Common Ancestor Of Mammals Research Articles

Comparative genomics of the T cell receptor μ locus in marsupials and monotremes.

T cells are a primary component of the vertebrate adaptive immune system. There are three mammalian T cell lineages based on their T cell receptors (TCR). The αβ T cells and γδ T cells are ancient and found broadly in vertebrates. The more recently discovered γμ T cells are uniquely mammalian and only found in marsupials and monotremes. In this study, we compare the TCRμ locus (TRM) across the genomes of two marsupials, the gray short-tailed opossum and Tasmanian devil, and one monotreme, the platypus. These analyses revealed lineage-specific duplications, common to all non-eutherian mammals described. There is conserved synteny in the TRM loci of both marsupials but not in the monotreme. Our results are consistent with an ancestral cluster organization which was present in the last common mammalian ancestor which underwent lineage-specific duplications and divergence among the non-eutherian mammals.

Evolutionary study of the extrinsic thoracic limb muscles of the domestic cat (Felis catus, Feliformia, Carnivora) based on their topology and innervation

AbstractExtrinsic thoracic limb muscles are a muscular group that supports the thoracic limb in mammals without the clavicle and serve to move the scapula and shoulder joint. However, there are few evolutionary studies of these muscles in Felis catus, which should take into account the topology and innervation of the muscles to hypothesize the muscle derivation from a common ancestor. The main objective of this study was to check the extrinsic thoracic limb muscles in ten cadavers. Intra‐ and interspecific anatomical variants were found with that formerly described and other felids. Based on the topology and innervation found in this study, the evolutionary derivation was hypothesized. Therefore, the omotransversarius and rhomboideus muscles are derived from the serratus ventralis cervicis muscle. The cleidobrachialis muscle is derived mainly from the m. deltoideus and accessorily from the supracoracoid muscular group. The pectoantebrachialis and pectoralis abdominalis muscles are derived from the pectoralis descendens and cutaneus trunci muscles, respectively. In conclusion, most extrinsic thoracic limb muscles of F. catus may have evolutionary derivations from the last common ancestor of mammals, while some of them are from the last common ancestor of carnivorans or within the family Felidae.

Getting out of a mammalian egg: the egg tooth and caruncle of the echidna

In the echidna, after development in utero, the egg is laid in the pouch and incubated for 10 days. During this time, the fetuses develop an egg tooth and caruncle to help them hatch. Using rare and unprecedented access to limited echidna pre- and post-hatching tissues, development of the egg tooth and caruncle were assessed by micro-CT, histology and immunofluorescence. Unlike therian tooth germs that develop by placode invagination, the echidna egg tooth developed by evagination, similar to the first teeth in some reptiles and fish. The egg tooth ankylosed to the premaxilla, rather than forming a tooth root with ligamentous attachment found in other mammals, with loss of the egg tooth associated with high levels of activity odontoclasts and apoptosis. The caruncle formed as a separate mineralisation from the adjacent nasal capsule, and as observed in birds and turtles, the nasal region epithelium on top of the nose expressed markers of cornification. Together, this highlights that the monotreme egg tooth shares many similarities with typical reptilian teeth, suggesting that this tooth has been conserved from a common ancestor of mammals and reptiles.

Evolution of the Short Form of DNMT3A, DNMT3A2, Occurred in the Common Ancestor of Mammals.

