Sequence shortening in the rodent ancestor

Insertions and deletions (indels), together with nucleotide substitutions, are major drivers of sequence evolution. An excess of deletions over insertions in genomic sequences-the so-called deletional bias-has been reported in a wide range of species, including mammals. However, this bias has not been found in the coding sequences of some mammalian species, such as human and mouse. To determine the strength of the deletional bias in mammals, and the influence of mutation and selection, we have quantified indels in both neutrally evolving noncoding sequences and protein-coding sequences, in six mammalian branches: human, macaque, ancestral primate, mouse, rat, and ancestral rodent. The results obtained with an improved algorithm for the placement of insertions in multiple alignments, Prank(+F), indicate that contrary to previous results, the only mammalian branch with a strong deletional bias is the rodent ancestral branch. We estimate that such a bias has resulted in an ~2.5% sequence loss of mammalian syntenic region in the ancestor of the mouse and rat. Further, a comparison of coding and noncoding sequences shows that negative selection is acting more strongly against mutations generating amino acid insertions than against mutations resulting in amino acid deletions. The strength of selection against indels is found to be higher in the rodent branches than in the primate branches, consistent with the larger effective population sizes of the rodents.     

Endogenous oxidative stress: relationship to aging,longevity and caloric restriction

Available studies are consistent with the possibility that oxygen radicals endogenously produced by mitochondria are causally involved in the determination of the rate of aging in homeothermic vertebrates. Oxidative damage to tissue macromolecules seems to increase during aging. The rate of mitochondrial oxygen radical generation of post-mitotic tissues is negatively correlated with animal longevity. In agreement with this, long-lived animals show lower levels of oxidative damage in their mitochondrial DNA (mtDNA) than short-lived ones, whereas this does not occur in nuclear DNA (nDNA). Caloric restriction, which decreases the rate of aging, also decreases mitochondrial oxygen radical generation and oxidative damage to mitochondrial DNA. This decrease in free radical generation occurs in complex I and is due to a decrease in the degree of electronic reduction of the complex I free radical generator, similarly to what has been described in various cases in long-lived animals. These results suggest that similar mechanisms have been used to extend longevity through decreases in oxidative stress in caloric restriction and during the evolution of species with different longevities.     

Evidence for an early appearance of modern post-switch immunoglobulin isotypes in mammalian evolution (II); cloning of IgE,IgG1 and IgG2 from a monotreme,the duck-billed platypus,Ornithorhynchus anatinus

To trace the emergence of the modern post-switch immunoglobulin (Ig) isotypes in vertebrate evolution we have studied Ig expression in mammals distantly related to eutherians. We here present an analysis of the Ig expression in an egg-laying mammal, a monotreme, the duck-billed platypus (Ornithorhynchus anatinus). Fragments of platypus IgG and IgE cDNA were obtained by a PCR-based screening using degenerate primers. The fragments obtained were used as probes to isolate full-length cDNA clones of three platypus post-switch isotypes, IgG1, IgG2, and IgE. Comparative amino acid sequence analysis against IgY, IgE and IgG from various animal species revealed that platypus IgE and IgG form branches that are clearly separated from those of their eutherian (placental) counterparts. However, the platypus IgE and IgG still conform to the general structure displayed by the respective Ig isotypes of eutherian and marsupial mammals. According to our findings, all of the major evolutionary changes in the expression array and basic Ig structure that have occurred since the evolutionary separation of mammals from the early reptile lineages, occurred prior to the separation of monotremes from marsupial and placental mammals. Hence, our results indicate that the modern post-switch isotypes appeared very early in the mammalian lineage, possibly already 310-330 million years ago.     

Using genomic data to unravel the root of the placental mammal phylogeny

The phylogeny of placental mammals is a critical framework for choosing future genome sequencing targets and for resolving the ancestral mammalian genome at the nucleotide level. Despite considerable recent progress defining superordinal relationships, several branches remain poorly resolved, including the root of the placental tree. Here we analyzed the genome sequence assemblies of human, armadillo, elephant, and opossum to identify informative coding indels that would serve as rare genomic changes to infer early events in placental mammal phylogeny. We also expanded our species sampling by including sequence data from >30 ongoing genome projects, followed by PCR and sequencing validation of each indel in additional taxa. Our data provide support for a sister-group relationship between Afrotheria and Xenarthra (the Atlantogenata hypothesis), which is in turn the sister-taxon to Boreoeutheria. We failed to recover any indels in support of a basal position for Xenarthra (Epitheria), which is suggested by morphology and a recent retroposon analysis, or a hypothesis with Afrotheria basal (Exafricoplacentalia), which is favored by phylogenetic analysis of large nuclear gene data sets. In addition, we identified two retroposon insertions that also support Atlantogenata and none for the alternative hypotheses. A revised molecular timescale based on these phylogenetic inferences suggests Afrotheria and Xenarthra diverged from other placental mammals approximately 103 (95-114) million years ago. We discuss the impacts of this topology on earlier phylogenetic reconstructions and repeat-based inferences of phylogeny.     

