Metabolic cold adaptation of polar fish based on measurements of aerobic oxygen consumption: fact or artefact? Artefact!

Whether metabolic cold adaptation in polar fish, based on measurements of aerobic standard metabolic rate, is a fact or an artefact has been a dispute since Holeton asked the question in 1974. So far polar fish had been considered to be metabolically cold adapted because they were reported to have a considerably elevated resting oxygen consumption, or standard metabolic rate, compared with oxygen consumption values of tropical or temperate fish extrapolated to similar low polar temperatures. Recent experiments on arctic and Antarctic fish, however, do not show elevated resting aerobic oxygen consumption values, or standard metabolic rate, and hence it is concluded that that metabolic cold adaptation in the traditional sense is an artefact.     

Habitat choice and recruitment of tropical fishes on temperate coasts of Japan

Tropical reef corals are expanding on Japanese temperate coasts in response to rising sea surface temperatures, and many tropical fish juveniles have been observed routinely in these coral habitats. The present study explored how offshore tropical fish larvae locate coral habitat on the temperate coasts of Japan. Settlement-stage larvae were sampled between July and October 2009–2011 with light traps anchored on coral-replete and coral-free habitats (rocky habitats) at two-level distance (distance between each habitat type was 6 km and 500 m, respectively). Larval abundance was significantly higher on the coral-dominated habitat than that on the rocky habitat at both short and long distance sites, suggesting that coral habitats attract offshore tropical fish larvae. In underwater visual survey, Chaetodontidae and Pomacentridae juveniles were more abundant in coral habitats than in rocky habitats at both the sites, and a laboratory habitat choice experiment demonstrated that these larvae showed a preference for corals rather than rocks. In contrast, densities of juvenile Mullidae did not differ between the coral and rocky habitats, and the larvae did not show a substrate preference in the habitat choice experiment. These observations suggest that habitat choice at settlement possibly accounts for the differences in settlement patterns of tropical fishes between the two habitats. Taken together, our results showed that most tropical fish larvae colonize their settlement coast at a scale of ~0.5 km, and that they may locate coral habitats after reaching a reef. Moreover, the results suggest that coral habitat expansion on temperate coasts will lead to an increase in coral-associated tropical fishes and will change assemblage structures of fishes on temperate coasts.     

No evidence for slow-down of molecular substitution rates at subzero temperatures in Antarctic serolid isopods (Crustacea, Isopoda, Serolidae)

The molecular slow-down hypothesis suggests a temperature-controlled slow-down of molecular substitution rates to be a common characteristic of polar poikilotherm organisms. There is evidence that metabolic rate may be controlling the rate of nucleotide substitution in many organisms. In this study, absolute rates of nucleotide change based on a geologically calibrated molecular clock from the 16S ribosomal RNA (LSU) gene of 12 species of serolid isopods living in Antarctic waters are calculated and compared with data from sesarmid crabs from tropical latitudes. Contrary to the prediction, no difference of molecular substitution rates between Crustacea from different latitudes can be detected. This result is corroborated by testing the relative rate in serolid isopods against other Crustacea from tropical, temperate and Antarctic waters. While an influence of temperature on the rate of spontaneous mutation cannot be dismissed, the results show that temperature is not the key determinant of the rate of nucleotide change as has been suggested by the molecular slow-down hypothesis.     

Validation of bacterial replication termination models using simulation of genomic mutations

In bacterial circular chromosomes and most plasmids, the replication is known to be terminated when either of the following occurs: the forks progressing in opposite directions meet at the distal end of the chromosome or the replication forks become trapped by Tus proteins bound to Ter sites. Most bacterial genomes have various polarities in their genomic structures. The most notable feature is polar genomic compositional asymmetry of the bases G and C in the leading and lagging strands, called GC skew. This asymmetry is caused by replication-associated mutation bias, and this "footprint" of the replication machinery suggests that, in contrast to the two known mechanisms, replication termination occurs near the chromosome dimer resolution site dif. To understand this difference between the known replication machinery and genomic compositional bias, we undertook a simulation study of genomic mutations, and we report here how different replication termination models contribute to the generation of replication-related genomic compositional asymmetry. Contrary to naive expectations, our results show that a single finite termination site at dif or at the GC skew shift point is not sufficient to reconstruct the genomic compositional bias as observed in published sequences. The results also show that the known replication mechanisms are sufficient to explain the position of the GC skew shift point.     

