Relationships Among Powered Flight,Metabolic Rate,Body Mass,Genome Size,and the Retrotransposon Complement of Volant Birds

Avian genomes are of interest because the rapid metabolic rate associated with powered flight requires small cells which constrain genome size. Consequently, flying birds tend to have small genomes relative to other vertebrates such as mammals. It thus stands to reason that flying birds should have smaller genomes than ground-dwelling birds with lower metabolic rates. Small genomes could be condensed but uncompromised in a number of ways, including smaller intergenic intervals, shorter introns, and/or a reduced transposable element (TE) complement. We evaluated genome size in light of the orthologous TE complement among 41 flying (FY) and seven ground-dwelling (GD) bird species to determine if a preponderance of deletions in orthologous TEs might explain the compact genomes of flying birds with high metabolic rates. We measured, across multiple loci in all 48 species, the lengths of 50 contemporary orthologous chicken repeat 1 (CR1, a non-LTR retrotransposon) copies relative to inferred ancestral CR1 sequences. We found genome sizes in GD birds were not different than those in FY birds, but the mean lengths of orthologous CR1 loci were significantly shorter in FY birds than in GD birds. Moreover, we observed a negative correlation between basal metabolic rate and length of orthologous CR1 loci. Finally, we observed positive correlations between body mass and both genome sizes as well as length of orthologous CR1 loci, which we expected given that body mass correlates negatively with metabolic rates. Our results support the contention that metabolism helps shape the avian TE complement and thus indirectly contributes to the compact genomes of birds.     

Genome size and wing parameters in passerine birds

Despite their status as the most speciose group of terrestrial vertebrates, birds exhibit the smallest and least variable genome sizes among tetrapods. It has been suggested that this is because powered flight imposes metabolic constraints on cell size, and thus on genome size. This notion has been supported by analyses of genome size and cell size versus resting metabolic rate and other parameters across birds, but most previous studies suffer from one or more limitations that have left the question open. The present study provides new insights into this issue through an examination of newly measured genome sizes, nucleus and cell sizes, body masses and wing parameters for 74 species of birds in the order Passeriformes. A positive relationship was found between genome size and nucleus/cell size, as well as between genome size and wing loading index, which is interpreted as an indicator of adaptations for efficient flight. This represents the single largest dataset presented for birds to date, and is the first to analyse a distinctly flight-related parameter along with genome size using phylogenetic comparative analyses. The results lend additional support to the hypothesis that the small genomes of birds are indeed related in some manner to flight, though the mechanistic and historical bases for this association remain an interesting area of investigation.     

Allometry of paracellular absorption in birds

Water-soluble nutrients can be absorbed across the intestinal epithelium by transcellular and paracellular processes. Recent studies suggest that small birds (<180 g) have more extensive paracellular absorption of glucose than nonflying mammals. This may be a feature that compensates for a reduced small intestine size because small birds have smaller mass-corrected intestinal length than do nonflying mammals, but the difference diminishes in larger birds. We hypothesized that if this explanation were correct, there would be a negative correlation between paracellular absorption and body mass in birds and that larger birds would have paracellular absorption comparable to that of nonflying mammals. We tested this hypothesis, using consistent methodology, by measuring the extent of absorption of a series of inert carbohydrate probes in heavier bird species (>300 g) selected from diverse taxa: American coots, mallards, pheasants, and pigeons. Absorption of carbohydrate probes was inversely related to body mass in birds, and absorption of these probes in large birds (>500 g) was comparable to absorption measurements in nonflying mammals. Higher paracellular uptake in the smaller avian species may offer a physiologically inexpensive means of nutrient absorption to compensate for a reduced small intestine size but may make those species more vulnerable to toxicant absorption.     

