Molecular Evolution of Amelogenin in Mammals

An evolutionary analysis of mammalian amelogenin, the major protein of forming enamel, was conducted by comparison of 26 sequences (including 14 new ones) representative of the main mammalian lineages. Amelogenin shows highly conserved residues in the hydrophilic N- and C-terminal regions. The central hydrophobic region (most of exon 6) is more variable, but it has conserved a high amount of proline and glutamine located in triplets, PXQ, indicating that these residues play an important role. This region evolves more rapidly, and is less constrained, than the other well-conserved regions, which are subjected to strong constraints. The comparison of the substitution rates in relation to the CpG richness confirmed that the highly conserved regions are subjected to strong selective pressures. The amino acids located at important sites and the residues known to lead to amelogenesis imperfecta when substituted were present in all sequences examined. Evolutionary analysis of the variable region of exon 6 points to a particular zone, rich in either amino acid insertion or deletion. We consider this region a hot spot of mutation for the mammalian amelogenin. In this region, numerous triplet repeats (PXQ) have been inserted recently and independently in five lineages, while most of the hydrophobic exon 6 region probably had its origin in several rounds of triplet insertions, early in vertebrate evolution. The putative ancestral DNA sequence of the mammalian amelogenin was calculated using a maximum likelihood approach. The putative ancestral protein was composed of 177 residues. It already contained all important amino acid positions known to date, its hydrophobic variable region was rich in proline and glutamine, and it contained triplet repeats PXQ as in the modern sequences.Reviewing Editor: Dr. Cecilia Saccone     

Regulation of Hemoglobin Function in Mammals

This survey of hemoglobin function in mammals reveals a broadrange in oxygen affinity. The concentration of red cell 2,3-DPGvaries widely among groups of mammals. Those animals (feloidsand ruminants) that have very low levels of this intracellularmediator have hemoglobins of intrinsically low oxygen affinitywhich fail to respond to the addition of 2,3-DPG. Mammals whichhave adapted to various types of hypoxia tend to have increasedoxygen affinity, primarily mediated through reduced levels ofred cell 2,3 DPG. In contrast mammals who are experimentallysubjected to low oxygen tensions develop decreased oxygen affinityowing to increased red cell 2,3-DPG. Mammals employ one of threedifferent mechanisms for the maintenance of higher oxygen affinityof fetal red cells, compared to maternal red cells. Many of these phenomena can be satisfactorily explained at themolecular level but their adaptational significance is lessclear.     

Episodic Evolution of Protein Hormones in Mammals

Pituitary growth hormone (GH) and prolactin have been shown previously to display a pattern of evolution in which episodes of rapid change are imposed on a low underlying basal rate (near-stasis). This study was designed to explore whether a similar pattern is seen in the evolution of other protein hormones in mammals. Seven protein hormones were examined (with the common α-subunit of the glycoprotein hormones providing an additional polypeptide for analysis)—those for which sequences from at least four eutherian orders are available with a suitable non-eutherian outgroup. Six of these (GH, prolactin, insulin, parathyroid hormone, glycoprotein hormone α-subunit, and luteinizing hormone β-subunit) showed markedly variable evolutionary rates in each case with a pattern of a slow basal rate and bursts of rapid change, the precise positions of the bursts varying from protein to protein. Two protein hormones (follicle-stimulating hormone β-subunit and thyroid-stimulating hormone β-subunit) showed no significant rate variation. Based on the sequences currently available, and pooling data from all eight proteins, the phase of slow basal change occupied about 85% of the sampled evolutionary time, but most evolutionary change (about 62% of the substitutions accepted) occurred during the episodes of rapid change. It is concluded that, in mammals at least, a pattern of prolonged periods of near-stasis with occasional episodes of rapid change provides a better model of evolutionary change for protein hormones than the one of constant evolutionary rates that is commonly favored. The mechanisms underlying this episodic evolution are not yet clear, and it may be that they vary from one group to another; in some cases, positive selection appears to underlie bursts of rapid change. Where gene duplication is associated with a period of accelerated evolution this often occurs at the end rather than the beginning of the episode. To what extent the type of pattern seen for protein hormones can be extended to other proteins remains to be established. Received: 10 October 2000 / Accepted: 18 December 2000     

Evolution of Acoustic Communication Signals of Mammals: Friendly Close-Range Vocalizations in Felidae (Carnivora)