Length and GC Content Variability of Introns among Teleostean Genomes in the Light of the Metabolic Rate Hypothesis

A comparative analysis of five teleostean genomes, namely zebrafish, medaka, three-spine stickleback, fugu and pufferfish was performed with the aim to highlight the nature of the forces driving both length and base composition of introns (i.e., bpi and GCi). An inter-genome approach using orthologous intronic sequences was carried out, analyzing independently both variables in pairwise comparisons. An average length shortening of introns was observed at increasing average GCi values. The result was not affected by masking transposable and repetitive elements harbored in the intronic sequences. The routine metabolic rate (mass specific temperature-corrected using the Boltzmann''s factor) was measured for each species. A significant correlation held between average differences of metabolic rate, length and GC content, while environmental temperature of fish habitat was not correlated with bpi and GCi. Analyzing the concomitant effect of both variables, i.e., bpi and GCi, at increasing genomic GC content, a decrease of bpi and an increase of GCi was observed for the significant majority of the intronic sequences (from ∼40% to ∼90%, in each pairwise comparison). The opposite event, concomitant increase of bpi and decrease of GCi, was counter selected (from <1% to ∼10%, in each pairwise comparison). The results further support the hypothesis that the metabolic rate plays a key role in shaping genome architecture and evolution of vertebrate genomes.     

Seasonality of peak metabolic rate in non‐migrant tropical birds

Birds that are year‐round residents of temperate and tropical regions have divergent life histories. Tropical birds have a slower ‘pace of life’, one characteristic of which includes lower peak metabolic rate and daily activity levels. Temperate resident birds are faced with seasonal variation in thermogenic demand. This challenge is met with seasonally increased peak metabolic rate during winter. These thermogenic demands are much lower in birds that are year‐round tropical residents. By measuring peak (summit) metabolic rate in tropical and temperate resident bird species during summer and winter, we asked whether tropical birds exhibit seasonality in peak metabolic rate, and if the direction of seasonality differs between tropical and temperate species. We measured summit metabolism in seven tropical and one temperate species during the winter and during the summer breeding season to test the hypothesis that summit metabolism of tropical residents would change seasonally. We consider whether metabolic seasonality is associated with breeding season for tropical species. We found that summit metabolism was significantly greater during the summer for most tropical residents, while the temperate resident matched several previous reports with higher summit metabolism in winter. We conclude that metabolic seasonality occurs in tropical residents and differs from temperate residents, suggesting that breeding during the summer may be driving relatively higher metabolism as compared to winter thermogenesis in temperate birds.     

Latitudinal variation in spongivorous fishes and the effectiveness of sponge chemical defenses

It has been proposed that predation pressure declines with increasing latitude and a positive correlation exists between predation intensity and the investment into chemical defenses. However, little direct evidence supports the idea that tropical species are better defended chemically than their temperate counterparts. Temperate reefs of the South Atlantic Bight (SAB) off Georgia, USA, provide a unique opportunity to study tropical sponges in a temperate environment. We documented sponge species richness and abundance, sponge predator density, and examined the ability of eight sponge species to chemically deter predation by fishes on two reefs in the SAB. We used rarefaction analysis and ANOVA to compare our results for sponge species richness and density, respectively, with similar published studies conducted on reefs of the sub-tropical Atlantic (i.e., Florida Keys). These analyses were combined with similar statistical comparisons for spongivorous fish species richness and density. Results showed that sponge species richness was lower, but sponge density was higher, on the temperate SAB reefs than on the subtropical reefs. Both spongivorous fish diversity and density were lower on the SAB reefs. The greater abundance of sponges and lower density of predators on SAB reefs suggest a lower frequency of predation on sponges on SAB reefs. Of the eight sponge species assayed from the SAB reefs, five possessed chemical extracts that were significantly less deterrent to fish predators than their tropical/subtropical conspecifics. When the results were combined across all sponge species, the chemical deterrence of fish predators was significantly lower for extracts obtained from the temperate sponge community as compared to the tropical/subtropical assemblage. These results support the more general hypothesis that a lower density and diversity of sponge predators occurs at high as compared to low latitudes in the western Atlantic and may contribute to decreased investment in chemical defenses.     