Do the fastest concepti have a shorter life span?

An evolutionary hypothesis based on an 'antagonist pleiotropy' or 'disposable soma' mechanism is put forward to explain differences in longevity between species, strains, and sexes. Data from several congenic mouse strains and mammalian species suggest that there may be an association between cleavage rate of concepti and longevity, in such a way that concepti from species, strains or the sex (male) with the fastest cleavage rates have shorter life spans. The major histocompatibility complex (MHC) and, in particular, the conceptus development gene (Ped) together with several Y-linked genes that are expressed during the preimplantation stages of development may play an important role in determining or modulating longevity in mammals. Notwithstanding, effects of other loci as well as environmental factors on conceptus development and longevity cannot be ignored.      

The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA.

We describe the complete sequence of the 16,596-nucleotide mitochondrial genome of the zebrafish (Danio rerio); contained are 13 protein genes, 22 tRNAs, 2 rRNAs, and a noncoding control region. Codon usage in protein genes is generally biased toward the available tRNA species but also reflects strand-specific nucleotide frequencies. For 19 of the 20 amino acids, the most frequently used codon ends in either A or C, with A preferred over C for fourfold degenerate codons (the lone exception was AUG: methionine). We show that rates of sequence evolution vary nearly as much within vertebrate classes as between them, yet nucleotide and amino acid composition show directional evolutionary trends, including marked differences between mammals and all other taxa. Birds showed similar compositional characteristics to the other nonmammalian taxa, indicating that the evolutionary trend in mammals is not solely due to metabolic rate and thermoregulatory factors. Complete mitochondrial genomes provide a large character base for phylogenetic analysis and may provide for robust estimates of phylogeny. Phylogenetic analysis of zebrafish and 35 other taxa based on all protein-coding genes produced trees largely, but not completely, consistent with conventional views of vertebrate evolution. It appears that even with such a large number of nucleotide characters (11,592), limited taxon sampling can lead to problems associated with extensive evolution on long phyletic branches.     

Higher levels of heat shock proteins in longer-lived mammals and birds

Cellular stress resistance is generally associated with longevity, but the mechanisms underlying this phenotype are not clear. In invertebrate models there is a clear role for heat shock proteins (Hsps) and organelle-specific unfolded protein responses (UPR) in longevity. However, this has not been demonstrated in vertebrates. Some Hsp amino acid sequences are highly conserved amongst mammals and birds. We used antibodies recognizing conserved regions of Hsp60 (primarily mitochondrial), Hsp70 (primarily cytosolic), GRP78 (Bip) and GRP94 (endoplasmic reticulum) to measure constitutive levels of these proteins in brain, heart and liver of 13 mammalian and avian species ranging in maximum lifespan from 3 to 30 years. In all three tissues, the expression of these proteins was highly correlated with MLSP, indicating higher basal levels of Hsp expression are characteristic of longer-lived species. We also quantified the levels of Hsp60, Hsp70 and GRP78 in brain and heart tissue of young adult (6-7 month old) Snell dwarf mice and normal littermates. Snell dwarf mice are characterized by a single gene mutation that is associated with an ～50% increase in lifespan. However, neither Hsp60, nor Hsp70, nor GRP78 levels were elevated in brain or heart tissue from Snell dwarf mice compared to normal littermates.     

The origin of human chromosome 1 and its homologs in placental mammals

Developing ordered gene maps from multiple mammalian species coupled with chromosome-painting data provide a powerful resource for resolving the evolutionary history of chromosomes and whole genomes. In this work, we recapitulate the evolutionary history of human chromosome 1 and its homologs in placental mammals, putatively the largest physical unit in the ancestral placental genome. Precise definition of translocation exchange breakpoints in human, carnivore, cetartiodactyl, and rodent-ordered gene maps demonstrate that chromosome breakpoints, previously considered as equivalent, actually represent distinct chromosome positions and exchange events. Multidirectional chromosome painting, using probes from homologs to chromosome 1 in seven mammal species from six orders of placental mammals, confirm the gene-mapping results and indicate that the multiple human chromosome 1 homologs in these species are derived from independent fissions of a single ancestral chromosome. Chromosome painting using human chromosome 1 probes identifies a single human chromosome 1 homolog in phylogenetically distant taxa, the two-toed sloth, cetaceans, and higher primates. The diverse phylogenetic occurrence of a single Hsa1 synteny among the major clades of placental mammals suggests that human chromosome 1 represents an intact ancestral chromosome, which was variously fissioned in the majority of placental species. We find that the number of human chromosome 1 fissions in a specific lineage reflects its general rate of genomic evolution. Further, historic chromosome exchange appears to have been disproportionately clustered in two breakpoint hotspots on the long arm.     

