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Morris Goodman

Publications and source records attributed to Morris Goodman.

At least 19 recordsLinked to original sources
PubMed2006

Functionally important glycosyltransferase gain and loss during catarrhine primate emergence.

A glycosyltransferase, alpha1,3galactosyltransferase, catalyzes the terminal step in biosynthesis of Galalpha1,3Galbeta1-4GlcNAc-R (alphaGal), an oligosaccharide cell surface epitope. This epitope or antigenically similar epitopes are widely distributed among the different forms of life. Although abundant in most mammals, alphaGal is not normally found in catarrhine primates (Old World monkeys and apes, including humans), all of which produce anti-alphaGal antibodies from infancy onward. Natural selection favoring enhanced resistance to alphaGal-positive pathogens has been the primary reason offered to account for the loss of alphaGal in catarrhines. Here, we question the primacy of this immune defense hypothesis with results that elucidate the evolutionary history of GGTA1 gene and pseudogene loci. One such locus, GGTA1P, a processed (intronless) pseudogene (PPG), is present in platyrrhines, i.e., New World monkeys, and catarrhines but not in prosimians. PPG arose in an early ancestor of anthropoids (catarrhines and platyrrhines), and GGTA1 itself became an unprocessed pseudogene in the late catarrhine stem lineage. Strong purifying selection, denoted by low nonsynonymous substitutions per nonsynonymous site/synonymous substitutions per synonymous site values, preserved GGTA1 in noncatarrhine mammals, indicating that the functional gene product is subjected to considerable physiological constraint. Thus, we propose that a pattern of alternative and/or more beneficial glycosyltransferase activity had to first evolve in the stem catarrhines before GGTA1 inactivation could occur. Enhanced defense against alphaGal-positive pathogens could then have accelerated the replacement of alphaGal-positive catarrhines by alphaGal-negative catarrhines. However, we emphasize that positively selected regulatory changes in sugar chain metabolism might well have contributed in a major way to catarrhine origins.

Animals↗
PubMed2006

Evolution of increased glia-neuron ratios in the human frontal cortex.

Evidence from comparative studies of gene expression and evolution suggest that human neocortical neurons may be characterized by unusually high levels of energy metabolism. The current study examined whether there is a disproportionate increase in glial cell density in the human frontal cortex in comparison with other anthropoid primate species (New World monkeys, Old World monkeys, and hominoids) to support greater metabolic demands. Among 18 species of anthropoids, humans displayed the greatest departure from allometric scaling expectations for the density of glia relative to neurons in layer II/III of dorsolateral prefrontal cortex (area 9L). However, the human glia-neuron ratio in this prefrontal region did not differ significantly from allometric predictions based on brain size. Further analyses of glia-neuron ratios across frontal areas 4, 9L, 32, and 44 in a sample of humans, chimpanzees, and macaque monkeys showed that regions involved in specialized human cognitive functions, such as "theory of mind" (area 32) and language (area 44) have not evolved differentially higher requirements for metabolic support. Taken together, these findings suggest that greater metabolic consumption of human neocortical neurons relates to the energetic costs of maintaining expansive dendritic arbors and long-range projecting axons in the context of an enlarged brain.

Animals↗
PubMed2006

Phylogenetic relationships and divergence times among New World monkeys (Platyrrhini, Primates).

Orthologous sequences of six nuclear genes were obtained for all recognized genera of New World monkeys (Primates: Platyrrhini) and outgroups to evaluate the phylogenetic relationships and to estimate divergence times. Phylogenetic relationships were reconstructed by maximum parsimony, maximum likelihood, and Bayesian approaches. All methods resolved with 100% branch support genus-level relationships, except for the grouping of Aotus as a sister taxa of Cebus and Saimiri, which was supported by low bootstrap percentages and posterior probability. All approaches depict three monophyletic New World monkey families: Atelidae, Cebidae, and Pitheciidae; also within each family, all approaches depict the same branching topology. However, the approaches differ in depicting the relationships of the three families to one another. Maximum parsimony depicts the Atelidae and Cebidae as sister families next joined by the Pitheciidae. Conversely, likelihood and Bayesian phylogenetic trees group families Atelidae and Pitheciidae together to the exclusion of Cebidae. Divergence time estimations using both local molecular clock and Bayesian approaches suggest the families diverged from one another over a short period of geological time in the late Oligocene-early Miocene.