Fish genomes and their evolution under the influence of ecology

Environmental interactions and the effects of such interactions on the evolution of genome attributes is an intriguing area of ongoing research. Several earlier studies have delved into how the genome size (GS) and the guanine-cytosine content (GC) of genomes are shaped by species’ ecology while largely disregarding other genome attributes, such as number of chromosomes (CR), number of genes (GE), and protein count (PC) from such comparisons. The present study was designed at understanding the influence of ecology––climate, habitat, and depth––on genome attributes by using the most current data on 579 whole fish genomes available at NCBI. Given the diverse and intricate roles of GS and GC in species adaptations to temperature, salinity, and hydrostatic pressure, the focus was on finding if and how the genomes responded to these stressors and if any common patterns existed in the genome-level responses. Our analyses exhibited some significant and intriguing trends for fishes as a whole while indicating strong effects of ecology on GS, GC, CR, and PC. Also, some very unique trends were observed on regressing GS and GC values across temperature, salinity, and depth clines. Accordingly, a very strong decline in the GS and a concomitant increase in GC were observed in species through the tropics/sub tropics to the temperate/poles, from freshwater to the marine habitats, and from the pelagic to bathydemersal depths. Observed patterns strongly support the notion that smaller GS and larger GC are associated with species inhabiting more stable environments and vice versa. The results also signify the effect of these patterns on protein flexibility and its role in tolerating stressful conditions. Observed patterns are discussed in the light of latitudinal biodiversity gradient, habitat complexity, and energy and metabolic expenditure hypothesis.     

The complete mitochondrial genome of the Antarctic sea spider Ammothea carolinensis (Chelicerata; Pycnogonida)

Mitochondria are responsible for the oxidative phosphorylation process. Accordingly, putatively adaptive changes in their genomic features have been variously associated with major eco-physiological shifts in animal evolution, including increased metabolic rates and heat adaptation. Antarctic pycnogonids offer an interesting system to test whether the selective pressure for heat production and increased aerobic metabolism may be driving genomic changes like: (a) unusual compositional biases at the nucleotide and amino acid level, possibly related to cold adaptation; (b) an accelerated rate of mutations/genomic rearrangements, possibly related to the mutagenic effects of oxygen intermediates. The complete mitochondrial genome (mtDNA) of the Antarctic sea spider Ammothea carolinensis Leach, 1814 (Arthropoda: Pycnogonida), the type species for the genus Ammothea, has been determined and is here compared to known genomes from Antarctic and temperate species. We describe a marked heterogeneity in base composition skewness parameters as well as a strong signature of purifying selection toward an increase in thymines at second codon positions, possibly associated with an increased stability of hydrophobic inter-membrane domains. We further observe a fairly high rate of genomic changes, including a possible hot spot of recombination at the level of tRNA-Q. Nevertheless, these features do not seem to be restricted to the two Antarctic pycnogonids analyzed, as to suggest a causal relationship between cold adaptation and genomic changes, and are better interpreted as basal features shared by the entire group. The relevance of the newly determined sequence for the phylogeny of pycnogonids, including its base composition and genomic rearrangements, is further discussed.     

Sleep in mammals

Quiet sleep (QS) was correlated with a different set of constitutional variables from those associated with active sleep (AS), in a sample of 69 species of mammals. The time spent in quiet sleep was negatively correlated with body size and basal metabolic rate. The latter relationship remained even after controlling for the effects of body weight. Neither the total time spent in active sleep, nor active sleep as a percentage of total sleep time was significantly correlated with body weight or metabolic rate. Altricial species spend more time in active sleep than do precocial species. The time between the onset of successive episodes of active sleep, the AS-QS cycle length, was positively correlated with body weight. For their body sizes, species that live in temperate regions have shorter AS-QS cycles than those living in tropical or sub-tropical regions. Correlations between patterns of sleep and adult brain weight probably result from the confounding effects of body weight. These findings were used to evaluate several explanations for interspecific differences in patterns of sleep among mammals.     

