Ulrich Zeller

The evolution of gene expression levels in mammalian organs

Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped by purifying selection, we identify numerous potentially selectively driven expression switches, which occurred at different rates across lineages and tissues and which probably contributed to the specific organ biology of various mammals.

The evolution of lncRNA repertoires and expression patterns in tetrapods

Only a very small fraction of long noncoding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but the absence of lncRNA annotations in non-model organisms has precluded comparative analyses. Here we present a large-scale evolutionary study of lncRNA repertoires and expression patterns, in 11 tetrapod species. We identify approximately 11,000 primate-specific lncRNAs and 2,500 highly conserved lncRNAs, including approximately 400 genes that are likely to have originated more than 300 million years ago. We find that lncRNAs, in particular ancient ones, are in general actively regulated and may function predominantly in embryonic development. Most lncRNAs evolve rapidly in terms of sequence and expression levels, but tissue specificities are often conserved. We compared expression patterns of homologous lncRNA and protein-coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network suggests potential functions for lncRNAs in fundamental processes such as spermatogenesis and synaptic transmission, but also in more specific mechanisms such as placenta development through microRNA production.

Retroviral envelope gene captures and syncytin exaptation for placentation in marsupials

Significance Syncytins are “captured” genes of retroviral origin, corresponding to the fusogenic envelope gene of endogenized retroviruses. They are present in a series of eutherian mammals, including humans and mice where they play an essential role in placentation. Here we show that marsupials—which diverged from eutherian mammals ∼190 Mya but still possess a primitive, short-lived placenta (rapidly left by the embryo for development in an external pouch)—have also captured such genes. The present characterization of the syncytin-Opo1 gene in the opossum placenta, together with the identification of two additional endogenous retroviral envelope gene captures, allow a recapitulation of the natural history of these unusual genes and definitely extends their “symbiotic niche” to all clades of placental mammals. Syncytins are genes of retroviral origin captured by eutherian mammals, with a role in placentation. Here we show that some marsupials—which are the closest living relatives to eutherian mammals, although they diverged from the latter ∼190 Mya—also possess a syncytin gene. The gene identified in the South American marsupial opossum and dubbed syncytin-Opo1 has all of the characteristic features of a bona fide syncytin gene: It is fusogenic in an ex vivo cell–cell fusion assay; it is specifically expressed in the short-lived placenta at the level of the syncytial feto–maternal interface; and it is conserved in a functional state in a series of Monodelphis species. We further identify a nonfusogenic retroviral envelope gene that has been conserved for >80 My of evolution among all marsupials (including the opossum and the Australian tammar wallaby), with evidence for purifying selection and conservation of a canonical immunosuppressive domain, but with only limited expression in the placenta. This unusual captured gene, together with a third class of envelope genes from recently endogenized retroviruses—displaying strong expression in the uterine glands where retroviral particles can be detected—plausibly correspond to the different evolutionary statuses of a captured retroviral envelope gene, with only syncytin-Opo1 being the present-day bona fide syncytin active in the opossum and related species. This study would accordingly recapitulate the natural history of syncytin exaptation and evolution in a single species, and definitely extends the presence of such genes to all major placental mammalian clades.

The kestrel (Falco tinnunculus L.) in Berlin: investigation of breeding biology and feeding ecology

Approximately 200–250 pairs of kestrels (Falco tinnunculus) breed in Berlin, preferentially in nest boxes. From 2002 to 2004, ten monitoring sites (breeding sites) characterised by different housing structure, land utilisation, vegetation cover and degree of building density were studied in Berlin: four in the city centre, three in a mixed zone and three in the outskirts. All pairs bred in nest boxes, so the reproductive success could easily be determined. Pellets, and feathers of bird prey species, were collected during the breeding seasons, and the food spectrum was determined based on these remains. There was no significant difference in the reproductive success of the kestrels between the three zones. Data on the number of fledged young indicated a sufficient food supply. In total, 9 species of mice and shrews, 23 bird species and 31 beetle species were identified as prey of kestrels. Urban kestrels specialise in hunting birds if mice and shrews are not readily available, with the house sparrow (Passer domesticus) as the favoured prey bird. Of note are anthropogenic food items, such as cutlet bones, that were found only in the city centre. This shows that the kestrel can adapt itself to humans with regard to its diet. There was no urban gradient with regard to reproductive success, but there was with the composition of food, such as the domination of bird prey in the city centre. The number of individual items of bird prey decreased from the centre to the outskirts. In conclusion, the results show that the kestrel is an opportunistic species which survives well anywhere in the city of Berlin.