Genomic imprinting is found in marsupial and eutherian mammals, but not in monotremes. While the primary regulator of genomic imprinting in eutherians is differential DNA methylation between parental alleles, conserved imprinted genes in marsupials tend to lack DNA methylation at their promoters. DNA methylation at eutherian imprinted genes is mainly catalyzed by a DNA methyltransferase (DNMT) enzyme, DNMT3A. There are two isoforms of eutherian DNMT3A: DNMT3A and DNMT3A2. DNMT3A2 is the primary isoform for establishing DNA methylation at eutherian imprinted genes and is essential for eutherian genomic imprinting. In this study, we investigated whether DNMT3A2 is also present in the two other mammalian lineages, marsupials and monotremes. We identified DNMT3A2 in both marsupials and monotremes, although imprinting has not been identified in monotremes. By analyzing genomic sequences and transcriptome data across vertebrates, we concluded that the evolution of DNMT3A2 occurred in the common ancestor of mammals. In addition, DNMT3A/3A2 gene and protein expression during gametogenesis showed distinct sexual dimorphisms in a marsupial, the tammar wallaby, and this pattern coincided with the sex-specific DNA methylation reprogramming in this species as it does in mice. Our results show that DNMT3A2 is present in all mammalian groups and suggests that the basic DNMT3A/3A2-based DNA methylation mechanism is conserved at least in therian mammals.

Vertebrate host phylogeny influences gut archaeal diversity

Commonly used 16S rRNA gene primers do not detect the full range of archaeal diversity present in the vertebrate gut. As a result, several questions regarding the archaeal component of the gut microbiota remain, including which Archaea are host-associated, the specificities of such associations and the major factors influencing archaeal diversity. Using 16S rRNA gene amplicon sequencing with primers that specifically target Archaea, we obtained sufficient sequence data from 185 gastrointestinal samples collected from 110 vertebrate species that span five taxonomic classes (Mammalia, Aves, Reptilia, Amphibia and Actinopterygii), of which the majority were wild. We provide evidence for previously undescribed Archaea–host associations, including Bathyarchaeia and Methanothermobacter, the latter of which was prevalent among Aves and relatively abundant in species with higher body temperatures, although this association could not be decoupled from host phylogeny. Host phylogeny explained archaeal diversity more strongly than diet, while specific taxa were associated with both factors, and cophylogeny was significant and strongest for mammalian herbivores. Methanobacteria was the only class predicted to be present in the last common ancestors of mammals and all host species. Further analysis indicated that Archaea–Bacteria interactions have a limited effect on archaeal diversity. These findings expand our current understanding of Archaea–vertebrate associations.

Transitions between foot postures are associated with elevated rates of body size evolution in mammals

Terrestrial mammals have evolved various foot postures: flat-footed (plantigrady), tiptoed (digitigrady), and hooved (unguligrady) postures. Although the importance of foot posture on ecology and body size of mammalian species has been widely recognized, its evolutionary trajectory and influence on body size evolution across mammalian phylogeny remain untested. Taking a Bayesian phylogenetic approach combined with a comprehensive dataset of foot postures in 880 extant mammalian species, we investigated the evolutionary history of foot postures and rates of body size evolution, within the same posture and at transitions between postures. Our results show that the common ancestor of mammals was plantigrade, and transitions predominantly occurred only between plantigrady and digitigrady and between digitigrady and unguligrady. At the transitions between plantigrady and digitigrady and between digitigrady and unguligrady, rates of body size evolution are significantly elevated leading to the larger body masses of digitigrade species (∼1 kg) and unguligrade species (∼78 kg) compared with their respective ancestral postures [plantigrady (∼0.75 kg) and digitigrady]. Our results demonstrate the importance of foot postures on mammalian body size evolution and have implications for mammalian body size increase through time. In addition, we highlight a way forward for future studies that seek to integrate morphofunctional and macroevolutionary approaches.

Discerning evolutionary trends in post-translational modification and the effect of intrinsic disorder: Analysis of methylation, acetylation and ubiquitination sites in human proteins.