Genome size and metabolic intensity in tetrapods: a tale of two lines

We show the negative link between genome size and metabolic intensity in tetrapods, using the heart index (relative heart mass) as a unified indicator of metabolic intensity in poikilothermal and homeothermal animals. We found two separate regression lines of heart index on genome size for reptiles-birds and amphibians-mammals (the slope of regression is steeper in reptiles-birds). We also show a negative correlation between GC content and nucleosome formation potential in vertebrate DNA, and, consistent with this relationship, a positive correlation between genome GC content and nuclear size (independent of genome size). It is known that there are two separate regression lines of genome GC content on genome size for reptiles-birds and amphibians-mammals: reptiles-birds have the relatively higher GC content (for their genome sizes) compared to amphibians-mammals. Our results suggest uniting all these data into one concept. The slope of negative regression between GC content and nucleosome formation potential is steeper in exons than in non-coding DNA (where nucleosome formation potential is generally higher), which indicates a special role of non-coding DNA for orderly chromatin organization. The chromatin condensation and nuclear size are supposed to be key parameters that accommodate the effects of both genome size and GC content and connect them with metabolic intensity. Our data suggest that the reptilian-birds clade evolved special relationships among these parameters, whereas mammals preserved the amphibian-like relationships. Surprisingly, mammals, although acquiring a more complex general organization, seem to retain certain genome-related properties that are similar to amphibians. At the same time, the slope of regression between nucleosome formation potential and GC content is steeper in poikilothermal than in homeothermal genomes, which suggests that mammals and birds acquired certain common features of genomic organization.     

Morphometrics of the avian small intestine compared with that of nonflying mammals: a phylogenetic approach

Flying animals may experience a selective constraint on gut volume because the energetic cost of flight increases and maneuverability decreases with greater digesta load. The small intestine is the primary site of absorption of most nutrients (e.g., carbohydrates, proteins, fat) in both birds and mammals. Therefore, we used a phylogenetically informed approach to compare small intestine morphometric measurements of birds with those of nonflying mammals and to test for effects of diet within each clade. We also compared the fit of nonphylogenetic and phylogenetic models to test for phylogenetic signal after accounting for effects of body mass, clade, and/or diet. We provide a new MATLAB program (Regressionv2.m) that facilitates a flexible model-fitting approach in comparative studies. As compared with nonflying mammals, birds had 51% less nominal small intestine surface area (area of a smooth bore tube) and 32% less volume. For animals <365 g in body mass, birds also had significantly shorter small intestines (20%-33% shorter, depending on body mass). Diet was also a significant factor explaining variation in small intestine nominal surface area of both birds and nonflying mammals, small intestine mass of mammals, and small intestine volume of both birds and nonflying mammals. On the basis of the phylogenetic trees used in our analyses, small intestine length and nominal surface area exhibited statistically significant phylogenetic signal in birds but not in mammals. Thus, for birds, related species tended to be similar in small intestine length and nominal surface area, even after accounting for relations with body mass and diet. A reduced small intestine in birds may decrease the capacity for breakdown and active absorption of nutrients. Birds do not seem to compensate for reduced digestive and absorptive capacity via a longer gut retention time of food, but we found some evidence that birds have an increased mucosal surface area via a greater villus area, although not enough to compensate for reduced nominal surface area. We predict that without increased rate of enzyme hydrolysis and/or mediated transport and without increased passive absorption of water-soluble nutrients, birds may operate with a reduced digestive capacity, compared with that of nonflying mammals, to meet an increase in metabolic needs (i.e., a reduced spare capacity).     

Genetic correlations between basal and maximum metabolic rates in a wild rodent: consequences for evolution of endothermy

According to the aerobic capacity model, endothermy in birds and mammals evolved as a correlated response to selection for an ability of sustained locomotor activity, rather than in a response to direct selection for thermoregulatory capabilities. A key assumption of the model is that aerobic capacity is functionally linked to basal metabolic rate (BMR). The assumption has been tested in several studies at the level of phenotypic variation among individuals or species, but none has provided a clear answer whether the traits are genetically correlated. Here we present results of a genetic analysis based on measurements of the basal and the maximum swim- and cold-induced oxygen consumption in about 1000 bank voles from six generations of a laboratory colony, reared from animals captured in the field. Narrow sense heritability (h2) was about 0.5 for body mass, about 0.4 for mass-independent basal and maximum metabolic rates, and about 0.3 for factorial aerobic scopes. Dominance genetic and common environmental (= maternal) effects were not significant. Additive genetic correlation between BMR and the swim-induced aerobic capacity was high and positive, whereas correlation resulting from specific-environmental effects was negative. However, BMR was not genetically correlated with the cold-induced aerobic capacity. The results are consistent with the aerobic capacity model of the evolution of endothermy in birds and mammals.     

