted Mest locus for a mutation inherited from the father spontaneously expressed the normally silenced allele from the mother. In addition, a newly acquired ability to overcome the deficit in maternal reproductive behaviour had occurred in the mutant mice, but this appeared not to be directly linked to the Mest mutation. Our results suggest that at least one allele of Mest expression is required in the somatic tissues of adult individuals and that under certain conditions (such as in the presence of a Mest insertional mutation or in an altered genetic background), somatically acquired alterations of allelic expression at the Mest locus may occur.

Retroelement demethylation associated with abnormal placentation in Mus musculus x Mus caroli hybrids

The proper functioning of the placenta requires specific patterns of methylation and the appropriate regulation of retroelements, some of which have been co-opted by the genome for placental-specific gene expression. Our inquiry was initiated to determine the causes of the placental defects observed in crosses between two species of mouse, Mus musculus and Mus caroli. M. musculus × M. caroli fetuses are rarely carried to term, possibly as a result of genomic incompatibility in the placenta. Taking into account that placental dysplasia is observed in Peromyscus and other Mus hybrids, and that endogenous retroviruses are expressed in the placental transcriptome, we hypothesized that these placental defects could result, in part, from failure of the genome defense mechanism, DNA methylation, to regulate the expression of retroelements. Hybrid M. musculus × M. caroli embryos were produced by artificial insemination, and dysplastic placentas were subjected to microarray and methylation screens. Aberrant overexpression of an X-linked Mus retroelement in these hybrid placentas is consistent with local demethylation of this retroelement, concomitant with genome instability, disruption of gene regulatory pathways, and dysgenesis. We propose that the placenta is a specific site of control that is disrupted by demethylation and retroelement activation in interspecific hybridization that occur as a result of species incompatibility of methylation machinery. To our knowledge, the present data provide the first report of retroelement activation linked to decreased methylation in a eutherian hybrid system.

Peromyscus as a Mammalian epigenetic model

Deer mice (Peromyscus) offer an opportunity for studying the effects of natural genetic/epigenetic variation with several advantages over other mammalian models. These advantages include the ability to study natural genetic variation and behaviors not present in other models. Moreover, their life histories in diverse habitats are well studied. Peromyscus resources include genome sequencing in progress, a nascent genetic map, and >90,000 ESTs. Here we review epigenetic studies and relevant areas of research involving Peromyscus models. These include differences in epigenetic control between species and substance effects on behavior. We also present new data on the epigenetic effects of diet on coat-color using a Peromyscus model of agouti overexpression. We suggest that in terms of tying natural genetic variants with environmental effects in producing specific epigenetic effects, Peromyscus models have a great potential.