Intrinsically disordered regions (IDRs) of proteins play significant biological functional roles despite lacking a well-defined 3D structure. For example, IDRs provide efficient housing for large numbers of post-translational modification (PTM) sites in eukaryotic proteins. Here, we study the distribution of more than 15,000 experimentally determined human methylation, acetylation and ubiquitination sites (collectively termed ‘MAU’ sites) in ordered and disordered regions, and analyse their conservation across 380 eukaryotic species. Conservation signals for the maintenance and novel emergence of MAU sites are examined at 11 evolutionary levels from the whole eukaryotic domain down to the ape superfamily, in both ordered and disordered regions. We discover that MAU PTM is a major driver of conservation for arginines and lysines in both ordered and disordered regions, across the 11 levels, most significantly across the mammalian clade. Conservation of human methylatable arginines is very strongly favoured for ordered regions rather than for disordered, whereas methylatable lysines are conserved in either set of regions, and conservation of acetylatable and ubiquitinatable lysines is favoured in disordered over ordered. Notably, we find evidence for the emergence of new lysine MAU sites in disordered regions of proteins in deuterostomes and mammals, and in ordered regions after the dawn of eutherians. For histones specifically, MAU sites demonstrate an idiosyncratic significant conservation pattern that is evident since the last common ancestor of mammals. Similarly, folding-on-binding (FB) regions are highly enriched for MAU sites relative to either ordered or disordered regions, with ubiquitination sites in FBs being highly conserved at all evolutionary levels back as far as mammals. This investigation clearly demonstrates the complex patterns of PTM evolution across the human proteome and that it is necessary to consider conservation of sequence features at multiple evolutionary levels in order not to get an incomplete or misleading picture.

Correlation between Hox code and vertebral morphology in the mouse: towards a universal model for Synapsida

BackgroundThe importance of the cervical vertebrae as part of the skull–neck system in facilitating the success and diversity of tetrapods is clear. The reconstruction of its evolution, however, is problematic because of the variation in the number of vertebrae, making it difficult to identify homologous elements. Quantification of the morphological differentiation in the neck of diverse archosaurs established homologous units of vertebrae (i.e. modules) resulting from Hox gene expression patterns within the cervical vertebral column. The present study aims to investigate the modularity of the cervical vertebral column in the mouse and to reveal the genetic patterns and changes underlying the evolution of the neck of modern mammals and their extinct relatives. In contrast to modern mammals, non-mammalian synapsids are characterized by a variable cervical count, the presence of free cervical ribs and the presence of a separate CV1 centrum. How might these evolutionary modifications be associated with changes in the Hox code?ResultsIn combination with up-to-date information on cervical Hox gene expression including description of the vertebral phenotype of Hox knock-out mutants, the 3D landmark-based geometric morphometric approach demonstrates a correlation between Hox code and vertebral morphology in the mouse. There is evidence that the modularity of the neck of the mouse had already been established in the last common ancestor of mammals, but differed from that of non-mammalian synapsids. The differences that likely occurred during the evolution of synapsids include an anterior shift in HoxA-5 expression in relation to the reduction of cervical ribs and an anterior shift in HoxD-4 expression linked to the development of the highly differentiated atlas-axis complex, whereas the remaining Hox genes may have displayed a pattern similar to that in mammals on the basis of the high level of conservatism in the axial skeleton of this lineage.ConclusionThus, the mouse Hox code provides a model for understanding the evolutionary mechanisms responsible for the great morphological adaptability of the cervical vertebral column in Synapsida. However, more studies in non-model organisms are required to further elucidate the evolutionary role of Hox genes in axial patterning of the unique mammalian body plan.