The evolution of body armor in mammals: plantigrade constraints of large body size

Predictions associated with opposing selection generating minimum variance in basal metabolic rate (BMR) in mammals at a constrained body mass (CBM; 358 g) were tested. The CBM is presumed to be associated with energetic constraints linked to predation and variable resources at intermediate sizes on a logarithmic mass scale. Opposing selection is thought to occur in response to energetic constraints associated with predation and unpredictable resources. As body size approaches and exceeds the CBM, mammals face increasing risks of predation and daily energy requirements. Fast running speeds may require high BMRs, but unpredictable and low resources may select for low BMRs, which also reduce foraging time and distances and thus predation risks. If these two selection forces oppose each other persistently, minimum BMR variance may result. However, extreme BMR outliers at and close to the CBM should be indicative of unbalanced selection and predator avoidance alternatives (escapers vs. defenders), and may therefore provide indirect support for opposing selection. It was confirmed that body armor in defenders evolves at and above the CBM, and armored mammals had significantly lower BMRs than their nonarmored counterparts. However, analyses comparing the BMR of escapers--the fastest nonarmored runners (Lagomorpha)--with similar-sized counterparts were inconclusive and were confounded by limb morphology associated with speed optimization. These analyses suggest that the risks and costs of predation and the speed limitations of the plantigrade foot may constrain the evolution of large body sizes in plantigrade mammals.     

The bat genome: GC-biased small chromosomes associated with reduction in genome size

Bats are distinct from other mammals in their small genome size as well as their high metabolic rate, possibly related to flight ability. Although the genome sequence has been published in two species, the data lack cytogenetic information. In this study, the size and GC content of each chromosome are measured from the flow karyotype of the mouse-eared bat, Myotis myotis (MMY). The smaller chromosomes are GC-rich compared to the larger chromosomes, and the relative proportions of homologous segments between MMY and human differ among the MMY chromosomes. The MMY genome size calculated from the sum of the chromosome sizes is 2.25 Gb, and the total GC content is 42.3 %, compared to human and dog with 41.0 and 41.2 %, respectively. The GC-rich small MMY genome is characterised by GC-biased smaller chromosomes resulting from preferential loss of AT-rich sequences. Although the association between GC-rich small chromosomes and small genome size has been reported only in birds so far, we show in this paper, for the first time, that the same phenomenon is observed in at least one group of mammals, implying that this may be a mechanism common to genome evolution in general.     

Genome size and developmental parameters in the homeothermic vertebrates.

Although unrelated to any intuitive notions of organismal complexity, haploid genome sizes (C values) are correlated with a variety of cellular and organismal parameters in different taxa. In some cases, these relationships are universal--notably, genome size correlates positively with cell size in each of the vertebrate classes. Other relationships are apparently relevant only in particular groups. For example, although genome size is inversely correlated with metabolic rate in both mammals and birds, no such relationship is found in amphibians. More recently, it has been suggested that developmental rate and (or) longevity are related to genome size in birds. In the present study, a large dataset was used to examine possible relationships between genome size and various developmental parameters in both birds and mammals. In neither group does development appear to be of relevance to genome size evolution (except perhaps indirectly in birds through the intermediation of body size and (or) within the rodents), a situation very different from that found in amphibians. These findings make it clear that genome size evolution cannot be understood without reference to the particular biology of the organisms under study.     