The distribution of the three friendly close-range vocalization types known in the Felidae was plotted on a recently published phylogeny of the cat family (Felidae) based on sequence comparisons of two mitochondrial DNA genes and other molecular and biochemical characters, with extrapolated divergence ages of its various lineages. It was found to be congruent with this phylogeny. One of the sound types is likely to be present in 30 species of the family (documented in 22 so far), another is present in 4, and the third in 2 species only; these sound types represent a phylogenetic transformation series. The latter two vocalization types also differ considerably from the first in the mode of sound production. From this, evolutionary conservatism over a long epoch for the one widespread vocalization type can be inferred, and less conservatism in the type present in four species, while the emergence of the least common type is evidence of relatively considerable and rapid evolutionary change. Thus, acoustic communication signals in a group of taxa can evolve at considerably different rates, and for a specific character this rate can differ between different lineages of that group. The ultimate causes of the evolutionary stability or of the subsequent relatively rapid change in sound structure and mode of sound production in these felid vocalizations are unknown.     

Monotremes as Pretribosphenic Mammals

An abundance of evidence points to the conclusion that monotremes are phyletically allied with pretribosphenic, rather than with tribosphenic, mammals. Monotremes do not have a tribosphenic dentition. Character analyses that apply tribosphenic cusp terminology to monotreme dentitions are implicitly limited thereby. A review of the molar dentition of living and fossil monotremes suggests that upper molars are composed of a strongly developed pretribosphenic paracone and metacone and a series of stylar cusps attached to them in a bicrescentic, or dilambdodont, fashion. The lower molars are composed of a trigonid, with a pretribosphenic protoconid, paraconid, and metaconid, and distal metacristid. The paraconid of m1 is reduced or lost. The talonid is composed of the pretribosphenic hypoconid, hypoconulid, and cristid obliqua. There is no evidence for a tribosphenic entoconid, nor for a talonid basin. There was no tribosphenic protocone. Monotremes are not related to other taxa included in Australosphenida. The dentition of Cretaceous taxa, such as Teinolophos and Steropodon, apparently still functioned by orthal mechanisms, whereas by the medial Paleocene (Monotrematum) and later (Obdurodon), monotremes appear to have accommodated a diet of soft-bodied organisms that left little trace of a mastication regime that had changed to apical wear via propalinal motion. Monotremes appear to be modern representatives of a Mesozoic radiation of pretribosphenic mammals centered largely in Gondwana, where they still reside today.     

Rhodopsin Molecular Evolution in Mammals Inhabiting Low Light Environments

The ecological radiation of mammals to inhabit a variety of light environments is largely attributed to adaptive changes in their visual systems. Visual capabilities are conferred by anatomical features of the eyes as well as the combination and properties of their constituent light sensitive pigments. To test whether evolutionary switches to different niches characterized by dim-light conditions coincided with molecular adaptation of the rod pigment rhodopsin, we sequenced the rhodopsin gene in twenty-two mammals including several bats and subterranean mole-rats. We compared these to thirty-seven published mammal rhodopsin sequences, from species with divergent visual ecologies, including nocturnal, diurnal and aquatic groups. All taxa possessed an intact functional rhodopsin; however, phylogenetic tree reconstruction recovered a gene tree in which rodents were not monophyletic, and also in which echolocating bats formed a monophyletic group. These conflicts with the species tree appear to stem from accelerated evolution in these groups, both of which inhabit low light environments. Selection tests confirmed divergent selection pressures in the clades of subterranean rodents and bats, as well as in marine mammals that live in turbid conditions. We also found evidence of divergent selection pressures among groups of bats with different sensory modalities based on vision and echolocation. Sliding window analyses suggest most changes occur in transmembrane domains, particularly obvious within the pinnipeds; however, we found no obvious pattern between photopic niche and predicted spectral sensitivity based on known critical amino acids. This study indicates that the independent evolution of rhodopsin vision in ecologically specialised groups of mammals has involved molecular evolution at the sequence level, though such changes might not mediate spectral sensitivity directly.     

