Temporal scaling of molecular evolution in primates and other mammals

Molecular clocks are routinely tested for linearity using a relative rate test and routinely calibrated against the geological time scale using a single or average paleontologically determined time of divergence between living taxa. The relative rate test is a test of parallel rate equality, not a test of rate constancy. Temporal scaling provides a test of rates, where scaling coefficients of 1.0 (isochrony) represent stochastic rate constancy. The fossil record of primates and other mammals is now known in sufficient detail to provide several independent divergence times for major taxonomic groups. Molecular difference should scale negatively or isochronically (scaling coefficients less than 1.0) with divergence time: where two or more divergence times are available, molecular difference appears to scale positively (scaling coefficient greater than 1.0). A minimum of four divergence times are required for adequate statistical power in testing the linear model: scaling is significantly nonlinear and positive in six of 11 published investigations meeting this criterion. All groups studied show some slowdown in rates of molecular change over Cenozoic time. The break from constant or increasing rates during the Mesozoic to decreasing rates during the Cenozoic appears to coincide with extraordinary diversification of placental mammals at the beginning of this era. High rates of selectively neutral molecular change may be concentrated in such discrete events of evolutionary diversification.      

The evolution of cathemerality in primates and other mammals: a comparative and chronoecological approach

Non-primate mammalian activity cycles are highly variable across and within taxonomic groups. In contrast, the order Primates has historically been recognized as displaying a diurnal-nocturnal dichotomy that mapped, for the most part, onto the taxonomic division between haplorhines and strepsirhines. However, it has become clear over the past two decades that activity cycles in primates are not quite so clear cut. Some primate species--like many large herbivorous mammals, mustelids, microtine rodents, and shrews--exhibit activity both at night and during the day. This activity pattern is often polyphasic or ultradian (several short activity bouts per 24-hour period), in contrast to the generally monophasic pattern (one long bout of activity per 24-hour period) observed in diurnal and nocturnal mammals. Alternatively, it can vary on a seasonal basis, with nocturnal activity exhibited during one season, and diurnal activity during the other season. The term now generally employed to describe the exploitation of both diurnal and nocturnal phases in primates is 'cathemeral'. Cathemerality has been documented in one haplorhine, the owl monkey, Aotus azarai, in the Paraguayan and Argentinian Chaco and in several Malagasy strepsirhines, including Eulemur spp., Hapalemur sp. and Lemur catta. In this paper, we review patterns of day-night activity in primates and other mammals and investigate the potential ecological and physiological bases underlying such 24-hour activity. Secondly, we will consider the role of cathemerality in primate evolution.     

Location of the X inactivation center in primates and other mammals

Summary In humans, the X chromosome inactivation center and an X inactivation-associated metaphase fold are at the same location (bands Xq1321) or are very closely associated. In other mammals, the location of the X inactivation center is unknown, but it has been suggested that the relationship between the inactivation center and the inactivation-associated fold may make it a useful marker for both identifying the inactivated X and locating the inactivation center in other mammalian species. If a similar metaphase fold is present in other mammals, the inactivation center would be located at the same site or very nearby. All of nine primate species did express an inactivation-associated fold. In most, the fold was located at the band homologous to human Xq13q21. In one of two chimpanzees, band Xq23q24 was implicated. In five other mammals an inactivation-associated fold was observed, but in two species, no fold was observed.     

Scaling of limb joint surface areas in anthropoid primates and other mammals

Recently it was reported that limb joint surface areas scale positively allometrically with body weight in anthropoid primates. This was attributed to the biomechanics of weight bearing: larger animals must require relatively larger joint surfaces to withstand relatively greater weight-related stresses on the joints. Our data on humeral and femoral geometry and joint surface areas in 73 species belonging to six mammalian orders (including primates) demonstrate that positive allometry of joint surface areas is not a general phenomenon for mammals and cannot have its basis among Anthropoidea in the biomechanics of weight bearing. We argue that, to the extent that positive allometric scaling of joint surface areas occurs in anthropoid primates, it is an artifact of differences in positional behaviour among distinct taxonomic groups that also happen to differ widely in body weight. Furthermore, we argue that, among mammals ranging in body size from sportive lemurs to giant pandas, functionally similar groups tend to exhibit: (1) linear dimensions (especially diameters and shaft circumferences) that scale in direct proportion to each other; and (2) joint surface areas that scale in direct proportion to the squares of linear dimensions and to the 2/3 power of body mass. In other words, limb bones of functionally similar animals fit the theoretical model of geometric similarity (or skeletal isometry). Differences in relative sizes of joint surface areas are related to differences in force transmission and movement potential among functionally distinct groups of animals.     

Associations between primates and other mammals in a central Amazonian forest landscape

Little information exists on mixed-species groups between primates and other mammals in Neotropical forests. In this paper, we describe three such associations observed during an extensive large-vertebrate survey in central Amazonia, Brazil. Mixed-species groups between a primate species and another mammal were observed on seven occasions between squirrel monkeys (Saimiri cf. ustus) and either South American coatis (Nasua nasua) or tayras (Eira barbara) and between brown capuchins (Cebus apella) and coatis. All associations were restricted to floodplain forest during its dry stage. We suggest that the associations involving the coatis are connected to foraging and vigilance but may be induced by a common alternative food resource at a time of food shortage.     