Brain size, development and metabolism in birds and mammals

Recent hypotheses that variation in brain size among birds and mammals result from differences in metabolic allocation during ontogeny are tested.
Indices of embryonic and post-embryonic brain growth are defined. Precocial birds and mammals have high embryonic brain growth indices which are compensated for by low post-embryonic indices (with the exception of Homo supiens ). In contrast, altricial birds and mammals have low embryonic and high post-embryonic indices. Altricial birds have relatively small brains at hatching and develop relatively large brains as adults, but among mammals there is no equivalent correlation between variation in adult relative brain sizes and state of neonatal development.
Compensatory brain development in both birds and mammals is associated with compensatory parental metabolic allocation. In comparison with altricial development, precocial development is characterized by higher levels of brain growth and parental metabolic allocation prior to hatching or birth and lower levels subsequently. Differences between degrees of postnatal investment by the parents in the young of precocial birds versus precocial mammals may result in the different patterns of adult brain size associated with precociality versus altriciality in the two groups.
The allometric exponent scaling brain on body size differs among taxonomic levels in birds. The exponent is higher for some parts of the brain than others, irrespective of taxonomic level. Unlike mammals, the exponents for birds do not show a general increase with taxonomic level. These pattcrns call into question recent interpretations of the allometric exponent in birds. and the reason for changes in exponent with taxonomic level.     

Metabolic rate and membrane fatty acid composition in birds: a comparison between long-living parrots and short-living fowl

Both basal metabolic rate (BMR) and maximum lifespan potential (MLSP) vary with body size in mammals and birds and it has been suggested that these are mediated through size-related variation in membrane fatty acid composition. Whereas the physical properties of membrane fatty acids affect the activity of membrane proteins and, indirectly, an animal’s BMR, it is the susceptibility of those fatty acids to peroxidation which influence MLSP. Although there is a correlation between body size and MLSP, there is considerable MLSP variation independent of body size. For example, among bird families, Galliformes (fowl) are relatively short-living and Psittaciformes (parrots) are unusually long-living, with some parrot species reaching maximum lifespans of more than 100 years. We determined BMR and tissue phospholipid fatty acid composition in seven tissues from three species of parrots with an average MLSP of 27 years and from two species of quails with an average MLSP of 5.5 years. We also characterised mitochondrial phospholipids in two of these tissues. Neither BMR nor membrane susceptibility to peroxidation corresponded with differences in MLSP among the birds we measured. We did find that (1) all birds had lower n-3 polyunsaturated fatty acid content in mitochondrial membranes compared to those of the corresponding tissue, and that (2) irrespective of reliance on flight for locomotion, both pectoral and leg muscle had an almost identical membrane fatty acid composition in all birds.     

Palaeogenomics of pterosaurs and the evolution of small genome size in flying vertebrates

The two living groups of flying vertebrates, birds and bats, both have constricted genome sizes compared with their close relatives. But nothing is known about the genomic characteristics of pterosaurs, which took to the air over 70 Myr before birds and were the first group of vertebrates to evolve powered flight. Here, we estimate genome size for four species of pterosaurs and seven species of basal archosauromorphs using a Bayesian comparative approach. Our results suggest that small genomes commonly associated with flight in bats and birds also evolved in pterosaurs, and that the rate of genome-size evolution is proportional to genome size within amniotes, with the fastest rates occurring in lineages with the largest genomes. We examine the role that drift may have played in the evolution of genome size within tetrapods by testing for correlated evolution between genome size and body size, but find no support for this hypothesis. By contrast, we find evidence suggesting that a combination of adaptation and phylogenetic inertia best explains the correlated evolution of flight and genome-size contraction. These results suggest that small genome/cell size evolved prior to or concurrently with flight in pterosaurs. We predict that, similar to the pattern seen in theropod dinosaurs, genome-size contraction preceded flight in pterosaurs and bats.     