High guanine-cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes

The causes of the variation between genomes in their guanine (G) and cytosine (C) content is one of the central issues in evolutionary genomics. The thermal adaptation hypothesis conjectures that, as G:C pairs in DNA are more thermally stable than adenonine:thymine pairs, high GC content may he a selective response to high temperature. A compilation of data on genomic GC content and optimal growth temperature for numerous prokaryotes failed to demonstrate the predicted correlation. By contrast, the GC content of Structural RNAs is higher at high temperatures. The issue that we address here is whether more freely evolving sites in exons (i.e. codonic third positions) evolve in the same manner as genomic DNA as a whole, Showing no correlated response, or like structural RNAs showing a strong correlation. The latter pattern would provide strong support for the thermal adaptation hypothesis, as the variation in GC content between orthologous genes is typically most profoundly seen at codon third sites (GC3). Simple analysis of completely sequenced prokaryotic genomes shows that GC3, but not genomic GC, is higher on average in thermophilic species. This demonstrates, if nothing else, that the results from the two measures cannot be presumed to be the same. A proper analysis, however, requires phylogenetic control. Here, therefore, we report the results of a comparative analysis of GC composition and optimal growth temperature for over 100 prokaryotes. Comparative analysis fails to show, in either Archea or Eubacteria, any hint of connection between optimal growth temperature and GC content in the genome as a whole, in protein-coding regions or, more crucially at GC. Conversely, comparable analysis confirms that GC content of structural RNA is strongly correlated with optimal temperature. Against the expectations of the thermal adaptation hypothesis, within prokaryotes GC content in protein-coding genies, even at relatively freely evolving sites, cannot be considered an adaptation to the thermal environment.     

Cold adaptation in marine organisms

Animals from polar seas exhibit numerous so called resistance adaptations that serve to maintain homeostasis at low temperature and prevent lethal freezing injury. Specialization to temperatures at or below 0 degrees C is associated with an inability to survive at temperatures above 3-8 degrees C. Polar fish synthesize various types of glycoproteins or peptides to lower the freezing point of most extracellular fluid compartments in a non-colligative manner. Antifreeze production is seasonal in boreal species and is often initiated by environmental cues other than low temperature, particularly short day lengths. Most of the adaptations that enable intertidal invertebrates to survive freezing are associated with their ability to withstand ariel exposure. Unique adaptations for freezing avoidance include the synthesis of low molecular mass ice-nucleating proteins that control and induce extracellular ice-formation. Marine poikilotherms also exhibit a range of capacity adaptations that increase the rate of some physiological processes so as to partially compensate for the effects of low temperature. However, the rate of embryonic development in a diverse range of marine organisms shows no evidence of temperature compensation. This results in a significant lengthening of the time from fertilization to hatching in polar, relative to temperate, species. Some aspects of the physiology of polar marine species, such as low metabolic and slow growth rates, probably result from a combination of low temperature and other factors such as the highly seasonal nature of food supplies. Although neuromuscular function shows a partial capacity adaptation in Antarctic fish, maximum swimming speeds are lower than for temperate and tropical species, particularly for early stages in the life history.     

Temperate macroalgae impacts tropical fish recruitment at forefronts of range expansion

Warming waters and changing ocean currents are increasing the supply of tropical fish larvae to temperature regions where they are exposed to novel habitats, namely temperate macroalgae and barren reefs. Here, we use underwater surveys on the temperate reefs of south-eastern (SE) Australia and western Japan (~33.5°N and S, respectively) to investigate how temperate macroalgal and non-macroalgal habitats influence recruitment success of a range of tropical fishes. We show that temperate macroalgae strongly affected recruitment of many tropical fish species in both regions and across three recruitment seasons in SE Australia. Densities and richness of recruiting tropical fishes, primarily planktivores and herbivores, were over seven times greater in non-macroalgal than macroalgal reef habitat. Species and trophic diversity (K-dominance) were also greater in non-macroalgal habitat. Temperate macroalgal cover was a stronger predictor of tropical fish assemblages than temperate fish assemblages, reef rugosities or wave exposure. Tropical fish richness, diversity and density were greater on barren reef than on reef dominated by turfing algae. One common species, the neon damselfish (Pomacentrus coelestis), chose non-macroalgal habitat over temperate macroalgae for settlement in an aquarium experiment. This study highlights that temperate macroalgae may partly account for spatial variation in recruitment success of many tropical fishes into higher latitudes. Hence, habitat composition of temperate reefs may need to be considered to accurately predict the geographic responses of many tropical fishes to climate change.