Fast Evolution of Interleukin-2 in Mammals and Positive Selection in Ruminants

Interleukin-2 (IL-2) is a cytokine involved in induction and regulation of the immune response in mammals. There have been numerous reports about the search for IL-2 in species other than mammals, and recently an IL-2-like gene has been isolated in chicken. Using PCR, we searched for IL-2 gene sequences in a wide variety of mammals, including marsupials and monotremes, as well as in birds. Although we can readily amplify IL-2 gene fragments in placental mammals, no amplification was obtained in other species. This is best explained by very high substitution rates. This suggest that strategies to isolate IL-2 homologous genes outside mammals should involve functional assays, as for the chicken gene, and not hybridization-based techniques. Nonsynonymous substitution rates are especially high in ruminants, due to positive selection acting on regions important in term of structure-function. We suggest that, although globally similar, the immune response of various mammals is not identical, mainly at the level of cytokine-mediated regulations. Received: 27 July 1999 / Accepted: 15 April 2000     

Correlated Evolution of Nucleotide Positions within Splice Sites in Mammals

Splice sites (SSs)—short nucleotide sequences flanking introns—are under selection for spliceosome binding, and adhere to consensus sequences. However, non-consensus nucleotides, many of which probably reduce SS performance, are frequent. Little is known about the mechanisms maintaining such apparently suboptimal SSs. Here, we study the correlations between strengths of nucleotides occupying different positions of the same SS. Such correlations may arise due to epistatic interactions between positions (i.e., a situation when the fitness effect of a nucleotide in one position depends on the nucleotide in another position), their evolutionary history, or to other reasons. Within both the intronic and the exonic parts of donor SSs, nucleotides that increase (decrease) SS strength tend to co-occur with other nucleotides increasing (respectively, decreasing) it, consistent with positive epistasis. Between the intronic and exonic parts of donor SSs, the correlations of nucleotide strengths tend to be negative, consistent with negative epistasis. In the course of evolution, substitutions at a donor SS tend to decrease the strength of its exonic part, and either increase or do not change the strength of its intronic part. In acceptor SSs, the situation is more complicated; the correlations between adjacent positions appear to be driven mainly by avoidance of the AG dinucleotide which may cause aberrant splicing. In summary, both the content and the evolution of SSs is shaped by a complex network of interdependences between adjacent nucleotides that respond to a range of sometimes conflicting selective constraints.     

Exploring the Potential Use of Seismic Waves as a Communication Channel by Elephants and Other Large Mammals

Bioseismic studies have previously documented the use of seismicstimuli as a method of communication in arthropods and smallmammals. Seismic signals are used to communicate intraspecificallyin many capacities such as mate finding, spacing, warning, resourceassessing, and in group cohesion. Seismic signals are also usedin interspecific mutualism and as a deterrent to predators.Although bioseismics is a significant mode of communicationthat is well documented for relatively small vertebrates, thepotential for seismic communication has been all but ignoredin large mammals. In this paper, we describe two modes of producingseismic waves with the potential for long distance transmission:1) locomotion by animals causing percussion on the ground and2) acoustic, seismic-evoking sounds that couple with the ground.We present recordings of several mammals, including lions, rhinoceroses,and elephants, showing that they generate similar acoustic andseismic vibrations. These large animals that produce high amplitudevocalizations are the most likely to produce seismic vibrationsthat propagate long distances. The elephant seems to be themost likely candidate to engage in long distance seismic communicationdue to its size and its high amplitude, low frequency, relativelymonotonic vocalizations that propagate in the ground and havethe potential to travel long distances. We review particularanatomical features of the elephant that would facilitate thedetection of seismic waves. We also assess low frequency soundsin the environment such as thunder and the likelihood of seismictransmission. In addition, we present the potential role ofseismic stimuli in human communication as well as the impactof modern anthropogenic effects on the seismic environment.     

Independent Evolution of Transcriptional Inactivation on Sex Chromosomes in Birds and Mammals

X chromosome inactivation in eutherian mammals has been thought to be tightly controlled, as expected from a mechanism that compensates for the different dosage of X-borne genes in XX females and XY males. However, many X genes escape inactivation in humans, inactivation of the X in marsupials is partial, and the unrelated sex chromosomes of monotreme mammals have incomplete and gene-specific inactivation of X-linked genes. The bird ZW sex chromosome system represents a third independently evolved amniote sex chromosome system with dosage compensation, albeit partial and gene-specific, via an unknown mechanism (i.e. upregulation of the single Z in females, down regulation of one or both Zs in males, or a combination). We used RNA-fluorescent in situ hybridization (RNA-FISH) to demonstrate, on individual fibroblast cells, inactivation of 11 genes on the chicken Z and 28 genes on the X chromosomes of platypus. Each gene displayed a reproducible frequency of 1Z/1X-active and 2Z/2X-active cells in the homogametic sex. Our results indicate that the probability of inactivation is controlled on a gene-by-gene basis (or small domains) on the chicken Z and platypus X chromosomes. This regulatory mechanism must have been exapted independently to the non-homologous sex chromosomes in birds and mammals in response to an over-expressed Z or X in the homogametic sex, highlighting the universal importance that (at least partial) silencing plays in the evolution on amniote dosage compensation and, therefore, the differentiation of sex chromosomes.     