Functional linkages for the pace of life, life-history, and environment in birds

For vertebrates, body mass underlies much of the variation in metabolism, but among animals of the same body mass, metabolism varies six-fold. Understanding how natural selection can influence variation in metabolism remains a central focus of Physiological Ecologists. Life-history theory postulates that many physiological traits, such as metabolism, may be understood in terms of key maturational and reproductive characteristics over an organism's life-span. Although it is widely acknowledged that physiological processes serve as a foundation for life-history trade-offs, the physiological mechanisms that underlie the diversification of life-histories remain elusive. Data show that tropical birds have a reduced basal metabolism (BMR), field metabolic rate, and peak metabolic rate compared with temperate counterparts, results consistent with the idea that a low mortality, and therefore increased longevity, and low productivity is associated with low mass-specific metabolic rate. Mass-adjusted BMR of tropical and temperate birds was associated with survival rate, in accordance with the view that animals with a slow pace of life tend to have increased life spans. To understand the mechanisms responsible for a reduced rate of metabolism in tropical birds compared with temperate species, we summarized an unpublished study, based on data from the literature, on organ masses for both groups. Tropical birds had smaller hearts, kidneys, livers, and pectoral muscles than did temperate species of the same body size, but they had a relatively larger skeletal mass. Direct measurements of organ masses for tropical and temperate birds showed that the heart, kidneys, and lungs were significantly smaller in tropical birds, although sample sizes were small. Also from an ongoing study, we summarized results to date on connections between whole-organism metabolism in tropical and temperate birds and attributes of their dermal fibroblasts grown in cell culture. Cells derived from tropical birds had a slower rate of growth, consistent with the hypothesis that these cells have a slower metabolism. We found that dermal fibroblasts from tropical birds resisted chemical agents that induce oxidative and non-oxidative stress better than do cells from temperate species, consistent with the hypothesis that birds that live longer invest more in self-maintenance such as antioxidant properties of cells.     

Intraspecific allometry of basal metabolic rate: relations with body size, temperature, composition, and circadian phase in the kestrel, Falco tinnunculus

The relationship between body size and basal metabolic rate (BMR) in homeotherms has been treated in the literature primarily by comparison between species of mammals or birds. This paper focuses on the intraindividual changes in BMR when body mass (W) varies with different maintenance regimens. BMR varied in individual kestrels in proportion to W1.67, which is considerably steeper than the mass exponents for homomorphic change (0.667; Heusner, 1984) for interspecific comparison among all birds (0.677) or raptors (0.678), for interindividual comparison of kestrels on ad libitum maintenance regimens (0.786), and for mass proportionality (1.00). The circadian range of telemetered core temperature also varied more strongly with intraindividual than with interspecific (Aschoff, 1981a) variation in mass. This was due to reduced nocturnal core temperature at low-maintenance regimens, which was, however, insufficient to account for the excessive reduction in BMR. kidney lean mass at Carcass analysis of eight birds sacrificed revealed a disproportionate reduction in heart and kidney lean mass at low-maintenance regimens. We surmise that variation in BMR primarily reflects variation in these metabolically highly active tissues. This may account for positive correlations found between heart, kidney, and BMR residuals relative to interspecific allometric prediction, and between alpha and rho residuals, as expected on the basis of the constant excess of BMR during alpha above BMR during rho (Aschoff & Pohl, 1970a).     

Metabolic ‘engines’ of flight drive genome size reduction in birds

The tendency for flying organisms to possess small genomes has been interpreted as evidence of natural selection acting on the physical size of the genome. Nonetheless, the flight–genome link and its mechanistic basis have yet to be well established by comparative studies within a volant clade. Is there a particular functional aspect of flight such as brisk metabolism, lift production or maneuverability that impinges on the physical genome? We measured genome sizes, wing dimensions and heart, flight muscle and body masses from a phylogenetically diverse set of bird species. In phylogenetically controlled analyses, we found that genome size was negatively correlated with relative flight muscle size and heart index (i.e. ratio of heart to body mass), but positively correlated with body mass and wing loading. The proportional masses of the flight muscles and heart were the most important parameters explaining variation in genome size in multivariate models. Hence, the metabolic intensity of powered flight appears to have driven genome size reduction in birds.     

Reptiles: a group of transition in the evolution of genome size and of the nucleotypic effect

