Course Of Mammalian Evolution Research Articles

Extensive Copy-Number Variation of the Human Olfactory Receptor Gene Family

As much as a quarter of the human genome has been reported to vary in copy number between individuals, including regions containing about half of the members of the olfactory receptor (OR) gene family. We have undertaken a detailed study of copy-number variation of ORs to elucidate the selective and mechanistic forces acting on this gene family and the true impact of copy-number variation on human OR repertoires. We argue that the properties of copy-number variants (CNVs) and other sets of large genomic regions violate the assumptions of statistical methods that are commonly used in the assessment of gene enrichment. Using more appropriate methods, we provide evidence that OR enrichment in CNVs is not due to positive selection but is because of OR preponderance in segmentally duplicated regions, which are known to be frequently copy-number variable, and because purifying selection against CNVs is lower in OR-containing regions than in regions containing essential genes. We also combine multiplex ligation-dependent probe amplification (MLPA) and PCR to assay the copy numbers of 37 candidate CNV ORs in a panel of approximately 50 human individuals. We confirm copy-number variation of 18 ORs but find no variation in this human-diversity panel for 16 other ORs, highlighting the caveat that reported intervals often overrepresent true CNVs. The copy-number variation we describe is likely to underpin significant variation in olfactory abilities among human individuals. Finally, we show that both homology-based and homology-independent processes have played a recent role in remodeling the OR family.

Comparative anatomical investigations of the postcranial skeleton of Henkelotherium guimarotae Krebs, 1991 (Eupantotheria, Mammalia) and their implications for its locomotion

The postcranial skeleton of the Late Jurassic Henkelotherium guimarotae exhibits a combination of primitive and modern characters, illuminating the early evolution of the therian “Grundplan”. Some of these characters (e.g., development of a supaspinous fossa) have been conserved in the later course of mammalian evolution, and have persisted to date with little variation in all therian taxa. Henkelotherium shares with certain small Recent mammals (Tupaiidae, Didelphidae) some primitive characters (e.g., asymmetric condyles of the femur), suggesting a mode of locomotion that is a similar to that in these living species. The small body size of Henkelotherium undoubtedly required some climbing abilities. This is supported by the paleoecological reconstruction of the Guimarota ecosystem indicating a densely vegetated environment. Henkelotherium shows features (e.g., elongated tail) that are interpreted here as adaptations for climbing. We suggest that Henkelotherium had a well developed capacity to move on discontinuous surfaces, displaying a flexible and versatile mode of locomotion.

Role of retrotransposon-derived imprinted gene, Rtl1, in the feto-maternal interface of mouse placenta

Eutherian placenta, an organ that emerged in the course of mammalian evolution, provides essential architecture, the so-called feto-maternal interface, for fetal development by exchanging nutrition, gas and waste between fetal and maternal blood. Functional defects of the placenta cause several developmental disorders, such as intrauterine growth retardation in humans and mice. A series of new inventions and/or adaptations must have been necessary to form and maintain eutherian chorioallantoic placenta, which consists of capillary endothelial cells and a surrounding trophoblast cell layer(s). Although many placental genes have been identified, it remains unknown how the feto-maternal interface is formed and maintained during development, and how this novel design evolved. Here we demonstrate that retrotransposon-derived Rtl1 (retrotransposon-like 1), also known as Peg11 (paternally expressed 11), is essential for maintenance of the fetal capillaries, and that both its loss and its overproduction cause late-fetal and/or neonatal lethality in mice.

CpG island density and its correlations with genomic features in mammalian genomes

A systematic analysis of CpG islands in ten mammalian genomes suggests that an increase in chromosome number elevates GC content and prevents loss of CpG islands.