Animals↗
PubMed2006

Evolution of the mammalian placenta revealed by phylogenetic analysis.

The placenta is essential for the success of therian mammalian reproduction. Intense selective pressure has shaped changes in placental anatomy and function during mammalian cladogenesis. Here we challenge the view that the hemochorial placenta is a derived feature in haplorhine primates. Using phylogenetic and statistical analyses of molecular and morphological data, we demonstrate that the ancestral eutherian mammalian placenta had the distinctive features of (i) hemochorial placental interface, (ii) a discoid shape, and (iii) a labyrinthine maternofetal interdigitation. These results reveal that the first eutherians had a deeply invasive placenta and imply that the major role of the placenta in sustaining pregnancy and promoting gestational development existed throughout the eutherian lineage that descended to humans from the last common ancestor of placental mammals. The ancestral state reconstructions demonstrate both clade-specific patterns of placentation and specific cases of convergent evolution within individual eutherian clades. Determining the mammalian pattern of change in placental morphology is important for understanding the evolutionary pressures faced by these lineages. The effects of selection pressures on the efficiency of placentation may stem from changes in nutritional demand, gestational length, number of embryos per pregnancy, uterine shape, and maternal body constitution. The influence of these factors on placental development needs further investigation.

Animals↗
PubMed2006

Phylogenetic comparisons suggest that distance from the locus control region guides developmental expression of primate beta-type globin genes.

Phylogenetic inferences drawn from comparative data on mammalian beta-globin gene clusters indicate that the ancestral primate cluster contained a locus control region (LCR) and five paralogously related beta-type globin loci (5'-LCR-epsilon-gamma-psieta-delta-beta-3'), with epsilon and gamma expressed solely during embryonic life. A gamma locus tandem duplication (5'-gamma(1)-gamma(2)-3') triggered gamma's evolution toward fetal expression but by a different trajectory in platyrrhines (New World monkeys) than in catarrhines (Old World monkeys and apes, including humans). In platyrrhine (e.g., Cebus) fetuses, gamma(1) at the ancestral distance from epsilon is down-regulated, whereas gamma(2) at increased distance is up-regulated. Catarrhine gamma(1) and gamma(2) acquired longer distances from epsilon (14 and 19 kb, respectively), and both are up-regulated throughout fetal life with gamma(1)'s expression predominating over gamma(2)'s. On enlarging the platyrrhine expression data, we find Aotus gamma is embryonic, Alouatta gamma is inactive at term, and in Callithrix, gamma(1) is down-regulated fetally, whereas gamma(2) is up-regulated. Of eight mammalian taxa now represented per taxon by embryonic, fetal, and postnatal beta-type globin gene expression data, four taxa are primates, and data for three of these primates are from this laboratory. Our results support a model in which a short distance (<10 kb) between epsilon and the adjacent gamma is a plesiomorphic character that allows the LCR to drive embryonic expression of both genes, whereas a longer distance (>10 kb) impedes embryonic activation of the downstream gene.

Animals↗
PubMed2005

Rapid electrostatic evolution at the binding site for cytochrome c on cytochrome c oxidase in anthropoid primates.

Cytochrome c (CYC) oxidase (COX), a multisubunit enzyme that functions in mitochondrial aerobic energy production, catalyzes the transfer of electrons from CYC to oxygen and participates in creating the electrochemical gradient used for ATP synthesis. Modeling three-dimensional structural data on COX and CYC reveals that 57 of the >1,500 COX residues can be implicated in binding CYC. Because of the functional importance of the transfer of electrons to oxygen, it might be expected that natural selection would drastically constrain amino acid replacement rates of CYC and COX. Instead, in anthropoid primates, although not in other mammals, CYC and COX show markedly accelerated amino acid replacement rates, with the COX acceleration being much greater at the positions that bind CYC than at those that do not. Specifically, in the anthropoid lineage descending from the last common ancestor of haplorhines (tarsiers and anthropoids) to that of anthropoids (New World monkeys and catarrhines) and that of catarrhines (Old World monkeys and apes, including humans), a minimum of 27 of the 57 COX amino acid residues that bind CYC were replaced, most frequently from electrostatically charged to noncharged residues. Of the COX charge-bearing residues involved in binding CYC, half (11 of 22) have been replaced with uncharged residues. CYC residues that interact with COX residues also frequently changed, but only two of the CYC changes altered charge. We suggest that reducing the electrostatic interaction between COX and CYC was part of the adaptive evolution underlying the emergence of anthropoid primates.

