Inverse relationship between evolutionary rate and age of mammalian genes

A large number of genes is shared by all living organisms, whereas many others are unique to some specific lineages, indicating their different times of origin. The availability of a growing number of eukaryotic genomes allows us to estimate which mammalian genes are novel genes and, approximately, when they arose. In this article, we classify human genes into four different age groups and estimate evolutionary rates in human and mouse orthologs. We show that older genes tend to evolve more slowly than newer ones; that is, proteins that arose earlier in evolution currently have a larger proportion of sites subjected to negative selection. Interestingly, this property is maintained when a fraction of the fastest-evolving genes is excluded or when only genes belonging to a given functional class are considered. One way to explain this relationship is by assuming that genes maintain their functional constraints along all their evolutionary history, but the nature of more recent evolutionary innovations is such that the functional constraints operating on them are increasingly weaker. Alternatively, our results would also be consistent with a scenario in which the functional constraints acting on a gene would not need to be constant through evolution. Instead, starting from weak functional constraints near the time of origin of a gene-as supported by mechanisms proposed for the origin of orphan genes-there would be a gradual increase in selective pressures with time, resulting in fewer accepted mutations in older versus more novel genes.     

Relative longevity and field metabolic rate in birds

Metabolism is a defining feature of all living organisms, with the metabolic process resulting in the production of free radicals that can cause permanent damage to DNA and other molecules. Surprisingly, birds, bats and other organisms with high metabolic rates have some of the slowest rates of senescence begging the question whether species with high metabolic rates also have evolved mechanisms to cope with damage induced by metabolism. To test whether species with the highest metabolic rates also lived the longest I determined the relationship between relative longevity (maximum lifespan), after adjusting for annual adult survival rate, body mass and sampling effort, and mass-specific field metabolic rate (FMR) in 35 species of birds. There was a strongly positive relationship between relative longevity and FMR, consistent with the hypothesis. This conclusion was robust to statistical control for effects of potentially confounding variables such as age at first reproduction, latitude and migration distance, and similarity in phenotype among species because of common phylogenetic descent. Therefore, species of birds with high metabolic rates senesce more slowly than species with low metabolic rates.     

Life history patterns in birds and mammals and their evolutionary interpretation

Summary It is argued that allometric principles account for most of the observed variation in the life history patterns amongst birds. To test this contention it is shown that traits such as incubation time, growth rates, age at first reproduction, lifespan, clutch weight and egg weight all scale to body weight with exponents similar to those found for analogous traits in mammals. It is then shown that most of the variation amongst bird taxa and between birds and mammals based on body weight allometry can be explained by variations in brain size, body temperature and metabolic rate, consistent with theories of growth and ageing derived from mammalian studies. Finally, it is suggested that the evidence for life histostory allometry is sufficiently strong that it argues for a more epigenetic view of life history patterns and their evolution than is generally conceded in most adaptation theories.     

Evolution of the lung surfactant proteins in birds and mammals

Phylogenetic analyses of the families of mammalian lung surfactant proteins (SP-A, SP-B, SP-C, and SP-D) supported the hypothesis that these proteins have diverged between birds and mammals as a result of lineage-specific gene duplications and deletions. Homologs of mammalian genes encoding SP-B, SP-C, and SP-D appear to have been deleted in chickens, whereas there was evidence of avian-specific duplications of the genes encoding SP-A and presaposin. Analysis of the genes closely linked to human SP-B, SP-C, and SP-D genes revealed that all three of these genes are closely linked to genes having orthologs on chicken chromosome 6 and also to genes lacking chicken orthologs. These relationships suggest that all of the lung surfactant protein genes, as well as certain related genes, may have been linked in the ancestor of humans and chickens. Further, they imply that the loss of surfactant protein genes in the avian lineages formed part of major genomic rearrangement events that involved the loss of other genes as well. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Different evolutionary histories underlie congruent species richness gradients of birds and mammals