Brain Evolution: Mammals,Primates, Chimpanzees,and Humans

Though many modern techniques are available for studying brains, they are difficult to use in evolutionary contexts that require examination of large numbers of specimens and species, and all major parts of the brain. Thus, evolutionary studies of many species and of whole brains still tend to be based upon simpler data such as sizes of brains and brain components. Such investigations, carried out over many decades, have usually employed univariate and bivariate analyses, though a few investigators used early multivariate methods. In mammals, these studies generally show the primacy of the relationship between brain and brain-part sizes with overall body size. More recent multivariate applications have confirmed this (Finlay, B. L., and Darlington, R. B. (1995). Science 268: 1578–1584) and some have also separated the highest level phylogenetic groups: strepsirrhines and haplorrhines (Barton, R. A., and Harvey, P. H. (2000). Nature 405: 1055–1058). Both findings were, in fact, evident in earlier multivariate studies (Holloway, R. L. (1979). In Hahn, M. E., Jensen C., and Dudek, B. C. (eds.), Development and Evolution of Brain Size: Behavioral Implications, Academic Press, New York, pp. 59–88; Sacher, G. A. (1970). In Noback, C. R., and Montagna, W. (eds.), The Primate Brain: Advances in Primatology. Vol. 1, Appleton-Century-Crofts, Educational Division, Meredith Corporation, New York, pp. 245–287). However, new studies employing proportional data aimed at conveying input/output relationships between brain components show further groupings of species that share convergences in lifestyles (de Winter, W., and Oxnard, C. E. (2001). Nature 409: 710–714). The convergences are brought about by combinations of brain variables that seem to be associated with brain functions implied by the specific lifestyles. Our most recent results demonstrate that chimpanzees and humans are especially different from one another, and the difference is not due to size alone. Part of this difference is merely a continuation, from chimpanzees towards humans, of a trend already present across all other primates that relates mainly to neocortical increase. But several other large and independent differences are not in the direction of the overall primate trend, but are differences of humans from all other mammals examined including all nonhuman primates. The combinations of brain variables associated with the latter differences are not related simply to enhancement of the neocortex, but seem to reflect other internal relationships. The overall separation of humans and chimpanzees is so large that it goes far beyond the conventional 98.6% commonality in their DNAs. It fits better with more recent molecular, developmental and evolutionary studies implying a considerably greater difference between chimpanzees and humans than usually recognized.     

Evolution of the Relaxin/Insulin-like Gene Family in Placental Mammals: Implications for Its Early Evolution

The relaxin (RLN) and insulin-like (INSL) gene family is a group of genes involved in a variety of physiological roles that includes bone formation, testicular descent, trophoblast development, and cell differentiation. This family appears to have expanded in vertebrates relative to non-vertebrate chordates, but the relative contribution of whole genome duplications (WGDs) and tandem duplications to the observed diversity of genes is still an open question. Results from our comparative analyses favor a model of divergence post vertebrate WGDs in which a single-copy progenitor found in the last common ancestor of vertebrates experienced two rounds of WGDs before the functional differentiation that gave rise to the RLN and INSL genes. One of the resulting paralogs was subsequently lost, resulting in three proto-RLN/INSL genes on three separate chromosomes. Subsequent rounds of tandem gene duplication and divergence originated the set of paralogs found on a given cluster in extant vertebrates. Our study supports the hypothesis that differentiation of the RLN and INSL genes took place independently in each RLN/INSL cluster after the two WGDs during the evolutionary history of vertebrates. In addition, we show that INSL4 represents a relatively old gene that has been apparently lost independently in all Euarchontoglires other than apes and Old World monkeys, and that RLN2 derives from an ape-specific duplication.