A primate-specific acceleration in the evolution of the caspase-dependent apoptosis pathway

Programmed cell death, or apoptosis, plays an essential role in mammalian development, especially the development of the nervous system. Here, we systematically examine the molecular evolution of the mammalian intrinsic apoptosis program. We divided the program into its several constituent pathways and examined the evolution of each pathway in diverse mammalian taxa spanning primates, rodents and carnivores. We observed that genes involved in the caspase-dependent apoptosis pathway stood out in several ways. First, these genes display an accelerated rate of protein sequence evolution in primates relative to rodents or carnivores. Secondly, this acceleration is most pronounced along the lineage leading to humans, and it is associated with signatures of positive selection. Finally, several genes in this pathway, including APAF1, CASP9 and CASP3, have been shown to be associated with dramatic defects in neuronal cell number and brain size when mutated in mice. These observations suggest the possibility that evolutionary changes in the caspase-dependent apoptosis pathway may have contributed to brain evolution in primates and humans. Our results also lend further support to the hypothesis that genes regulating brain size during development might have played a particularly important role in transforming brain size during evolution.     

Evidence for an early appearance of modern post-switch isotypes in mammalian evolution; cloning of IgE,IgG and IgA from the marsupial Monodelphis domestica

In birds, reptiles and amphibians the IgY isotype exhibits the functional characteristics of both of IgG and IgE. Hence, the gene for IgY most likely duplicated some time during early mammalian evolution and formed the ancestor of present day IgG and IgE. To address the question of when IgY duplicated and formed two functionally distinct isotypes, and to study when IgG and IgA lost their second constant domains, we have examined the Ig expression in a non-placental mammal, the marsupial Monodelphis domestica (grey short-tailed opossum). Screening of an opossum spleen cDNA library revealed the presence of all three isotypes in marsupials. cDNA clones encoding the entire constant regions of opossum IgE (ϵ chain), IgG (γ chain) and IgA (α chain) were isolated, and their nucleotide sequences were determined. A comparative analysis of the amino acid sequences for IgY, IgA, IgE and IgG from various animal species showed that opossum IgE, IgG and IgA on the phylogenetic tree form branches clearly separated from their eutherian counterparts. However, they still conform to the general structure found in eutherian IgE, IgG and IgA. Our findings indicate that all the major evolutionary changes in the Ig isotype repertoire, and in basic Ig structure that have occurred since the evolutionary separation of mammals from the early reptile lineages, occurred prior to the evolutionary separation of marsupials and placental mammals.     

Mutation hot spots in mammalian mitochondrial DNA

Animal mitochondrial DNA is characterized by a remarkably high level of within-species homoplasy, that is, phylogenetic incongruence between sites of the molecule. Several investigators have invoked recombination to explain it, challenging the dogma of maternal, clonal mitochondrial inheritance in animals. Alternatively, a high level of homoplasy could be explained by the existence of mutation hot spots. By using an exhaustive mammalian data set, we test the hot spot hypothesis by comparing patterns of site-specific polymorphism and divergence in several groups of closely related species, including hominids. We detect significant co-occurrence of synonymous polymorphisms among closely related species in various mammalian groups, and a correlation between the site-specific levels of variability within humans (on one hand) and between Hominoidea species (on the other hand), indicating that mutation hot spots actually exist in mammalian mitochondrial coding regions. The whole data, however, cannot be explained by a simple mutation hot spots model. Rather, we show that the site-specific mutation rate quickly varies in time, so that the same sites are not hypermutable in distinct lineages. This study provides a plausible mutation model that potentially accounts for the peculiar distribution of mitochondrial sequence variation in mammals without the need for invoking recombination. It also gives hints about the proximal causes of mitochondrial site-specific hypermutability in humans.     