Long terminal repeats of porcine endogenous retroviruses in Sus scrofa

Using PCR, sequencing, and bioinformatic approaches with the genomic DNAs of Korean pigs (domestic, wild, and hybrid with Yorkshire), twelve solitary PERV long terminal repeat elements were identified and analyzed. Structure analysis of the LTR elements indicated that they have different repeat sequences in the U3 region. The PERV-A6-KWP1 and -KWP2 elements bear seven and eight 39-bp repeats, respectively. The R region of the PERV LTR elements was highly conserved in pig and mouse genomes, suggesting that they seem to have originated from a common exogenous viral element and then evolved independently throughout the course of mammalian evolution.

Microbes and the Developing Gastrointestinal Tract

During the course of mammalian evolution, there has been a close relationship between microbes residing in the gastrointestinal (GI) tract and the mammalian host. Although the host provides the microbes with a warm environment and nutrients, they, in turn, undergo various metabolic processes that aid the host. The host has developed weapons against microbes that are considered foreign, as well as mechanisms to tolerate and live synergistically with most of the microbes in the GI tract. This relationship is proving to be important not only in the neonatal period and during infancy, but it is becoming increasingly evident that microbial colonization in early life may affect the individual's health throughout life. Here we will review this relationship in terms of health and disease, with a focus on the aspects of this relationship during maturation of the host.

Genomic imprinting in mammals: emerging themes and established theories.

The epigenetic events that occur during the development of the mammalian embryo are essential for correct gene expression and cell-lineage determination. Imprinted genes are expressed from only one parental allele due to differential epigenetic marks that are established during gametogenesis. Several theories have been proposed to explain the role that genomic imprinting has played over the course of mammalian evolution, but at present it is not clear if a single hypothesis can fully account for the diversity of roles that imprinted genes play. In this review, we discuss efforts to define the extent of imprinting in the mouse genome, and suggest that different imprinted loci may have been wrought by distinct evolutionary forces. We focus on a group of small imprinted domains, which consist of paternally expressed genes embedded within introns of multiexonic transcripts, to discuss the evolution of imprinting at these loci.

Short interspersed elements (SINEs) are a major source of canine genomic diversity.

SINEs are retrotransposons that have enjoyed remarkable reproductive success during the course of mammalian evolution, and have played a major role in shaping mammalian genomes. Previously, an analysis of survey-sequence data from an individual dog (a poodle) indicated that canine genomes harbor a high frequency of alleles that differ only by the absence or presence of a SINEC_Cf repeat. Comparison of this survey-sequence data with a draft genome sequence of a distinct dog (a boxer) has confirmed this prediction, and revealed the chromosomal coordinates for >10,000 loci that are bimorphic for SINEC_Cf insertions. Analysis of SINE insertion sites from the genomes of nine additional dogs indicates that 3%-5% are absent from either the poodle or boxer genome sequences--suggesting that an additional 10,000 bimorphic loci could be readily identified in the general dog population. We describe a methodology that can be used to identify these loci, and could be adapted to exploit these bimorphic loci for genotyping purposes. Approximately half of all annotated canine genes contain SINEC_Cf repeats, and these elements are occasionally transcribed. When transcribed in the antisense orientation, they provide splice acceptor sites that can result in incorporation of novel exons. The high frequency of bimorphic SINE insertions in the dog population is predicted to provide numerous examples of allele-specific transcription patterns that will be valuable for the study of differential gene expression among multiple dog breeds.

Ancestry of the Mammalian Preplate and its Derivatives: Evolutionary Relicts or Embryonic Adaptations?