A comparison between genome size and some phenotypic parameters, such as developmental length and metabolic rate, showed in reptiles a nucleotypic correlation similar to the one observed in birds and mammals. Indeed, like homeotherms, reptiles exhibit a highly significant, inverse correlation of genome size with metabolic rate but unlike amphibians, no relationship with developmental length. Several lines of evidence suggest that these nucleotypic correlations are influenced by body temperature, which also affects the guanine + cytosine nuclear percentage, and that they play an important role in the adaptation of these amniotes. However, the reptilian suborders exhibit differences in the quantitative and compositional characters of the genome that do not completely correspond to differences in the phenotypic parameters commonly involved in the nucleotypic effect. Thus, additional factors could have influenced genome size in this class. These data could be explained with the model of Hartl and Petrov, who observed an inverse correlation between genome size, non-coding portion of the genome and rate of DNA loss and hypothesized a strong role for different spectra of spontaneous insertions and deletions (indels) in the variations of genome size. It is thus reasonable to surmise that variations in the reptilian genome were initially influenced by different indels spectra typical of the diverse lineages, possibly related to different chromosome compartmentalizations. The consequent size increases or decreases would have influenced various morphological and functional cell parameters, and through these some phenotypic characteristics of the whole organism, especially the metabolic rate, very important for environmental adaptation and thus subject to natural selection. Through this "nucleotypic" bond, natural selection would also have controlled genome size variations.     

Basal metabolic rate: history, composition, regulation, and usefulness

The concept of basal metabolic rate (BMR) was developed to compare the metabolic rate of animals and initially was important in a clinical context as a means of determining thyroid status of humans. It was also important in defining the allometric relationship between body mass and metabolic rate of mammals. The BMR of mammals varies with body mass, with the same allometric exponent as field metabolic rate and with many physiological and biochemical rates. The membrane pacemaker theory proposes that the fatty acid composition of membrane bilayers is an important determinant of a species BMR. In both mammals and birds, membrane polyunsaturation decreases and monounsaturation increases with increasing body mass and a decrease in mass-specific BMR. The secretion and production of thyroid hormones in mammals are related to body mass, with the allometric exponent similar to BMR; yet there is no body size-related variation in either total or free concentrations of thyroid hormones in plasma of mammals. It is suggested that in different-sized mammals, the secretion/production of thyroid hormones is a result of BMR differences rather than their cause. BMR is a useful concept in some situations but not in others.     

The demands of incubation and avian clutch size

We reviewed information on the demands of incubation to examine whether these could influence the optimal clutch size of birds. The results indicate that appreciable metabolic costs of incubation commonly exist, and that the incubation of enlarged clutches can impose penalties on birds. In 23 studies on 19 species, incubation metabolic rate (IMR) was not elevated above the metabolic rate of resting non-incubating birds (RMR), but contrary to the physiological predictions of King and others, IMR was greater than RMR in 15 studies on 15 species. Across species, IMR was substantially above basal metabolic rate (BMR), averaging 1.606 × BMR. Of six studies on three species performed under thermo-neutral conditions, none found IMR to be in excess of RMR. IMRs measured exclusively within the thermo-neutral zone averaged only 1.08 × BMR contrasting with the significantly higher figure of 1.72 × BMR under wider conditions. 16 of 17 studies on procellariiforms found IMR below RMR, indicating a significant difference between this and other orders. We could find no other taxonomic, or ecological factors which had clear effects on IMR. Where clutch size was adjusted experimentally during incubation, larger clutches were associated with: significantly lower percentage hatching success in 11 of 19 studies; longer incubation periods in eight of ten studies; greater loss of adult body condition in two of five studies; and higher adult energy expenditure in eight of nine studies. Given that incubation does involve metabolic costs and given that the demands of incubation increase sufficiently with clutch size to affect breeding performance, we propose that the optimal clutch size of birds may in part by shaped by the number of eggs the parents can afford to incubate.     

Individual variation and repeatability of basal metabolism in the bank vole, Clethrionomys glareolus

Basal metabolic rate (BMR) is a fundamental energetic trait and has been measured in hundreds of birds and mammals. Nevertheless, little is known about the consistency of the population-average BMR or its repeatability at the level of individual variation. Here, we report that average mass-independent BMR did not differ between two generations of bank voles or between two trials separated by one month. Individual differences in BMR were highly repeatable across the one month interval: the coefficient of intraclass correlation was 0.70 for absolute log-transformed values and 0.56 for mass-independent values. Thus, BMR can be a meaningful measure of an individual physiological characteristic and can be used to test hypotheses concerning relationships between BMR and other traits. On the other hand, mass-independent BMR did not differ significantly across families, and the coefficient of intraclass correlation for full sibs did not differ from zero, which suggests that heritability of BMR in voles is not high.