Accumulation of cardiac lipofuscin in mammals: correlation between sexual maturation and the first appearance of lipofuscin

Accumulation of lipofuscin is an important phenomenon of the cellular aging process. The first appearance of cardiac lipofuscin showed a good correlation with sexual maturation, which was correlated with maximum life-span of mammals. Large metabolic changes occurred at sexual maturation. From these results, it is suggested that sexual maturation of mammals is the initiation period of the aging process. Correlation between sexual maturation and longevity was re-evaluated using many mammals. Domestic and laboratory animals showed an earlier sexual maturation than other mammals, including rodents.     

Plasma IGF-1 is negatively correlated with body mass in a comparison of 36 mammalian species

In mammals, insulin-like growth factor-1 (IGF-1) is positively correlated with adult body mass, in comparisons made within a given species. In mice, IGF-1 deficiency is associated with dwarfism, whereas IGF-1 overproduction in transgenic animals causes gigantism. Surprisingly, the opposite is true in an inter-species context. We collected published plasma total IGF-1 data for adults of 36 mammalian species and analyzed it with respect to body mass. In contrast to the intra-species observation, this analysis revealed a significant negative correlation of plasma IGF-1 with body mass. Interestingly, IGF-1 is negatively correlated with longevity, and suppression of IGF-1 signalling in worms, flies and mice increases lifespan. Smaller mouse strains, for example, tend to have lower plasma IGF-1 levels and to be longer-lived. However, when plasma total IGF-1 was analyzed relative to the maximum lifespans of the 36 species examined here, there was no statistically significant correlation. Low plasma IGF-1 levels in larger mammalian species may be physiologically significant, considering the roles of this hormone in metabolism, tissue regeneration, and cancer incidence.     

The molecular basis by which dietary restricted feeding reduces mitochondrial reactive oxygen species generation

Restricted feeding regimes in rodents that extend longevity lower the rate of mitochondrial reactive oxygen species generation. This effect is not dependent upon the depression of the state III and IV mitochondrial respiration rates. Mitochondria from liver, skeletal muscle and brown adipose tissue adapt to DR feeding with a lowered membrane potential that results from an enhanced proton leak across the inner membrane. Mitochondrial ROS generation is very sensitive to the magnitude of the membrane potential and the enhanced proton leak and ROS generation rates are reversible by exogenous insulin in liver and heart mitochondria. The adenine nucleotide translocase (ANT) was shown to be the dominant proton leak channel induced under DR feeding regimes in these tissues, while in brown fat mitochondria, UCP1 was activated, but this was not sensitive to exogenous insulin treatment. The effect of DR to modify the proton leak, membrane potential and ROS generation rate can be simulated by a range of non-esterified free fatty acids (NEFA) acting on the ANT to enhance its protonophoric activity. Mobilisation of NEFA under DR feeding, when insulin plasma concentrations are extremely low, explains the indirect action of insulin to counteract the effects of DR feeding on mitochondrial ROS generation.     

Is the mitochondrial free radical theory of aging intact?

The present state of the mitochondrial free radical theory of aging is reviewed. Available studies do not support the hypothesis that antioxidants control the rate of aging because: (a) they correlate inversely with maximum longevity in vertebrates, and (b) increasing their concentration by different methods does not increase maximum lifespan. On the other hand, comparative studies consistently show that long-lived mammals and birds have low rates of mitochondrial reactive oxygen species (ROS) production and low levels of oxidative damage in their mitochondrial DNA. Furthermore, caloric restriction, which extends longevity, also decreases mitochondrial ROS production at complex I and lowers mtDNA oxidative damage. Recent data show that these changes can also be obtained with protein restriction without strong caloric restriction. Another trait of long-lived mammals and birds is the possession of low degrees of unsaturation in their cellular membranes. This is mainly due to minimizing the presence of highly unsaturated fatty acids such as 22:6n-3 and emphasizing the presence of less unsaturated fatty acids such as 18:2n-6 in long-lived animals, without changing the total amount of polyunsaturated fatty acids. This leads to lower levels of lipid peroxidation and lipoxidation-derived protein modification in long-lived species. Taken together, available information is consistent with the predictions of the mitochondrial free radical theory of aging, although definitive proof and many mechanistic details are still lacking.     

