The genomics of placenta evolution in livebearing fish

During vertebrate evolution, complex organs have evolved several times. The development of these organs is encoded in the genome. However, it is currently unclear how new complex organs, consisting of multiple interlocking parts, can evolve as a result of genomic change. In this thesis, I aim to find the genomic basis of one such newly evolved organ: the placenta in the livebearing fish family Poeciliidae. In this family, a placenta has evolved nine times independently, allowing for the investigation of multiple evolutionary origins of the same organ within a single group of species. First, I sequence and assemble the genomes of both placental and non-placental poeciliid species. Then, I compare the genomes of placental species with the genomes of non-placental species, aiming to find consistent genomic differences between placental and non-placental species that can be associated with placenta evolution. I show that indeed, placental species show consistent mutations in both protein-coding and regulatory regions of the genome. Protein-coding mutations occur mainly around structural and metabolic genes, while regulatory changes occur mainly around developmental genes. I also show that, contrary to some predictions, gene duplications are not associated with placenta evolution in poeciliid fish. Finally, I show that allele-specific DNA methylation is present in the poeciliid fish Poeciliopsis gracilis, and that its inheritance is non-random but instead depends on parent-of-origin of the methylated allele, suggesting genomic imprinting. Together I provide a comprehensive overview of genome evolution in the fish family Poeciliidae, and provide new insights into the evolution of complex traits

Data from: Resistance and recovery of methane-oxidizing communities depends on stress regime and history; a microcosm study

Although soil microbes are responsible for important ecosystem functions, and soils are under increasing environmental pressure, little is known about their resistance and resilience to multiple stressors. Here, we test resistance and recovery of soil methane-oxidizing communities to two different, repeated, perturbations: soil drying, ammonium addition and their combination. In replicated soil microcosms we measured methane oxidation before and after perturbations, while monitoring microbial abundance and community composition using quantitative PCR assays for the bacterial 16S rRNA and pmoA gene, and sequencing of the bacterial 16S rRNA gene. Although microbial community composition changed after soil drying, methane oxidation rates recovered, even after four desiccation events. Moreover, microcosms subjected to soil drying recovered significantly better from ammonium addition compared to microcosms not subjected to soil drying. Our results show the flexibility of microbial communities, even if abundances of dominant populations drop, ecosystem functions can recover. In addition, a history of stress may induce changes in community composition and functioning, which may in turn affect its future tolerance to different stressors

Molecular Signatures of Placentation and Secretion Uncovered in Poeciliopsis Maternal Follicles

Placentation evolved many times independently in vertebrates. Although the core functions of all placentas are similar, we know less about how this similarity extends to the molecular level. Here, we study Poeciliopsis, a unique genus of live-bearing fish that have independently evolved complex placental structures at least three times. The maternal follicle is a key component of these structures. It envelops yolk-rich eggs and is morphologically simple in lecithotrophic species but has elaborate villous structures in matrotrophic species. Through sequencing, the follicle transcriptome of a matrotrophic, Poeciliopsis retropinna, and lecithotrophic, P. turrubarensis, species we found genes known to be critical for placenta function expressed in both species despite their difference in complexity. Additionally, when we compare the transcriptome of different river populations of P. retropinna, known to vary in maternal provisioning, we find differential expression of secretory genes expressed specifically in the top layer of villi cells in the maternal follicle. This provides some of the first evidence that the placental structures of Poeciliopsis function using a secretory mechanism rather than direct contact with maternal circulation. Finally, when we look at the expression of placenta proteins at the maternal-fetal interface of a larger sampling of Poeciliopsis species, we find expression of key maternal and fetal placenta proteins in their cognate tissue types of all species, but follicle expression of prolactin is restricted to only matrotrophic species. Taken together, we suggest that all Poeciliopsis follicles are poised for placenta function but require expression of key genes to form secretory villi.</p

Parallel genomic changes drive repeated evolution of placentas in live-bearing fish