     

Compositional properties of nuclear genes from cold-blooded vertebrates

Summary We have investigated the compositional properties of coding sequences from cold-blooded vertebrates and we have compared them with those from warm-blooded vertebrates. Moreover, we have studied the compositional correlations of coding sequences with the genomes in which they are contained, as well as the compositional correlations among the codon positions of the genes analyzed.The distribution of GC levels of the third codon positions of genes from cold-blooded vertebrates are distinctly different from those of warm-blooded vertebrates in that they do not reach the high values attained by the latter. Moreover, coding sequences from cold-blooded vertebrates are either equal, or, in most cases, lower in GC (not only in third, but also in first and second codon positions) than homologous coding sequences from warm-blooded vertebrates; higher values are exceptional. These results at the gene level are in agreement with the compositional differences between cold-blooded and warm-blooded vertebrates previously found at the whole genome (DNA) level (Bernardi and Bernardi 1990a,b).Two linear correlations were found: one between the GC levels of coding sequences (or of their third codon positions) and the GC levels of the genomes of cold-blooded vertebrates containing them; and another between the GC levels of third and first+ second codon positions of genes from cold-blooded vertebrates. The first correlation applies to the genomes (or genome compartments) of all vertebrates and the second to the genes of all living organisms. These correlations are tantamount to a genomic code.     

Whole genome re‐sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera)

Sacred lotus (Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystems. As a foundation for exploring genomic variation and evolution among different germplasms, we re‐sequenced 19 individuals from three cultivated temperate lotus subgroups (rhizome, seed and flower lotus), one wild temperate lotus subgroup (wild lotus), one tropical lotus group (Thai lotus) and an outgroup (Nelumbo lutea). Through genetic diversity and polymorphism analysis by non‐missing SNP sites widely distributed in the whole genome, we confirmed that wild and Thai lotus exhibited greater differentiation with a higher genomic diversity compared to cultivated lotus. Rhizome lotus had the lowest genomic diversity and a closer relationship to wild lotus, whereas the genomes of seed and flower lotus were admixed. Genes in energy metabolism process and plant immunity evolved rapidly in lotus, reflecting local adaptation. We established that candidate genes in genomic regions with significant differentiation associated with temperate and tropical lotus divergence always exhibited highly divergent expression pattern. Together, this study comprehensive and credible interpretates important patterns of genetic diversity and relationships, gene evolution, and genomic signature from ecotypic differentiation of sacred lotus.     

Metabolic rate is negatively linked to adult survival but does not explain latitudinal differences in songbirds

Survival rates vary dramatically among species and predictably across latitudes, but causes of this variation are unclear. The rate‐of‐living hypothesis posits that physiological damage from metabolism causes species with faster metabolic rates to exhibit lower survival rates. However, whether increased survival commonly observed in tropical and south temperate latitudes is associated with slower metabolic rate remains unclear. We compared metabolic rates and annual survival rates that we measured across 46 species, and from literature data across 147 species of birds in northern, southern and tropical latitudes. High metabolic rates were associated with lower survival but survival varied substantially among latitudinal regions independent of metabolism. The inability of metabolic rate to explain latitudinal variation in survival suggests (1) species may evolve physiological mechanisms that mitigate physiological damage from cellular metabolism and (2) extrinsic rather than intrinsic sources of mortality are the primary causes of latitudinal differences in survival.     

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.     