389. Muscular Dystrophy Genes and the Early Metazoan Transition from Dynein- to Myosin-Powered Locomotion

During early animal evolution, the primary source of locomotive mechanical power shifted from axonemal (flagellar) dynein to densely arrayed class II myosin. Although the emergence of muscle conferred the advantage of three-dimensional scalability, the transition brought with it the evolutionarily unprecedented problem of safely transmitting huge forces across rapidly deforming cell membranes. This task in vertebrates is accomplished in part through the dystrophin-dystroglycan-sarcoglycan complex (DGC), which is implicated in most forms of muscular dystrophy. We present the inferred earliest steps in the molecular evolution of these cell surface and cortical cytoskeletal proteins, using genome sequence data from all early branching metazoan phyla and a broad sampling of unicellular taxa. Results: Surprisingly, the phylogeny suggests that a DGC emerged before the “sarcomeric” clade of myosins, implying conserved function(s) among unicellular lineages closely related to the Metazoa. Furthermore, linkage of the DGC to the cytoskeleton occurred before the massive tandem-repeat expansions (>200) seen in sarcomeric scaffolding proteins of the titin superfamily. The rod-like domains of dystrophin and utrophin were coopted at their full length from a rapidly lengthening cytoskeletal protein with an unrelated function, that of connecting actin filaments to microtubules at large physical distances. Finally, intron positions in the inferred dystrophin gene in a common ancestor to all Bilateria provide clues to the molecular basis of Duchenne muscular dystrophy and to emerging therapies. Conclusions: Our reconstruction suggests that evolution of membrane-spanning “muscular dystrophy protein complexes” was an essential process as one geometric constraint on power transduction was traded for another. 80% of the length of dystrophin is attributable to tandem DNA duplications that pre-dated the evolutionary emergence of sarcomeres. This chronology implies that escalating power output from striated muscle played no role in providing selective pressure for the serial expansion of “spectrin-like” repeats. This finding has therapeutic implications, as it suggests that minimal length dystophins or utrophins may fully complement the physiological role of full length dystrophin in vertebrates as long as the deletional juxtaposition of triple helical repeats does not disrupt force transmission. This interpretation is consistent with the clinical findings of Becker Muscular Dystrophy in selected patients with in-frame exon duplications. In this view, the evolutionary stability of the length of the dystrophin rod is driven by the incompatibility, when placed in close physical proximity by deletion, of divergent triple helical repeats. The evolutionary translocation of the protein to the cytoskeletal cortex as part of the DGC may have greatly reduced the metabolic load associated with synthesis of the strong but scarce protein, also facilitating evolutionary drift to the enormous size of the gene in a common mammalian ancestor.

Evolutionary origin of Tbr2‐expressing precursor cells and the subventricular zone in the developing cortex

ABSTRACTThe subventricular zone (SVZ) is greatly expanded in primates with gyrencephalic cortices and is thought to be absent from vertebrates with three‐layered, lissencephalic cortices, such as the turtle. Recent work in rodents has shown that Tbr2‐expressing neural precursor cells in the SVZ produce excitatory neurons for each cortical layer in the neocortex. Many excitatory neurons are generated through a two‐step process in which Pax6‐expressing radial glial cells divide in the VZ to produce Tbr2‐expressing intermediate progenitor cells, which divide in the SVZ to produce cortical neurons. We investigated the evolutionary origin of SVZ neural precursor cells in the prenatal cerebral cortex by testing for the presence and distribution of Tbr2‐expressing cells in the prenatal cortex of reptilian and avian species. We found that mitotic Tbr2+ cells are present in the prenatal cortex of lizard, turtle, chicken, and dove. Furthermore, Tbr2+ cells are organized into a distinct SVZ in the dorsal ventricular ridge (DVR) of turtle forebrain and in the cortices of chicken and dove. Our results are consistent with the concept that Tbr2+ neural precursor cells were present in the common ancestor of mammals and reptiles. Our data also suggest that the organizing principle guiding the assembly of Tbr2+ cells into an anatomically distinct SVZ, both developmentally and evolutionarily, may be shared across vertebrates. Finally, our results indicate that Tbr2 expression can be used to test for the presence of a distinct SVZ and to define the boundaries of the SVZ in developing cortices. J. Comp. Neurol. 524:433–447, 2016. © 2015 Wiley Periodicals, Inc.