Adaptation, Physiological↗
PubMed2005

The phylogenetic history of New World monkey beta globin reveals a platyrrhine beta to delta gene conversion in the atelid ancestry.

Orthologues of the beta globin gene locus from 10 New World monkey species were sequenced and aligned against available beta and delta globin sequences from rabbit and other primates. Where needed, additional primate sequencing was performed. Phylogenetic analysis identified a beta to delta conversion in the stem of the Anthropoidea, stretching from the 3' part of the proximal promotor to the 5' start of intron 2, consistent with earlier findings. No further conversion appeared to have occurred in the descent of the catarrhines. Within the New World monkey lineage that led to spider monkey and other atelids, another shorter gene conversion was found, spanning adjacent parts of exon 1 and intron 1. The analysis also confirmed that galago beta had replaced galago delta, that an earlier loriform-specific gene conversion extended over intron 2, and that gene conversion throughout the main gene conversion region occurred in the tarsiiform lineage. Platyrrhine phylogenetic relationships were investigated with beta sequences restricted to those that were not involved in gene conversions. This phylogeny generally agreed with results from other nuclear genes. The one exception was that the beta sequences did not place the callitrichine clade within the Cebidae but weakly joined the callitrichine and atelid clades.

Animals↗
PubMed2005

Rapid nonsynonymous evolution of the iron-sulfur protein in anthropoid primates.

Cytochrome c (CYC) and 9 of the 13 subunits of cytochrome c oxidase (complex IV; COX) were previously shown to have accelerated rates of nonsynonymous substitution in anthropoid primates. Cytochrome b, the mtDNA encoded subunit of ubiquinol-cytochrome c reductase (complex III), also showed an accelerated nonsynonymous substitution rate in anthropoid primates but rate information about the nuclear encoded subunits of complex III has been lacking. We now report that phylogenetic and relative rates analysis of a nuclear encoded catalytically active subunit of complex III, the iron-sulfur protein (ISP), shows an accelerated rate of amino acid replacement similar to cytochrome b. Because both ISP and subunit 9, whose function is not directly related to electron transport, are produced by cleavage into two subunits of the initial translation product of a single gene, it is probable that these two subunits of complex III have essentially identical underlying rates of mutation. Nevertheless, we find that the catalytically active ISP has an accelerated rate of amino acid replacement in anthropoid primates whereas the catalytically inactive subunit 9 does not.

Amino Acid Sequence↗
PubMed2005

Moving primate genomics beyond the chimpanzee genome.

The comparative DNA sequence data that already exist on individual genomic loci depict the phylogenetic relationships of nearly all extant primate genera. Such a phylogenetic representation of the primates, validated by many sequenced primate genomes, and encompassing the full adaptive diversity of the order, is a prerequisite for identifying the genetic basis of humankind, and for testing the proposed human uniqueness of these traits. Some of these traits have been discovered recently, particularly in genes encoding proteins that are important for brain function.

Animals↗
PubMed2004

Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles.

Gene expression profiles from the anterior cingulate cortex (ACC) of human, chimpanzee, gorilla, and macaque samples provide clues about genetic regulatory changes in human and other catarrhine primate brains. The ACC, a cerebral neocortical region, has human-specific histological features. Physiologically, an individual's ACC displays increased activity during that individual's performance of cognitive tasks. Of approximately 45,000 probe sets on microarray chips representing transcripts of all or most human genes, approximately 16,000 were commonly detected in human ACC samples and comparable numbers, 14,000-15,000, in gorilla and chimpanzee ACC samples. Phylogenetic results obtained from gene expression profiles contradict the traditional expectation that the non-human African apes (i.e., chimpanzee and gorilla) should be more like each other than either should be like humans. Instead, the chimpanzee ACC profiles are more like the human than like the gorilla; these profiles demonstrate that chimpanzees are the sister group of humans. Moreover, for those unambiguous expression changes mapping to important biological processes and molecular functions that statistically are significantly represented in the data, the chimpanzee clade shows at least as much apparent regulatory evolution as does the human clade. Among important changes in the ancestry of both humans and chimpanzees, but to a greater extent in humans, are the up-regulated expression profiles of aerobic energy metabolism genes and neuronal function-related genes, suggesting that increased neuronal activity required increased supplies of energy.