The evolutionary origin of complex organs defies empirical study because most evolved hundreds of millions of years ago. The placenta of live-bearing fish in the family Poeciliidae represents a unique opportunity to study the origin of complexity : in this family, placentas evolved at least nine times, vary in the scope of their development and are sometimes of recent origin, with closely related species with and without placentas. It is currently unknown whether convergent genomic changes underlie this repeated evolution. Here we compare whole genomes of 26 poeciliid species representing six independent origins of placentation. We show that the evolution of placentas is accompanied by convergent changes in the evolutionary rate of both protein-coding genes, as well as convergent changes in non-coding regulatory elements. Shifts in evolutionary rate that correlate with placentation were mainly observed in transporter- and vesicle-located genes, while shuffling of regulatory elements occurred mainly around developmental genes. We conclude that convergent genomic changes in both protein-coding and regulatory regions may underlie the repeated evolution of the placenta in the Poeciliidae

Parallel Genomic Changes Drive Repeated Evolution of Placentas in Live-Bearing Fish

The evolutionary origin of complex organs challenges empirical study because most organs evolved hundreds of millions of years ago. The placenta of live-bearing fish in the family Poeciliidae represents a unique opportunity to study the evolutionary origin of complex organs, because in this family a placenta evolved at least nine times independently. It is currently unknown whether this repeated evolution is accompanied by similar, repeated, genomic changes in placental species. Here, we compare whole genomes of 26 poeciliid species representing six out of nine independent origins of placentation. Evolutionary rate analysis revealed that the evolution of the placenta coincides with convergent shifts in the evolutionary rate of 78 protein-coding genes, mainly observed in transporter- and vesicle-located genes. Furthermore, differences in sequence conservation showed that placental evolution coincided with similar changes in 76 noncoding regulatory elements, occurring primarily around genes that regulate development. The unexpected high occurrence of GATA simple repeats in the regulatory elements suggests an important function for GATA repeats in developmental gene regulation. The distinction in molecular evolution observed, with protein-coding parallel changes more often found in metabolic and structural pathways, compared with regulatory change more frequently found in developmental pathways, offers a compelling model for complex trait evolution in general: changing the regulation of otherwise highly conserved developmental genes may allow for the evolution of complex traits.</p

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Resistance and Recovery of Methane-Oxidizing Communities Depends on Stress Regime and History; A Microcosm Study

Although soil microbes are responsible for important ecosystem functions, and soils are under increasing environmental pressure, little is known about their resistance and resilience to multiple stressors. Here, we test resistance and recovery of soil methaneoxidizing communities to two different, repeated, perturbations: soil drying, ammonium addition and their combination. In replicated soil microcosms we measured methane oxidation before and after perturbations, while monitoring microbial abundance and community composition using quantitative PCR assays for the bacterial 16S rRNA and pmoA gene, and sequencing of the bacterial 16S rRNA gene. Although microbial community composition changed after soil drying, methane oxidation rates recovered, even after four desiccation events. Moreover, microcosms subjected to soil drying recovered significantly better from ammonium addition compared to microcosms not subjected to soil drying. Our results show the flexibility of microbial communities, even if abundances of dominant populations drop, ecosystem functions can recover. In addition, a history of stress may induce changes in community composition and functioning, which may in turn affect its future tolerance to different stressors

Whole genome sequencing of Heterandria formosa reveals information about the evolution of the placenta in the livebearing fish family Poeciliidae

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. Studying this process requires closely related species that vary in the complexity of their organs. This is the case for the placenta in the livebearing fish family Poeciliidae, as members of this family vary markedly in their placental complexity. Here, we look for the genomic basis underlying this phenotypic variation in the genome of 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 play 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 information of a placental poeciliid. We looked for signatures of adaptive evolution by comparing its gene sequences to those of three non-placental live-bearing relatives. We found 18 positively selected genes exclusive to H. formosa, as well as 5 gene duplications. 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

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.</p