Multiple groups of endogenous betaretroviruses in mice, rats, and other mammals

Betaretroviruses exist in endogenous and exogenous forms in hosts that are widely distributed and evolutionarily distantly related. Here we report the discovery and characterization of several previously unknown betaretrovirus groups in the genomes of Mus musculus and Rattus norvegicus. Each group contains both mouse and rat elements, and several of the groups are more closely related to previously known betaretroviruses from nonmurine hosts. Some of the groups also include members from hosts which were not previously known to harbor betaretroviruses, such as the gray mouse lemur (Microcebus murinus) and Seba's short-tailed bat (Carollia perspicillata). Some of the mouse and rat elements possess intact open reading frames for gag, pro, pol, and/or env genes and display characteristics of having retrotransposed recently. We propose a model whereby betaretroviruses have been evolving within the genomes of murid rodents for at least the last 20 million years and, subsequent to (or concomitant with) the global spread of their murid hosts, have occasionally been transmitted to other species.     

Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates

Background  

Unitary pseudogenes are a class of unprocessed pseudogenes without functioning counterparts in the genome. They constitute only a small fraction of annotated pseudogenes in the human genome. However, as they represent distinct functional losses over time, they shed light on the unique features of humans in primate evolution.     

Comparison of arginase activity in red blood cells of lower mammals, primates, and man: evolution to high activity in primates.

Arginase activity in red blood cells (RBC) of various mammalian species including man was determined. In nonprimate species, the activity generally fell below the level of detectability of the assay: less than 1.0 mumol urea/g hemoglobin per hr. Activities in higher nonhuman primates were equal to or of the same order of magnitude as those in man (approximately 950 mumol/g hemoglobin per hr). RBC arginase deficiency with normal liver arginase activity has been shown to segregate as an autosomal codominant trait in Macaca fascicularis established and bred in captivity. This study confirms the presence of this polymorphism in wild populations trapped in several geographic areas and demonstrates the absence of immunologically cross-reactive material in the RBC of RBC arginase-deficient animals. These data when taken together suggest that the expression of arginase in RBC is the result of a regulatory alteration, has evolved under positive selective pressure, and is not an example of the vestigial persistence of an arcane function. The expression of arginase in the RBC results in a marked drop in the arginine content of these cells.     

Origin and evolution of the grazing guild in new world terrestrial mammals

Although vertebrate herbivory has existed on land for about 300 million years, the grazingadaptation, principally developed in mammals, did not appear until the middle Cenozoic about 30 million years ago. Paleontological evidence indicates that grazing mammals diversified at the time of the spread of grasslands. Recently revised fossil calibrations reveal that the grazing mammal guild originated during the early Miocene in South America about 10-15 million years earlier than it did during the late Miocene in the northern hemisphere. Carbon isotopic analyses of extinct grazers' teeth reveal that this guild originated predominantly in C(3) terrestrial ecosystems. The present-day distribution of C(3) and C(4) grasslands evolved on the global ecological landscape since the late Miocene, after about 7 million years ago.     

Comparative and functional morphology of musculus canalis ani in tetrapod mammals and primates]

Comparative anatomy of structure and function of the M. canalis ani in tetrapode mammals and primates is described for the first time. The muscle itself lies on the sphincter ani internus in the area between the anorectal ("pectinate") and anocutaneal ("white") lines and its circumference is intact around the entire anal canal. The canalis ani muscle orginates from the superior part of the sphincter ani internus and concomitantly receives additional fibers from the longitudinal muscle. Caudally the muscle dips back into the sphincter ani internus and, at the same time, a small portion of the fibers go to the longitudinal muscle and, likewise, a portion also sets itself on the perinaal skin. On the basis of its morphological relationship to the convoluted vessels of the rectal venous plexus, the canalis ani muscle appears to be able to complete the closing of the anus in the continence phase to such an extent that a complete closing of the anal lumen is guaranted.     

Characterization of the functional gene and several processed pseudogenes in the human triosephosphate isomerase gene family.

The functional gene and three intronless pseudogenes for human triosephosphate isomerase were isolated from a recombinant DNA library and characterized in detail. The functional gene spans 3.5 kilobase pairs and is split into seven exons. Its promoter contains putative TATA and CCAAT boxes and is extremely rich in G and C residues (76%). The pseudogenes share a high degree of homology with the functional gene but contain mutations that preclude the synthesis of an active triosephosphate isomerase enzyme. Sequence divergence calculations indicate that these pseudogenes arose approximately 18 million years ago. We present evidence that there is a single functional gene in the human triosephosphate isomerase gene family.     

A comparative analysis of vibrissa count and infraorbital foramen area in primates and other mammals

Vibrissae are specialized sensory “hairs” that respond to mechanical stimuli. Sensory information from vibrissae is transmitted to the brain via the infraorbital nerve, which passes through the infraorbital foramen (IOF). Several analyses have documented that primates have smaller IOFs than non-primate mammals, and that haplorhines have smaller IOFs than strepsirrhines. These grade shifts in IOF area were attributed to differences in “vibrissa development.” Following earlier analyses, IOF area has been used to derive a general estimate of “whiskeredness” in extinct primates, and consequently, IOF area has been used in phylogenetic and paleoecological interpretations. Yet, the relationship between IOF area and vibrissa count has not been tested, and little is known about how IOF area and vibrissa counts vary among mammals. This study explores how relative IOF area and vibrissa count differ among 25 mammalian orders, and tests for a correlation between IOF area and vibrissa count. Results indicate that primates and dermopterans (Primatomorpha) have smaller IOFs than most non-primate mammals, but they do not have fewer vibrissae. In addition, strepsirrhines and haplorhines do not differ from one another in relative IOF area or vibrissa counts. Despite different patterns documented for IOF area and vibrissa count variation across mammals, results from this study do confirm that vibrissa count and IOF area are significantly and positively correlated (p < 0.0001). However, there is considerable scatter in the data, suggesting that vibrissa counts cannot be predicted from IOF area. There are three implications of these finding. First, IOF area reflects all mechanoreceptors in the maxillary region, not just vibrissae. Second, IOF area may be an informative feature in interpretations of the fossil record. Third, paleoecological interpretations based on vibrissae are not recommended.