Coding principles of the canonical cortical microcircuit in the avian brain

Mammalian neocortex is characterized by a layered architecture and a common or "canonical" microcircuit governing information flow among layers. This microcircuit is thought to underlie the computations required for complex behavior. Despite the absence of a six-layered cortex, birds are capable of complex cognition and behavior. In addition, the avian auditory pallium is composed of adjacent information-processing regions with genetically identified neuron types and projections among regions comparable with those found in the neocortex. Here, we show that the avian auditory pallium exhibits the same information-processing principles that define the canonical cortical microcircuit, long thought to have evolved only in mammals. These results suggest that the canonical cortical microcircuit evolved in a common ancestor of mammals and birds and provide a physiological explanation for the evolution of neural processes that give rise to complex behavior in the absence of cortical lamination.

Evolution of mammalian sensorimotor cortex: thalamic projections to parietal cortical areas in Monodelphis domestica.

The current experiments build upon previous studies designed to reveal the network of parietal cortical areas present in the common mammalian ancestor. Understanding this ancestral network is essential for highlighting the basic somatosensory circuitry present in all mammals, and how this basic plan was modified to generate species specific behaviors. Our animal model, the short-tailed opossum (Monodelphis domestica), is a South American marsupial that has been proposed to have a similar ecological niche and morphology to the earliest common mammalian ancestor. In this investigation, we injected retrograde neuroanatomical tracers into the face and body representations of primary somatosensory cortex (S1), the rostral and caudal somatosensory fields (SR and SC), as well as a multimodal region (MM). Projections from different architectonically defined thalamic nuclei were then quantified. Our results provide further evidence to support the hypothesized basic mammalian plan of thalamic projections to S1, with the lateral and medial ventral posterior thalamic nuclei (VPl and VPm) projecting to S1 body and S1 face, respectively. Additional strong projections are from the medial division of posterior nucleus (Pom). SR receives projections from several midline nuclei, including the medial dorsal, ventral medial nucleus, and Pom. SC and MM show similar patterns of connectivity, with projections from the ventral anterior and ventral lateral nuclei, VPm and VPl, and the entire posterior nucleus (medial and lateral). Notably, MM is distinguished from SC by relatively dense projections from the dorsal division of the lateral geniculate nucleus and pulvinar. We discuss the finding that S1 of the short-tailed opossum has a similar pattern of projections as other marsupials and mammals, but also some distinct projections not present in other mammals. Further we provide additional support for a primitive posterior parietal cortex which receives input from multiple modalities.

Mammalian skull heterochrony reveals modular evolution and a link between cranial development and brain size.

The multiple skeletal components of the skull originate asynchronously and their developmental schedule varies across amniotes. Here we present the embryonic ossification sequence of 134 species, covering all major groups of mammals and their close relatives. This comprehensive data set allows reconstruction of the heterochronic and modular evolution of the skull and the condition of the last common ancestor of mammals. We show that the mode of ossification (dermal or endochondral) unites bones into integrated evolutionary modules of heterochronic changes and imposes evolutionary constraints on cranial heterochrony. However, some skull-roof bones, such as the supraoccipital, exhibit evolutionary degrees of freedom in these constraints. Ossification timing of the neurocranium was considerably accelerated during the origin of mammals. Furthermore, association between developmental timing of the supraoccipital and brain size was identified among amniotes. We argue that cranial heterochrony in mammals has occurred in concert with encephalization but within a conserved modular organization.

Insights into the evolution of mammalian telomerase: Platypus TERT shares similarities with genes of birds and other reptiles and localizes on sex chromosomes