Animals↗
PubMed2004

Accelerated evolution of the electron transport chain in anthropoid primates.

Mitochondria are both the power plant of the cell and a central integrator of signals that govern the lifespan, replication and death of the cell. Perhaps as a consequence, genes that encode components of the mitochondrial electron transport chain (ETC) are generally conserved. Therefore, it is surprising that many of these genes in anthropoid primates (New World monkeys, Old World monkeys and apes, including humans) have been major targets of darwinian positive selection. Sequence comparisons have provided evidence that marked increases of non-synonymous substitution rates occurred in anthropoid ETC genes that encode subunits of Complex III and IV, and the electron carrier molecule cytochrome c (CYC). Two important questions are: (i) how has evolution altered ETC function? and; (ii) how might functional changes in the ETC be linked to evolution of an expanded neocortical brain?

Animals↗
PubMed2003

Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: enlarging genus Homo.

What do functionally important DNA sites, those scrutinized and shaped by natural selection, tell us about the place of humans in evolution? Here we compare approximately 90 kb of coding DNA nucleotide sequence from 97 human genes to their sequenced chimpanzee counterparts and to available sequenced gorilla, orangutan, and Old World monkey counterparts, and, on a more limited basis, to mouse. The nonsynonymous changes (functionally important), like synonymous changes (functionally much less important), show chimpanzees and humans to be most closely related, sharing 99.4% identity at nonsynonymous sites and 98.4% at synonymous sites. On a time scale, the coding DNA divergencies separate the human-chimpanzee clade from the gorilla clade at between 6 and 7 million years ago and place the most recent common ancestor of humans and chimpanzees at between 5 and 6 million years ago. The evolutionary rate of coding DNA in the catarrhine clade (Old World monkey and ape, including human) is much slower than in the lineage to mouse. Among the genes examined, 30 show evidence of positive selection during descent of catarrhines. Nonsynonymous substitutions by themselves, in this subset of positively selected genes, group humans and chimpanzees closest to each other and have chimpanzees diverge about as much from the common human-chimpanzee ancestor as humans do. This functional DNA evidence supports two previously offered taxonomic proposals: family Hominidae should include all extant apes; and genus Homo should include three extant species and two subgenera, Homo (Homo) sapiens (humankind), Homo (Pan) troglodytes (common chimpanzee), and Homo (Pan) paniscus (bonobo chimpanzee).

Animals↗
PubMed2003

Adaptive evolution of cytochrome c oxidase subunit VIII in anthropoid primates.

Cytochrome c oxidase (COX) is a 13-subunit protein complex that catalyzes the last step in mitochondrial electron transfer in mammals. Of the 10 subunits encoded by nuclear DNA (three are mtDNA products), some are expressed as tissue- and/or development-specific isoforms. For COX subunit VIII, previous work showed that expression of the contractile muscle-specific isoform gene, COX8H, is absent in humans and Old World monkeys, and the other isoform gene, COX8L, is expressed ubiquitously. Here, we show that COX8H is transcribed in most primate clades, but its expression is absent in catarrhines, that is, in Old World monkeys and hominids (apes, including humans), having become a pseudogene in the stem of the catarrhines. The ubiquitously expressed isoform, COX8L, underwent nonsynonymous rate acceleration and elevation in the ratio of nonsynonymous/synonymous changes in the stem of anthropoid primates (New World monkeys and catarrhines), possibly setting the stage for loss of the heart-type (H) isoform. The most rapidly evolving region of VIII-L is one that interacts with COX I, suggesting that the changes are functionally coadaptive. Because accelerated rates of nonsynonymous substitutions in anthropoids such as observed for COX8L are also shown by genes for at least 13 other electron transport chain components, these encoded amino acid replacements may be viewed as part of a series of coadaptive changes that optimized the anthropoid biochemical machinery for aerobic energy metabolism. We argue that these changes were linked to the evolution of an expanded neocortex in anthropoid primates.