Ultrastructure of the placenta of the tammar wallaby, Macropus eugenii: comparison with the grey short-tailed opossum, Monodelphis domestica

The ultrastructure of the tammar placenta was studied throughout pregnancy. The uterine epithelium grows from a columnar to an enlarged, undulating epithelium between early gestation and mid‐gestation when the shell coat that surrounds the marsupial conceptus ruptures. Trophectoderm and uterine epithelium do not form syncytia, nor does invasion of the endometrium occur at any stage of pregnancy. Uterine secretion is provided to both the bilaminar and the trilaminar side of the yolk sac placenta up to birth. Fenestrations, abundant vesicles and lumenal processes of maternal capillaries, as well as deep basal folds of the uterine epithelium, suggest that there is transfer of hemotrophes adjacent to both parts of the yolk sac. In contrast, in the grey short‐tailed opossum, these structures are lacking. The yolk sacs of adjacent embryos fuse to form a common yolk sac cavity, thus losing most of the bilaminar yolk sac. The bilaminar and trilaminar components of the yolk sac placenta of the tammar are less different in structure and function than those of the grey short‐tailed opossum, but both types are fully functional placentas. The extended secretory phase of the tammar uterus and the maternal recognition of early pregnancy appear to be derived characters of macropodid marsupials.

Postnatal lung and metabolic development in two marsupial and four eutherian species

Two marsupial species (Monodelphis domestica, Macropus eugenii) and four eutherian species (Mesocricetus auratus, Suncus murinus, Tupaia belangeri and Cavia aperea) were examined to compare and contrast the timing of lung and metabolic development during the postnatal maturation of the mammalian respiratory apparatus. Using light, scanning and transmission electron microscopy, the lung structural changes were correlated with indirect calorimetry to track the metabolic development. Marsupial and eutherian species followed the same pattern of mammalian lung development, but differed in the developmental pace. In the two newborn marsupial species, the lung parenchyma was at the early terminal sac stage, with large terminal air sacs, and the lung developed slowly. In contrast, the newborn eutherian species had more advanced lungs at the late terminal sac stage in altricial species (M. auratus, S. murinus) and at the alveolar stage in precocial species (T. belangeri, C. aperea). Postnatal lung development proceeded rapidly in eutherian species. The marsupial species had a low metabolic rate at birth and achieved adult metabolism late in postnatal development. In contrast, newborn eutherian species had high metabolic rates and reached adult metabolism during the first week of life. The time course of the metabolic development is thus tightly linked to the structural differentiation of the lungs and the timing of postnatal lung development. These differences in the neonatal lung structure and the timing of postnatal lung maturation between marsupial and eutherian species reflect their differing reproductive strategies.

Lung and metabolic development in mammals: contribution to the reconstruction of the marsupial and eutherian morphotype

Marsupials represent only 6% of all living mammals. Marsupialia and Placentalia are distinguished mainly by their modes of reproduction. In particular, the differences in the stage of development of the neonates may be one explanation for the divergent evolutionary success. In this respect one important question is whether the survivability of the neonate depends on the degree of maturation of the respiratory system relative to the metabolic capacity at the time of birth. Therefore, this review highlights the differences in lung morphology and metabolic development of extant Marsupialia and Placentalia. The Marsupial neonate is born with a low birth weight and is highly immature. The neonatal lung is characterized by large terminal sacs, a poorly developed bronchial system and late formation of alveoli. Marsupialia have a low metabolic rate at birth and attain adult metabolic rate and thermoregulatory capacity late in postnatal development. In contrast, the eutherian neonate is born with a relative high birth weight and is always more mature than marsupial neonates. The neonatal lung has small terminal sacs, the bronchial system is well developed and the formation of alveoli begins few days after birth. Placentalia have a high metabolic rate at birth and attain adult metabolic rate and thermoregulatory capacity early in postnatal development. The differences in the developmental degree of the newborn lung between Marsupialia and Placentalia have consequences for their metabolic and thermoregulatory capacity. These differences could be advantageous for Placentalia in the changing environments in which they evolved.