台湾海峡鱼类组成及其生态区系

本文依据台湾海峡鱼类物种的相关历史调查资料和文献, 分析了台湾海峡鱼类物种组成及其生态类型和区系特征, 探讨全球变化背景下台湾海峡鱼类物种组成变化。结果显示, 台湾海峡共有鱼类1,697种, 分隶40目206科740属, 其中, 目级分类阶元种类数最多的为鲈形目, 科级分类阶元种类数最多的为鰕虎科; 从适温性上看, 暖水性鱼类最多, 有1,560种, 其次为暖温性鱼类(128种)和冷温性鱼类(9种); 栖息地生态类型则以大陆架砂泥质底层鱼类和岩礁性鱼类种类数最多, 各有596种, 其后依次是大陆架近底层鱼类(249种)、大陆架中上层鱼类(158种)和大洋性鱼类(98种), 洄游性鱼类181种, 经济性鱼类735种; 海区间鱼类种类数对比显示, 台湾海峡鱼类与南海鱼类共有种最多, 共有种比例高达91.9%, 其次为东海(69.3%)和黄海(19.4%), 多为印度—西太平洋海区分布种, 仅288种广泛分布于中国各海区。由此, 台湾海峡鱼类区系特征兼有热带和亚热带海区鱼类区系特点, 属于印度—西太平洋暖水区系中—日亚区和印度—马来亚区的过渡海区, 其分界区域在台湾浅滩东部外缘至澎湖列岛偏北海域。     

Isochore patterns and gene distributions in fish genomes

The compositional approach developed in our laboratory many years ago revealed a large-scale compositional heterogeneity in vertebrate genomes, in which GC-rich and GC-poor regions, the isochores, were found to be characterized by high and low gene densities, respectively. Here we mapped isochores on fish chromosomes and assessed gene densities in isochore families. Because of the availability of sequence data, we have concentrated our investigations on four species, zebrafish (Brachydanio rerio), medaka (Oryzias latipes), stickleback (Gasterosteus aculeatus), and pufferfish (Tetraodon nigroviridis), which belong to four distant orders and cover almost the entire GC range of fish genomes. These investigations produced isochore maps that were drastically different not only from those of mammals (in that only two major isochore families were essentially present in each genome vs five in the human genome) but also from each other (in that different isochore families were represented in different genomes). Gene density distributions for these fish genomes were also obtained and shown to follow the expected increase with increasing isochore GC. Finally, we discovered a remarkable conservation of the average size of the isochores (which match replicon clusters in the case of human chromosomes) and of the average GC levels of isochore families in both fish and human genomes. Moreover, in each genome the GC-poorest isochore families comprised a group of "long isochores" (2-20 Mb in size), which were the lowest in GC and varied in size distribution and relative amount from one genome to the other.     

Compositional evolution of noncoding DNA in the human and chimpanzee genomes

We have examined the compositional evolution of noncoding DNA in the primate genome by comparison of lineage-specific substitutions observed in 1.8 Mb of genomic alignments of human, chimpanzee, and baboon with 6542 human single-nucleotide polymorphisms (SNPs) rooted using chimpanzee sequence. The pattern of compositional evolution, measured in terms of the numbers of GC-->AT and AT-->GC changes, differs significantly between fixed and polymorphic sites, and indicates that there is a bias toward fixation of AT-->GC mutations, which could result from weak directional selection or biased gene conversion in favor of high GC content. Comparison of the frequency distributions of a subset of the SNPs revealed no significant difference between GC-->AT and AT-->GC polymorphisms, although AT-->GC polymorphisms in regions of high GC segregate at slightly higher frequencies on average than GC-->AT polymorphisms, which is consistent with a fixation bias favoring high GC in these regions. However, the substitution data suggest that this fixation bias is relatively weak, because the compositional structure of the human and chimpanzee genomes is becoming homogenized, with regions of high GC decreasing in GC content and regions of low GC increasing in GC content. The rate and pattern of nucleotide substitution in 333 Alu repeats within the human-chimpanzee-baboon alignments are not significantly affected by the GC content of the region in which they are inserted, providing further evidence that, since the time of the human-chimpanzee ancestor, there has been little or no regional variation in mutation bias.