Aim The global species richness patterns of birds and mammals are strongly congruent. This could reflect similar evolutionary responses to the Earth’s history, shared responses to current climatic conditions, or both. We compare the geographical and phylogenetic structures of both richness gradients to evaluate these possibilities. Location Global. Methods Gridded bird and mammal distribution databases were used to compare their species richness gradients with the current environment. Phylogenetic trees (resolved to family for birds and to species for mammals) were used to examine underlying phylogenetic structures. Our first prediction is that both groups have responded to the same climatic gradients. Our phylogenetic predictions include: (1) that both groups have similar geographical patterns of mean root distance, a measure of the level of the evolutionary development of faunas, and, more directly, (2) that richness patterns of basal and derived clades will differ, with richness peaking in the tropics for basal clades and in the extra‐tropics for derived clades, and that this difference will hold for both birds and mammals. We also explore whether alternative taxonomic treatments for mammals can generate patterns matching those of birds. Results Both richness gradients are associated with the same current environmental gradients. In contrast, neither of our evolutionary predictions is met: the gradients have different phylogenetic structures, and the richness of birds in the lowland tropics is dominated by many basal species from many basal groups, whereas mammal richness is attributable to many species from both few basal groups and many derived groups. Phylogenetic incongruence is robust to taxonomic delineations for mammals. Main conclusions Contemporary climate can force multiple groups into similar diversity patterns even when evolutionary trajectories differ. Thus, as widely appreciated, our understanding of biodiversity must consider responses to both past and present climates, and our results are consistent with predictions that future climate change will cause major, correlated changes in patterns of diversity across multiple groups irrespective of their evolutionary histories.     

The relationship between 'dehydrin-like' proteins and seed longevity in Ranunculus sceleratus L.

The relationship between the abundance of proteins homologousto the dehydrin/RAB group of LEAs and seed longevity has beenstudied in Ranunculus sceleratus L. The presence of these ‘dehydrin-like’proteins was not related to increases in seed longevity associatedwith seed development or priming treatments. Similarly, a drying-inducedincrease in the amount of ‘dehydrin-like’ proteinswas not accompanied by an improvement in longevity. Key words: Dehyclrin, LEA, longevity, R. sceleratus, seed     

The relationship between relative solvent accessibility and evolutionary rate in protein evolution

Recent work with Saccharomyces cerevisiae shows a linear relationship between the evolutionary rate of sites and the relative solvent accessibility (RSA) of the corresponding residues in the folded protein. Here, we aim to develop a mathematical model that can reproduce this linear relationship. We first demonstrate that two models that both seem reasonable choices (a simple model in which selection strength correlates with RSA and a more complex model based on RSA-dependent amino acid distributions) fail to reproduce the observed relationship. We then develop a model on the basis of observed site-specific amino acid distributions and show that this model behaves appropriately. We conclude that evolutionary rates are directly linked to the distribution of amino acids at individual sites. Because of this link, any future insight into the biophysical mechanisms that determine amino acid distributions will improve our understanding of evolutionary rates.     

Specific metabolic rate, longevity and "Rubner constant" for birds

An assumption was made that age constituent alpha x(beta) of mortality of individuals in a population in Weibull equation mx = m0 + alpha x(beta) (Ricklefs, 2000) reflects change of specific metabolic rate of one individual with age. Based upon that hypothesis a formula was proposed for relationship of specific metabolic rate of an adult individual after cessation of growth, when mass W is attained, and age t: q(t) = q0(1-omega(beta) + 1t(beta)) where q0 = aW(-b) is value q(t) at the moment of growth cessation and omega = alpha(1/(beta + 1)) is "ageing rate", determined and estimated by R. Ricklefs. Maximum longevity of an individual was determined as [equation: see text], where qcrit is specific metabolic rate at the age tmax. Parameter beta and relationships omega(W) and (qcrit/q0)(W) were approximated for birds from data of Ricklefs. Statistical comparison of results of calculations of tmax was carried out on the basis of the above formula and other known formulas for groups of Passeriformes and non-Passeriformes. Rubner constant [equation: see text] was calculated assuming that body mass of an adult individual (W) is attained in the first year of life (tA = 0). Average values of 602.4 +/- 2.5 kcal g(-1) (n = 83) for non-Passeriformes and 963 +/- 6.3 kcal g(-1) (n = 41) for Passeriformes were obtained.     

An explanation of the relationships between mass, metabolic rate and characteristic skeletal length for birds and mammals

A theory explaining the relationships between metabolic rate and body mass for birds and mammals is developed in terms of the mitochondrion theory of aerobic metabolism, the sliding filament theory of muscle contraction, simple models of vertebrate anatomy and activity, and other propositions. Both body mass and metabolic rates are shown to result from a homogeneous vertebrate design quantitatively expressed in terms of a set of nearly invariant parameters with five degrees of freedom: propulsion technique, mitochondrion capability, non-skeletal muscle mass exponent, characteristic skeletal length, and sturdiness factor. The first three of the degrees of freedom are phylogenetic group specific. The last two vary considerably even within a single species. The theory is shown to agree satisfactorily with placental mammal, marsupial mammal, passerine bird and nonpasserine bird data. Algorithms for determining metabolic rates and body mass as functions of skeletal characteristic length are developed and quantitative estimates of the constants occurring in the algorithms are given.     