Lung Development of Monotremes: Evidence for the Mammalian Morphotype

The reproductive strategies and the extent of development of neonates differ markedly between the three extant mammalian groups: the Monotremata, Marsupialia, and Eutheria. Monotremes and marsupials produce highly altricial offspring whereas the neonates of eutherian mammals range from altricial to precocial. The ability of the newborn mammal to leave the environment in which it developed depends highly on the degree of maturation of the cardio‐respiratory system at the time of birth. The lung structure is thus a reflection of the metabolic capacity of neonates. The lung development in monotremes (Ornithorhynchus anatinus, Tachyglossus aculeatus), in one marsupial (Monodelphis domestica), and one altricial eutherian (Suncus murinus) species was examined. The results and additional data from the literature were integrated into a morphotype reconstruction of the lung structure of the mammalian neonate. The lung parenchyma of monotremes and marsupials was at the early terminal air sac stage at birth, with large terminal air sacs. The lung developed slowly. In contrast, altricial eutherian neonates had more advanced lungs at the late terminal air sac stage and postnatally, lung maturation proceeded rapidly. The mammalian lung is highly conserved in many respects between monotreme, marsupial, and eutherian species and the structural differences in the neonatal lungs can be explained mainly by different developmental rates. The lung structure of newborn marsupials and monotremes thus resembles the ancestral condition of the mammalian lung at birth, whereas the eutherian newborns have a more mature lung structure. Anat Rec, 2009.

Inner ear labyrinth anatomy of monotremes and implications for mammalian inner ear evolution

The monophyletic clade Monotremata branches early from the rest of the mammalian crown group in the Jurassic and members of this clade retain many ancestral mammalian traits. Thus, accurate and detailed anatomical descriptions of this group can offer unique insight into the early evolutionary history of Mammalia. In this study, we examine the inner ear anatomy of two extant monotremes, Ornithorhynchus anatinus and Tachyglossus aculeatus, with the primary goals of elucidating the ancestral mammalian ear morphology and resolving inconsistencies found within previous descriptive literature. We use histological serial sections and high‐resolution microcomputed tomography (µCT) for correlating soft tissue features of the vestibule and cochlea to the osseous labyrinth endocast. We found that in both monotremes the scala tympani coils to a lesser degree than scala vestibuli and scala media, although all three scalae show an apical coil inside the osseous cochlear tube. The helicotrema (conduit between scala tympani and scala vestibuli) is in subapical position, and the cochlear and lagenar ganglia and their associated nerve fibers are not enclosed by bone. In comparison, in extant therian mammals (i.e., marsupials and placentals) the helicotrema is located at the apex of the osseous cochlear canal, the three scalae coil to the same degree and the cochlear ganglion is enclosed by the primary bony lamina. Whether the lagenar ganglion is lost in therian mammals or integrated into the cochlear ganglion is still debated. The presence of a sensory lagenar macula at the apex of the membranous cochlear duct, innervated by a separate lagenar nerve and ganglion is a plesiomorphic condition of amniotes that monotremes share. A separate osseous lagenar canaliculus for the lagenar nerve, and the coiling of the distended lagenar sac at the end of the cochlear duct are autapomorphies of monotremes. Based on our findings we hypothesize that the ancestral inner ear of stem mammaliaforms is characterized by a straight or slightly curved osseous cochlear canal, a lagenar macula, lagenar nerve fibers separated from a larger bundle of cochlear nerve fibers, the presence of an organ of Corti and an intra‐otic cochlear ganglion suspended by membranous connective tissue. Among the major Mesozoic clades of crown mammals, cladotherians and gondwanatherians most likely acquired a fully functioning organ of Corti but lost the sensory lagenar macula, like extant therians. However, Mesozoic spalacotherioids, multituberculates and eutriconodonts likely retained the mammaliaform condition. J. Morphol. 278:236–263, 2017.

The Placentation of Eulipotyphla—Reconstructing a Morphotype of the Mammalian Placenta

Placentation determines the developmental status of the neonate, which can be considered as the most vulnerable stage in the mammalian life cycle. In this respect, the different evolutionary and ecological adaptations of marsupial and placental mammals have most likely been associated with the different reproductive strategies of the two therian clades. The morphotypes of marsupial and placental neonates, as well as the placental stem species pattern of Marsupialia, have already been reconstructed. To contribute to a better understanding of the evolution of Placentalia, a histological and ultrastructural investigation of the placenta in three representatives of Eulipotyphla, that is, core insectivores, has been carried out in this study. We studied the Musk shrew (Suncus murinus), the four‐toed hedgehog (Atelerix albiventris), and the Iberian mole (Talpa occidentalis). As a result, a eulipotyphlan placental morphotype consisting of a compact and invasive placenta was reconstructed. This supports the widely accepted hypothesis that the stem lineage of Placentalia is characterized by an invasive, either endothelio‐ or hemochorial placenta. Evolutionary transformations toward a diffuse, noninvasive placenta occurred in the stem lineages of lower primates and cetartiodactyles and were associated with prolonged gestation and the production of few and highly precocial neonates. Compared to the choriovitelline placenta of Marsupialia, the chorioallantoic placenta of Placentalia allows for a more intimate contact and is associated with more advanced neonates. J. Morphol. 275:1122–1144, 2014.