Amino Acid Sequence↗
PubMed2003

Retention of a duplicate gene through changes in subcellular targeting: an electron transport protein homologue localizes to the golgi.

Cytochrome c oxidase (COX), the terminal enzyme complex of the electron transport chain, contains 13 subunits, 3 encoded by mitochondrial DNA and 10 by nuclear. Several of the nuclear subunits, including subunit VIIa, are known to have two tissue- and development-specific isoforms in mammals. A recently identified third member of the gene family, COX7AR, encodes a protein previously thought to function in mitochondria. However, observation of fluorescent pCOX7AR C-terminal fusion proteins in HeLa cells showed that pCOX7AR is localized to the Golgi apparatus. Sequence analyses indicate that the duplication of COX7AR occurred prior to the origin of the Euteleostomi (bony vertebrates) and that pCOX7AR is more highly conserved than the two other isoforms. These results indicate that, after gene duplication and modification of the mitochondrial targeting signal, pCOX7AR was evolutionarily altered to a new and apparently important function in the Golgi. These results also suggest that predictions of function from homology can be misleading and show that specialization and modification of subcellular localization are similar to cis-element subfunctionalization. In cis-element subfunctionalization, complementary null mutations occur to the cis-elements of the descendents of a gene duplication, causing both descendent genes to be obligate. In the process described in this paper, which could be termed subcellular subfunctionalization, complementary null mutations can occur to the subcellular localization signals of the descendants of a gene duplication, causing both descendent genes to be similarly obligate. Noncomplementary null mutations could also uncover an alternate localization, which is the more likely case for pCOX7AR.

Electron Transport Complex IV↗
PubMed2002

Amino acid replacement is rapid in primates for the mature polypeptides of COX subunits, but not for their targeting presequences.

We examined inferred amino acid replacements for 16 genes that encode the proteins of the cytochrome c oxidase (COX) holoenzyme in eight vertebrate species. Phylogeny-based analysis revealed that the human lineage (primates) has had an unusually large, statistically significant, number of amino acid replacements in the mature protein coding region of these genes. This finding is similar to earlier observations of an accelerated non-synonymous substitution rate for some lineages of primates for COX1, COX2, COX4, and COX7AH. In contrast, the mitochondrial targeting presequences of these same proteins have not undergone a concomitant rate change. This more comprehensive analysis suggests that COX5A, COX6B, COX6C, COX7C, and COX8L have also undergone an acceleration in amino acid replacement rates in anthropoid primates. Some of these rate accelerations (e.g. in COX5A and COX7C) are so pronounced that non-human mammalian sequences are more similar to sequences from Xenopus or zebrafish than they are to human. Since the functions of the targeting and mature proteins of these polypeptides are different, the mature portions of these genes are likely to have undergone a functionally significant change that is adaptive in nature.

Amino Acid Sequence↗
PubMed2002

Regulation of fetal versus embryonic gamma globin genes: appropriate developmental stage expression patterns in the presence of HS2 of the locus control region.

The gamma genes provide the major contribution to beta-like globin chain production in the fetal liver of humans. However, the expression of gamma genes in the fetus is a recent evolutionary trend seen only in the primate lineage. In a previous study, it was shown that galago and human gamma genes retain their characteristic stage-specific expression patterns in transgenic mice (galago gamma is expressed exclusively in the embryo, whereas human gamma is expressed in the fetus). In that experiment, human and galago gamma genes were linked to hypersensitive site 3 (HS3) of the locus control region. To rule out the possibility that HS3 is required for these differential expression profiles, additional transgenic lines were tested in which human or galago gamma genes were linked to HS2. Once again, the galago gamma gene was embryonic and the human gamma gene was fetal, indicating that the stage specificity of these genes is driven by elements located within the 4-kb fragments that contain the human and galago gamma genes proper.

Age Factors↗