The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals

Background  

During the last ten years, major advances have been made in characterizing and understanding the evolution of mitochondrial DNA, the most popular marker of molecular biodiversity. Several important results were recently reported using mammals as model organisms, including (i) the absence of relationship between mitochondrial DNA diversity and life-history or ecological variables, (ii) the absence of prominent adaptive selection, contrary to what was found in invertebrates, and (iii) the unexpectedly large variation in neutral substitution rate among lineages, revealing a possible link with species maximal longevity. We propose to challenge these results thanks to the bird/mammal comparison. Direct estimates of population size are available in birds, and this group presents striking life-history trait differences with mammals (higher mass-specific metabolic rate and longevity). These properties make birds the ideal model to directly test for population size effects, and to discriminate between competing hypotheses about the causes of substitution rate variation.     

On the relationship between handedness and longevity

Abstract

During the past five years, there have been numerous studies of the relationship between handedness and longevity. In this report, I review previous contributions and use methods of survival analysis on a set of 4,448 males to determine the strength of the relationship between handedness and longevity. The results indicate that left‐handers have small, yet significant, declines in survival probabilities between the ages of 65 and 85.     

Behavioral thermoregulation in mammals and birds

Thermoregulation in homoiotherms is achieved by physiological and behavioural adjustments which involve the musculature, skin, sensory capacities, hypothalamus and endocrine glands. Under thermal stress animals exhibit anorexia, body extension, gasping, languor, lethargy, excessive drinking, bathing, decreased locomotor activities, group dispersion, and shade seeking. When exposed to cold, animals show body flexure, huddling, hyperphagia, extra locomotor activities, depressed respiration and nest building. Species and breed differences in the behavioural adjustments to unfavourable climates are related to habitat, morphological characteristics of body covering, degree of physiological adaptability, degree of physiological immaturity at birth or hatching, and the number of young.     

Strong variations of mitochondrial mutation rate across mammals--the longevity hypothesis

Mitochondrial DNA (mtDNA) is the most popular marker of molecular diversity in animals, primarily because of its elevated mutation rate. After >20 years of intensive usage, the extent of mitochondrial evolutionary rate variations across species, their practical consequences on sequence analysis methods, and the ultimate reasons for mtDNA hypermutability are still largely unresolved issues. Using an extensive cytochrome b data set, fossil data, and taking advantage of the decoupled dynamics of synonymous and nonsynonymous substitutions, we measure the lineage-specific mitochondrial mutation rate across 1,696 mammalian species and compare it with the nuclear rate. We report an unexpected 2 orders of magnitude mitochondrial mutation rate variation between lineages: cytochrome b third codon positions are renewed every 1-2 Myr, in average, in the fastest evolving mammals, whereas it takes >100 Myr in slow-evolving lineages. This result has obvious implications in the fields of molecular phylogeny, molecular dating, and population genetics. Variations of mitochondrial substitution rate across species are partly explained by body mass, longevity, and age of female sexual maturity. The classical metabolic rate and generation time hypothesis, however, do not fully explain the observed patterns, especially a stronger effect of longevity in long-lived than in short-lived species. We propose that natural selection tends to decrease the mitochondrial mutation rate in long-lived species, in agreement with the mitochondrial theory of aging.     

Density-dependent dispersal in birds and mammals

Density‐dependent dispersal can be caused by various mechanisms, from competition inducing individuals to emigrate (positive density‐dependence) to social crowding effects impeding free movement (negative density‐dependence). Various spatial population models have incorporated positively density‐dependent dispersal algorithms, and recent theoretical models have explored the conditions for density‐dependent dispersal (DD) to evolve. However, while the existence of DD is well documented in some taxa such as insects, there is no clear picture on its generality in vertebrates. Here I review the available empirical data on DD in birds and mammals, focusing mainly on variation in dispersal between years and on experimental density manipulations. Surprisingly few studies have explicitly focused on DD, and interpretation of the available data is often hampered by differences in approach, small sample sizes and/or statistical shortcomings. Positive DD was reported in 50 and 33% of the selected mammal and bird studies, respectively, while two studies on mammals (out of eight) reported negative DD. Among bird studies, DD was more often reported for emigration rates or long‐distance recoveries than for average distances within finite study areas. Experimental studies manipulating densities (mainly on mammals) have consistently generated positive DD, typically showing reduced emigration in response to partial population removal. Studies that examined dispersal in relation to seasonal changes in density (small mammals only) have more often reported negative DD. Studies that compared dispersal between sites differing in density, also show a mixture of positive and negative DD. This suggests that dispersal changes in a more complex way with seasonal and spatial density variation than with annual densities, and/or that these results are confounded by other factors differing between seasons and sites, such as habitat quality. I conclude that both correlational and experimental studies support the existence of positive, rather than negative, density‐dependent dispersal in birds and mammals.     