Mammalian cortical development is preceded by the elaboration of a transient preplate, which is split into a superficial marginal zone and a deep subplate after the arrival of the cortical plate. There has been some controversy in the evolutionary interpretation of this transient structure, as some propose it to represent the ancestral cortex or pallium of non-mammals, while others consider it to be a phylogenetic novelty. The preplate and its derivatives contain components derived by both tangential and radial migration. Tangentially migrating elements include pioneer neurons and interneurons, both of subpallial origin, and Cajal-Retzius cells, mostly of pallial origin. Pioneer neurons were probably present in the ancestors of mammals, but may have changed their original superficial position to one below the developing cortex, thus attracting thalamic afferents in the subcortical white matter, and making them penetrate the cortex radially. In mammals, Cajal-Retzius cells appear to have increased both in number and on their level of reelin expression, perhaps in the context of controlling the final stages of migration in a radially expanding neoocortex. Radial-migrating cells are partly represented by the pyramidal-like cells of the subplate. These neurons resemble the excitatory elements of the adult reptilian cortex, but is not clear whether they are their true homologues. One possibility is that these cells appeared by virtue of a heterochronic process in which the earliest radial elements of the cortical plate began to be produced at progressively earlier developmental stages. Thus, we conclude that the mammalian preplate and its derivatives contain both ancestral and derived elements, all of which have been modified in the course of mammalian evolution to support an increasingly complex cortical plate development.

Evolutionary constraints on CD1 structure: insights from comparative genomic analysis

It is well established that the CD1 family of proteins present lipid antigens to T cells. However, in vivo studies of CD1 function have been carried out almost exclusively using mouse models, despite the fact that mice lack most of the CD1 genes that are found in humans and other mammals. To understand why there is a difference in the number of CD1 genes observed between humans and mice, we used comparative genomic analysis to examine differences at the CD1 locus. This analysis reveals a significant genomic deletion in mice that provides a probable explanation for the disparity. Furthermore, we propose a hypothesis in which functionally convergent evolution could have a role in at least partially compensating for the loss of certain CD1 isoforms during the course of mammalian evolution.

Mammary tumors in mice conditionally mutant for Brca1 exhibit gross genomic instability and centrosome amplification yet display a recurring distribution of genomic imbalances that is similar to human breast cancer.

BRCA1 mutation carriers have an increased susceptibility to breast and ovarian cancer. Excision of exon 11 of Brca1 in the mouse, using a conditional knockout (Cre-loxP) approach, results in mammary tumor formation after long latency. To characterize the genomic instability observed in these tumors, to establish a comparative map of chromosomal imbalances and to contribute to the validation of this mouse model of breast cancer, we have characterized chromosomal imbalances and aberrations using comparative genomic hybridization (CGH), and spectral karyotyping (SKY). We found that all tumors exhibit chromosome instability as evidenced by structural chromosomal aberrations and aneuploidy, yet they display a pattern of chromosomal gain and loss that is similar to the pattern in human breast carcinomas. Of note, nine of 15 tumors exhibited a gain of distal chromosome 11, a region that is orthologous to human chromosome 17q11-qter, the mapping position of Erbb2. However, our analysis suggests that genes distal to Erbb2 are the main targets of amplification. Four of the tumors also exhibited a copy number loss of proximal chromosome 11 (11A-B), a region orthologous to human 17p. In eight of the tumors we observed whole or partial gain of chromosome 15 centering on 15D2-D3 (orthologous to human chromosome 8q24), the map location of the c-Myc gene, and six of the tumors exhibited copy number loss of whole or partial chromosome 14, including 14D3, the map location of Rb1. We conclude that despite the tremendous shuffling of chromosomes during the course of mammalian evolution, the pattern of genomic imbalances is conserved between BRCA1-associated mammary gland tumors in mice and humans. Western blot analysis showed that while p53 is absent or mutated in some tumors, at least two tumors revealed wild-type protein, suggesting that other genetic events may lead to tumorigenesis. Similar to BRCA1-deficient mouse embryonic fibroblasts, the tumor cells contained supernumerary functional centrosomes with intact centrioles whose presence results in multipolar mitoses and aneuploidy.