BackgroundThe TERT gene encodes the catalytic subunit of the telomerase complex and is responsible for maintaining telomere length. Vertebrate telomerase has been studied in eutherian mammals, fish, and the chicken, but less attention has been paid to other vertebrates. The platypus occupies an important evolutionary position, providing unique insight into the evolution of mammalian genes. We report the cloning of a platypus TERT (OanTERT) ortholog, and provide a comparison with genes of other vertebrates.ResultsThe OanTERT encodes a protein with a high sequence similarity to marsupial TERT and avian TERT. Like the TERT of sauropsids and marsupials, as well as that of sharks and echinoderms, OanTERT contains extended variable linkers in the N-terminal region suggesting that they were present already in basal vertebrates and lost independently in ray-finned fish and eutherian mammals. Several alternatively spliced OanTERT variants structurally similar to avian TERT variants were identified. Telomerase activity is expressed in all platypus tissues like that of cold-blooded animals and murine rodents. OanTERT was localized on pseudoautosomal regions of sex chromosomes X3/Y2, expanding the homology between human chromosome 5 and platypus sex chromosomes. Synteny analysis suggests that TERT co-localized with sex-linked genes in the last common mammalian ancestor. Interestingly, female platypuses express higher levels of telomerase in heart and liver tissues than do males.ConclusionsOanTERT shares many features with TERT of the reptilian outgroup, suggesting that OanTERT represents the ancestral mammalian TERT. Features specific to TERT of eutherian mammals have, therefore, evolved more recently after the divergence of monotremes.

The Temporal Sequence of the Mammalian Neocortical Neurogenetic Program Drives Mediolateral Pattern in the Chick Pallium

The six-layered neocortex permits complex information processing in all mammalian species. Because its homologous region (the pallium) in nonmammalian amniotes has a different architecture, the ability of neocortical progenitors to generate an orderly sequence of distinct cell types was thought to have arisen in the mammalian lineage. This study, however, shows that layer-specific neuron subtypes do exist in the chick pallium. Deep- and upper-layer neurons are not layered but are segregated in distinct mediolateral domains in vivo. Surprisingly, cultured chick neural progenitors produce multiple layer-specific neuronal subtypes in the same chronological sequence as seen in mammals. These results suggest that the temporal sequence of the neocortical neurogenetic program was already inherent in the last common ancestor of mammals and birds and that mammals use this conserved program to generate a uniformly layered neocortex, whereas birds impose spatial constraints on the sequence to pattern the pallium.

Emergence of mammals by emergency: exaptation

With the development of molecular embryology and the coming of the post-genomic era, the molecular mechanisms of morphological evolution have recently begun to be elucidated. Whole genome sequences of many vertebrate species have been determined, and comparative genomics has suggested that one source of biodiversity is conserved non-coding elements (CNEs), which may be involved in generating new networks of gene expression. Nishihara et al. (Genome Res. 2006; 16, 864) discovered retroposon (AmnSINE1s)-derived CNEs in the human genome, and suggested that the AmnSINE1s obtained their function (i.e., exapted) in a common mammalian ancestor and are involved in generating mammalian-specific morphology. Therefore, investigation of the function of AmnSINE1-derived CNEs in morphogenesis helps us understand the molecular events of how mammals obtained their specific morphological characters by exaptation that occurred when the first mammalian ancestor emerged about 250 Ma (million years ago). Because there are more than 100 AmnSINE1-derived CNE loci in the mammalian genome, a burst of exaptation of AmnSINE1s must have occurred, possibly triggered by the Permian-Triassic mass extinction 250 Ma. In this review, we discuss morphological evolution of the mammalian-specific characters including brain that were exapted after retrotransposition of AmnSINE1s by referring to two CNE loci described by Sasaki et al.

Evolution of the regulatory control of vertebrate striated muscle: the roles of troponin I and myosin binding protein-C

Troponin I (TnI) and myosin binding protein-C (MyBP-C) are key regulatory proteins of contractile function in vertebrate muscle. TnI modulates the Ca(2+) activation signal, while MyBP-C regulates cross-bridge cycling kinetics. In vertebrates, each protein is distributed as tissue-specific paralogs in fast skeletal (fs), slow skeletal (ss), and cardiac (c) muscles. The purpose of this study is to characterize how TnI and MyBP-C have changed during the evolution of vertebrate striated muscle and how tissue-specific paralogs have adapted to different physiological conditions. To accomplish this we have completed phylogenetic analyses using the amino acid sequences of all known TnI and MyBP-C isoforms. This includes 99 TnI sequences (fs, ss, and c) from 51 different species and 62 MyBP-C sequences from 26 species, with representatives from each vertebrate group. Results indicate that the role of protein kinase A (PKA) and protein kinase C (PKC) in regulating contractile function has changed during the evolution of vertebrate striated muscle. This is reflected in an increased number of phosphorylatable sites in cTnI and cMyBP-C in endothermic vertebrates and the loss of two PKC sites in fsTnI in a common ancestor of mammals, birds, and reptiles. In addition, we find that His(132), Val(134), and Asn(141) in human ssTnI, previously identified as enabling contractile function during cellular acidosis, are present in all vertebrate cTnI isoforms except those from monotremes, marsupials, and eutherian mammals. This suggests that the replacement of these residues with alternative residues coincides with the evolution of endothermy in the mammalian lineage.