A comparative analysis of the evolutionary relationship between diet and enzyme targeting in bats, marsupials and other mammals

The subcellular distribution of the enzyme alanine:glyoxylate aminotransferase (AGT) in the livers of different mammals appears to be related to their natural diets. Thus, AGT tends to be mitochondrial in carnivores, peroxisomal in herbivores, and both mitochondrial and peroxisomal in omnivores. To what extent this relationship is an incidental consequence of phylogenetic structure or an evolutionarily meaningful adaptive response to changes in dietary selection pressure is unknown. In order to distinguish between these two possibilities, we have determined the subcellular distribution of AGT in the livers of 22 new mammalian species, including members of three orders not studied before. In addition, we have analysed the statistical relationship between AGT distribution and diet in all 77 mammalian species, from 12 different orders, for which the distribution is currently known. Our analysis shows that there is a highly significant correlation between AGT distribution and diet, independent of phylogeny. This finding is compatible with the suggestion that the variable intracellular targeting of AGT is an adaptive response to episodic changes in dietary selection pressure. To our knowledge, this is the first example of such a response being manifested at the molecular and cellular levels across the breadth of Mammalia.     

The ribonuclease A superfamily of mammals and birds: identifying new members and tracing evolutionary histories

The RNase A superfamily has been important in biochemical, structural, and evolutionary studies and is believed to be the sole vertebrate-specific enzyme family. To understand the origin and diversification of the superfamily, we here determine its entire repertoire in the sequenced genomes of human, mouse, rat, and chicken. We report a previously unnoticed gene cluster in mouse chromosome 10 and a number of new genes, including mammalian RNases 11-13, which are close relatives of the recently identified RNases 9 and 10. Gene expression data imply male-reproductive functions for RNases 9-13, although their sequences suggest the lack of ribonucleolytic activities. In contrast to the presence of 13-20 functional genes in mammals, chicken has only 3 RNase genes, which are evolutionarily close to mammalian RNase 5, like other nonmammalian RNases. This and other evidence suggests that the RNase A superfamily originated from an RNase 5-like gene and expanded in mammals. Together with the fact that multiple lineages of the superfamily, including RNases 2, 3, 5, and 7, have antipathogenic activities, we suggest that the superfamily started off as a host-defense mechanism in vertebrates. Consistent with this hypothesis, all members of the superfamily exhibit high rates of amino acid substitution as is commonly observed in immunity genes.     

Encephalization and the evolution of longevity in mammals

Allometric principles account for most of the observed variation in maximum life span among mammals. When body-size effects are controlled for, most of the residual variance in mammalian life span can be explained by variations in brain size, metabolic rate and body temperature. It is shown that species with large brains for a given body size and metabolic rate, such as anthropoid primates, also have long maximum life spans. Conversely, mammals with relatively high metabolic rates and low levels of encephalization, as in most insectivores and rodents, tend to have short life spans. The hypothesis is put forward that encephalization and metabolic rate, which may govern other life history traits, such as growth and reproduction, are the primary determinants directing the evolution of mammalian longevity.     

The relationship between kinship marriages and longevity in Azerbaijan

In order to elucidate the role of inbreeding in human longevity, the individuals of both sexes aged 80-100 and more, all residents of the Azerbaijan SSR, were exposed to a genealogical examination. It was found that 22.46% of men and 12.92% of women were born in kinship marriages. The familial longevity indices appeared to be high in this examination. The inbreeding in the presence of favourable heredity does not reduce the level of longevity in the above region.     

Variability and size in mammals and birds

Body size, its variability, and their ecological correlates have long been important topics in evolutionary biology. Yet, the question of whether there is a general relationship between size and size-relative variability has not previously been addressed. Through an analysis of body-mass and length measurements from 65 074 individuals from 351 mammalian species, we show that size-relative variability increases significantly with mean species body size. Analysis of mean body mass and standard deviations for 237 species of birds revealed the same pattern. We present three plausible alternatives explanations and eliminate several others. Of these, the hypothesis that the increase in size-relative variability with mean body mass is related to the scaling of body mass components is most strongly supported. In effect, larger mammals and birds are more variable because their body mass is composed to greater relative degree of components with higher intrinsic variability (bone, fat, and muscle). In contrast, smaller mammals and birds have lower body mass variability because they are composed to a greater relative extent of components (viscera and nervous system) in which size variation is more highly constrained by energetic and functional factors.