An Unusual Form of Purifying Selection in a Sperm Protein

Protamines are small, highly basic DNA-binding proteins found in the sperm of animals. Interestingly, the proportion of arginine residues in one type of protamine, protamine P1, is about 50% in mammals. Upon closer examination, it was found that both the total number of amino acids and the positions of arginine residues have changed considerably during the course of mammalian evolution. This evolutionary pattern suggests that protamine P1 is under an unusual form of purifying selection, in which the high proportion of arginine residues is maintained but the positions may vary. In this case, we would expect that the rate of nonsynonymous substitution is not particularly low compared with that of synonymous substitution, despite purifying selection. We would also expect that the selection for a high arginine content results in a high frequency of the nucleotide G in the coding region of this gene, because all six arginine codons contain at least one G. These expectations were confirmed in our study of mammalian protamine genes. Analysis of nonmammalian vertebrate genes also showed essentially the same patterns of evolutionary changes, suggesting that this unusual form of purifying selection has been active since the origin of bony vertebrates. The protamine gene of an insect species shows similar patterns, although its purifying selection is less intense. These observations suggest that arginine-rich selection is a general feature of protamine evolution. The driving force for arginine-rich selection appears to be the DNA-binding function of protamine P1 and an interaction with a protein kinase in the fertilized egg.

Cloning and nucleotide sequence of retroposons specific to hominoid primates derived from an endogenous retrovirus (HERV-K).

595 ENDOGENOUS RETROVIRUSES comprise approximately 1% of the human genome.1 Although most human endogenous retroviruses (HERVs) are defective, one class, HERV-K (homologous to mouse mammary tumor virus [MMTV]), encodes viral proteins and particles3 and is highly expressed in germ cell tumors. Retroposons (a retroelementso and a retrovirus-like elements,o which multiply in the genome by retrotransposition) are distinguished from retroviruses by the absence of one or both long terminal repeats (LTRs). These repetitive elements are classified into two groupsÐshort (up to 600 bp) interspersed nuclear elements (SINEs) and long (about 6 kg) interspersed nuclear elements (LINEs)Ð that include a number of families that have diverged in the course of mammalian evolution.4 One class of SINEs, the Alu sequences, is specific to primates. Another class, termed SINE-R (for retrovirus), which is derived from the HERV-K sequence, has apparently undergone modification in the hominoid lineage.5 Such elements are a potential agency of genome change.1,6,7 The human-specific retroposon SINE-R.C2, a member of the SINE-R retroposon family (present at 4000 to 5000 copies per haploid human genome), was discovered in an investigation of the variable number of tandem repeats (VNTR) locus within intron 3 of the gene for C2, the second component of complement, located in class III of the major histocompatibility complex on the short arm of human chromosome 6.8,9 Other members of the SINE-R family in the human genome, SINER11, -14, and -19, were isolated by colony blot hybridization with an HERV-K10 probe. By BLAST search, schizophrenic brain S11 cDNA (GenBank, accession No. AA772777) was also found to have high homology with the 39 LTR of HERV-K10. Therefore, specific polymerase chain reaction (PCR) primers, JS902 and JS903, were designed from S11 cDNA. Using these primers, the sequences HS307 (GenBank, accession No. AB016781) and HS408 (GenBank, accession No. AB016782), which have a high degree of homology to the SINE-R.C2, -R11, -R14, and -R19 retroposons, were identified in an investigation of the Xq21.3 region that has been tentatively linked to schizophrenia and schizo-affective disorder by Laval et al.10 and Kim et al. Each of these retroposons derives from the 3 9 long terminal repeat and the small upstream flanking regions of the human endogenous retrovirus HERV-K10,5 the entire sequence of which has been reported as a candidate autoimmune gene in type I diabetes.11 The HERV-K10 (present at 50 copies per haploid human genome) has been found to be present in all primates except for New World monkeys, whereas SINE-R.C2 is present only in Homo sapiens. Other members of the SINER family have been found to be present in the human, chimpanzee, and gorilla genomes by Southern blot analysis.12 To obtain sequence information relating to SINE-R-type retroposons in hominoid primates, genomic DNAs from the chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), orangutan (Pongo pygmaeus), and agile gibbon (Hylobates agilis) were amplified by PCR using primers JS902 (5 9 -GAGA ATGGGCCATGATGAC-3 9 , bases 4±22) and JS903 (59 GATCATTCTTGGATGTTTCT-3 9 , bases 466±485) derived from schizophrenic brain S11 cDNA (GenBank, accession No. AA772777). The PCR conditions followed were those of Kim et al. with an annealing temperature of 56°C. PCR products were separated on a 1.8% agarose gel, purified with the QIAEX II gel extraction kit (Qiagen, Chatsworth, CA) and cloned into the T-khs307 vector.14 Plasmid DNA was isolated by the alkali lysis method, using the High Pure plasmid isolation kit (Boehringer Mannheim, Indianapolis, IN). Individual plasmid DNAs were screened for inserts by PCR and positive samples were subjected to sequence analyses on both strands with T7 and M13 reverse primers using an automated DNA sequencer (model 373A; Applied Biosystems, Foster City, CA) and the DyeDeoxy terminator kit. Sequence analyses were done with the aid of GAP and PILEUP from the GCG program. The neighbor-joining phylogenetic analysis was performed with the CLUSTAL W program.15 We searched for sequence homology using the BLAST network server.16 Using genomic DNA from hominoid primates, SINE-R-type retroposons were amplified and nucleotide sequences deter-