Statistical evidence for ancestral correlation patterns

Statistical correlations in DNA sequences are an important source of information for processes of genome evolution. As a special case of such correlations and building up on our previous work, here we study, how short-range correlations in Eukaryotic genomes change under elimination of various classes of repetitive DNA. Our main result is that a residual correlation pattern, common to most mammalian species, emerges under elimination of all repetitive DNA, suggesting features of an ancestral correlation signature. Furthermore, using this general framework, we find classes of repeats, which upon deletion move the correlation pattern towards this residual pattern (simple repeats and SINEs) or away from this residual pattern (LINEs). These findings suggest that the common correlation pattern visible in the mammalian species after repeat elimination can be associated with a common mammalian ancestor.

Ultraconserved Elements: Analyses of Dosage Sensitivity, Motifs and Boundaries

Ultraconserved elements (UCEs) are sequences that are identical between reference genomes of distantly related species. As they are under negative selection and enriched near or in specific classes of genes, one explanation for their ultraconservation may be their involvement in important functions. Indeed, many UCEs can drive tissue-specific gene expression. We have demonstrated that nonexonic UCEs are depleted among segmental duplications (SDs) and copy number variants (CNVs) and proposed that their ultraconservation may reflect a mechanism of copy counting via comparison. Here, we report that nonexonic UCEs are also depleted among 10 of 11 recent genomewide data sets of human CNVs, including 3 obtained with strategies permitting greater precision in determining the extents of CNVs. We further present observations suggesting that nonexonic UCEs per se may contribute to this depletion and that their apparent dosage sensitivity was in effect when they became fixed in the last common ancestor of mammals, birds, and reptiles, consistent with dosage sensitivity contributing to ultraconservation. Finally, in searching for the mechanism(s) underlying the function of nonexonic UCEs, we have found that they are enriched in TAATTA, which is also the recognition sequence for the homeodomain DNA-binding module, and bounded by a change in A + T frequency.

MiRNA Profile of a Triassic Common Mammalian Ancestor and PremiRNA Evolution in the Three Mammalian Reproductive Lineages

MicroRNAs (miRNAs) are major factors in the regulation of gene expression. Recent evolutionary studies of miRNAs indicate that important biological innovations, such as the advent of bilateral symmetry and placental reproduc- tion, are accompanied by bursts of miRNA creation which are subsequently conserved via purifying selection. The emer- gence of eutherian (placental) mammals followed by as much as fifty million years the appearance of the first true mam- mals in the late Triassic, some 230 million years ago. We have utilized microRNA inventories of eutherian, metatherian (marsupial), monotreme (platypus), and chicken genomes to assemble a minimal microRNA profile of the last common ancestor of all mammals consisting of 171 miRNAs. This profile suggests that the rise of placental reproduction launched a more than three-fold expansion of microRNAs. In addition to expansion of the microRNA repertoire, the conserved mi- croRNAs from five mammalian and one avian genome show evidence for conforming to a canonical phylogenetic history as well as dramatic deviations from the assumptions of molecular clock-like rates and the equality of substitution rates among lineages. We also show that many of these basal mammalian miRNAs are highly expressed in eutherian placenta thus creating an opportunity to gain insight on how microRNAs acquire new targets and new functions.