Comparative analyses of the role of postnatal development on the expression of play fighting

Whether it is that animals are young so that they can play, or whether it is that they play because they are young, play should be more prevalent in species that have a greater degree of postnatal development. This hypothesis is tested by comparative analyses within two mammalian orders (primates and muroid rodents) using independent contrasts. This technique can account for the relative degree of relatedness among the species. For both orders, the complexity or prevalence of play fighting is compared to the degree of prenatal development (neonatal weight/adult weight). In addition, the prevalence of play in primates is compared to prenatal brain development (neonatal brain weight/adult brain weight). Significant negative regressions show that 30% of the variance in the distribution of play in the rodents is accounted for by the degree of prenatal development of body size, and 60% of the variance in play in the primates is accounted for by prenatal brain growth. The findings are thus consistent with the prediction. Species with a greater proportion of their growth occurring postnatally play more and have more complex play than do species with more of their growth occurring prenatally.     

Hepcidins in amphibians and fishes: Antimicrobial peptides or iron-regulatory hormones?

Hepcidin, originally identified as a 25 amino acid peptide antibiotic produced in the liver, is a key regulator of iron balance and recycling in humans and mice. Closely related hepcidin genes and peptides also have been identified in other mammals, amphibians, and a number of fish species. We hypothesize that hepcidin, the iron-regulatory hormone in humans, may have evolved from an antimicrobial peptide in fishes. In this review we will highlight the evidence that indicates hepcidin evolved from an antimicrobial peptide to an iron-regulatory hormone in vertebrate evolution. This evidence includes the discovery of hepcidin as an antimicrobial peptide and iron-regulatory hormone, structural comparison of mammalian hepcidins and nonmammalian hepcidins, and the cellular and molecular evidence indicating that, while some fish hepcidins may serve only as antimicrobial peptides, other fish and amphibian hepcidins may function as iron regulators.     

Deal in the womb: fetal opiates, parent-offspring conflict, and the future of midwifery

This paper argues that parent-offspring conflict is mediated by placental beta-endorphins in placental mammals, i.e., foetuses make their mothers endorphin-dependent then manipulate them to increase nutrient allocation to the placenta. This hypothesis predicts that: (1) anatomic position of endorphin production should mirror its presumed role in fetal-maternal conflict; (2) endorphin levels should co-vary positively with nutrient carrying capacity of maternal blood system; (3) postpartum psychological symptoms (postpartum blues, depression and psychosis) in humans are side-effects of this mechanism that can be interpreted as endorphin-deprivation symptoms; (4) shortly after parturition, placentophagia could play an adaptive role in decreasing the negative side-effects of fetal manipulation; (5) later, breast-feeding induced endorphin excretion of the maternal pituitary saves mother from further deprivation symptoms. Finally, whatever the molecular mechanism of fetal manipulation is, widespread and intense medical care (such as caesarean section and use of antidepressants) affects the present and future evolution of mother-foetus conflict in the human species (and also in domestic animals) to increase 'fetal aggressiveness' and thus technology-dependency of reproduction.     

Blastocysts prepare for the race to be male

Recent findings in different mammalian species have demonstratedthat XY embryos grow faster than XX embryos before the gonadsare differentiated. In mice and cattle, accelerated developmentis already evident in XY blastocysts, while in the rat and inhuman fetuses a quantitative sex difference has been shown tobe present before testicular differentiation has occurred. Thesedata demonstrate that in these species the histological differentiationof the testis, which occurs early and rapidly, is preceded byan increased growth rate of the embryo. This may be expectedto increase the probability of the gonad reaching the thresholdfor testis development, since it is known that developmentaldelay can result in ovarian differentiation. It is postulatedthat the fast development of the male may be an adaptation tothe reproductive biology of eutherian mammals, in which developmentof both sexes occurs in the hormonal environment of the uterus.The question is raised as to a possible connection between sex-relatedgrowth and other sex differences, such as longevity.     

The evolution of orbit orientation and encephalization in the Carnivora (Mammalia)

Evolutionary change in encephalization within and across mammalian clades is well-studied, yet relatively few comparative analyses attempt to quantify the impact of evolutionary change in relative brain size on cranial morphology. Because of the proximity of the braincase to the orbits, and the inter-relationships among ecology, sensory systems and neuroanatomy, a relationship has been hypothesized between orbit orientation and encephalization for mammals. Here, we tested this hypothesis in 68 fossil and living species of the mammalian order Carnivora, comparing orbit orientation angles (convergence and frontation) to skull length and encephalization. No significant correlations were observed between skull length and orbit orientation when all taxa were analysed. Significant correlations were observed between encephalization and orbit orientation; however, these were restricted to the families Felidae and Canidae. Encephalization is positively correlated with frontation in both families and negatively correlated with convergence in canids. These results indicate that no universal relationship exists between encephalization and orbit orientation for Carnivora. Braincase expansion impacts orbit orientation in specific carnivoran clades, the nature of which is idiosyncratic to the clade itself.