The lysine-binding function of Lp(a).

The atherogenicity of Lp(a) is attributable to the binding of its apolipoprotein(a) component to fibrin and other plasminogen substrates. It can attenuate the activation of plasminogen, diminishing plasmin-dependent fibrinolysis and transforming growth factor-beta activation. Apolipoprotein(a) contains a major lysine-binding site in one of its kringle domains. Destroying this site by site-directed mutagenesis greatly reduces the binding of apolipoprotein(a) to lysine and fibrin. Transgenic mice expressing wild-type apolipoprotein(a) have a 5-fold increase in the development of lipid lesions, as well as a large increase in the focal deposition of apolipoprotein(a) in the aorta, compared to the lysine-binding site mutant strain and to non-transgenic litter mates. Although the adaptive function of apolipoprotein(a) remains obscure, a gene with similar structure has evolved by independent remodeling of the plasminogen twice during the course of mammalian evolution.

Protein phosphatase X has been highly conserved during mammalian evolution

Complementary DNA encoding human protein phosphatase X (PPX, also designated PPP4 in the human genome nomenclature) was isolated from a teratocarcinoma library. The deduced amino acid sequence of human PPX differs from that of rabbit PPX in only two in 307 amino acids, demonstrating that the structure of PPX has been highly conserved during the course of mammalian evolution.

PCR derived cDNA clones for X-linked phosphoglycerate kinase-1 in a marsupial, the tammar wallaby ( Macropus eugenii)

cDNA clones for the X-linked PGK-1 were obtained from a tammar wallaby liver by PCR and sequenced. The PGK-1 gene published here is the consensus sequence of those clones. The sequence represents an open reading frame of 1251 bp. Sequence comparisons to X-linked and autosomal sequences showed the greatest homology with the X-linked PGK-1 genes in eutherian species. This sequence opens the way for studying the paternal X inactivation phenomenon in marsupials and will assist in defining the time course of mammalian evolution.

The Language Bioprogram Hypothesis and Singaporean English

In his rather controversial book "Roots of Language" 1981, Bickerton claims that 'many of the prerequisites for human language were laid down in the course of mammalian evolution, and that the most critical of those prerequisites... was the capacity to construct quite elaborate mental representations of the external world....' (Bickerton 1981:294-295). The Language Bioprogram Hypothesis (LBH) concerns 'a biological' or 'a species-specific program for language, genetically coded and expressed in ways still largely myste rious, in the structures and modes of operation of the human brain' (Bickerton 1984:173). Among the important distinctions of the LBH are those between state and process, punctual and non-punctual, specific and non-specific and causative and non-causative. Such dis tinctions are clearly evident when a pidgin becomes a creole. The in nate punctual/non-punctual distinction is manifested in Bickerton's investigation of past tense marking in 2 decreolizing situations- Guyana and Hawaii. Verbs which were used non-punctually received a lower marking for past tense than verbs that were used punctually. What are the factors which influence variation in past tense marking of Chinese Singaporeans? The substratum language may have a strong influence since in Chinese there is no morphological change to the past form of the verb. Or it could be that the innate Language Bioprogram has an influence as well. Naturally, other fac tors such as teaching and general language learning strategies cannot be ignored. This paper is based on an empirical investigation of recordings of spontaneous speech of a hundred ethnically Chinese Singaporeans who have had English-medium education and discusses variation in past tense marking in Singaporean English as well as pedagogical im plications of the LBH for second language acquisition.

Neocortical Expansion: An Attempt toward Relating Phylogeny and Ontogeny

The neocortex is the most characteristic feature of the human brain. On gross inspection, its convoluted surfaces can be seen to have overgrown and covered most other brain structures. In the functional sphere, it is to the neocortex that we attribute those behaviors assumed to be most uniquely human such as cognition and linguistic behavior. This essay is an attempt to understand how this structure expanded during the course of mammalian evolution. At present, any attempt must be more speculative than definitive, but it is offered in the hope that it will generate more discussion on a topic that is central to all neurobiology, as well as a number of allied disciplines. I will proceed by outlining current views on the evolution of the brain, briefly review the organization of the somatosensory cortex in several mammalian forms, and then discuss in some detail ontogenetic mechanisms that may have some bearing on neocortical phylogeny. The primary proposition put forth is that the mammalian neocortex is relatively unspecified by strict genetic means, and that this allowed the neocortex to expand and adapt to a variety of circumstances during the course of phylogeny.

Flexible recognition of rapidly evolving promoter sequences by mitochondrial transcription factor 1.

Transcriptional promoters of mitochondrial DNA have diverged extensively in the course of mammalian evolution. Nevertheless, the transcriptional machinery and the overall mechanisms of transcriptional control and regulation seem to be conserved. We have compared the human and murine homologs of the major DNA-binding transcriptional activator, mitochondrial transcription factor 1 (mtTF1), with unexpected results. Both proteins have similar chromatographic and transcriptional properties and are the same size. Both recognize and bind sequences between -12 and -39 within their respective homologous promoters. However, the sequences that they recognize are markedly divergent; although the base pairs they contact are situated similarly or identically with respect to the transcriptional start site, sequence identity between the two species' contact points is less than 50%. Interestingly, the two proteins are functionally interchangeable; each can bind to the heterologous light-strand promoter and can activate transcription by the heterologous mitochondrial RNA polymerase. Thus, the RNA polymerase or some as yet undetected transcription factor, rather than mTF1, may determine the strict species specificity of mitochondrial transcription. Flexible DNA sequence recognition by mtTF1, on the other hand, may be a principal facilitating mechanism for rapid control sequence evolution.

Differences in evolutionary stability among mammalian H1 subtypes. Implications for the roles of H1 subtypes in chromatin.

The metabolic and developmental properties that differentiate five H1 subtypes of the mouse, H1a-H1e, are shown to have been conserved in the course of mammalian evolution. The structures of the subtypes, however, as judged by their mobilities in two-dimensional gel electrophoresis, have been conserved to varying extents. H1a and H1c have undergone the most structural variation, each having a different electrophoretic mobility in every species examined. H1b is much less varied, while H1d and H1e are invariant by these electrophoretic criteria. These results suggest that H1a and -c differ fundamentally from H1b, -d, and -e in their interactions with other chromatin components. It is suggested that this difference is in the ability to promote the coiling of 10-nm chromatin fibers into higher order chromatin structures.