We analyze published data from 592 AC microsatellite loci from 98 species in five vertebrate classes including fish, reptiles, amphibians, birds, and mammals. We use these data to address nine major questions about microsatellite evolution. First, we find that larger genomes do not have more microsatellite loci and therefore reject the hypothesis that microsatellites function primarily to package DNA into chromosomes. Second, we confirm that microsatellite loci are relatively rare in avian genomes, but reject the hypothesis that this is due to physical constraints imposed by flight. Third, we find that microsatellite variation differs among species within classes, possibly relating to population dynamics. Fourth, we reject the hypothesis that microsatellite structure (length, number of alleles, allele dispersion, range in allele sizes) differs between poikilotherms and homeotherms. The difference is found only in fish, which have longer microsatellites and more alleles than the other classes. Fifth, we find that the range in microsatellite allele size at a locus is largely due to the number of alleles and secondarily to allele dispersion. Sixth, length is a major factor influencing mutation rate. Seventh, there is a directional mutation toward an increase in microsatellite length. Eighth, at the species level, microsatellite and allozyme heterozygosity covary and therefore inferences based on large-scale studies of allozyme variation may also reflect microsatellite genetic diversity. Finally, published microsatellite loci (isolated using conventional hybridization methods) provide a biased estimate of the actual mean repeat length of microsatellites in the genome.

Corresponding Editor: B. Bowen

The study of phenotypic integration concerns the modular nature of organismal phenotypes. The concept provides a rationale for why certain subsets of phenotypic traits show particularly high levels of association over development and/or evolution. The techniques detailed in this report facilitate the generation and testing of hypotheses of phenotypic integration and trait interaction. The approach advocated for exploring patterns of interaction among traits is based on the statistical notion of conditional independence, incorporated in a technique known as graphical modeling. The use of graphical models is illustrated with an application to a well-known biological dataset of fowl skeletal measurements, previously analyzed by Sewall Wright. A definition of phenotypic modularity is given, based on a notion of mutual information, which provides a consistent criterion for recognizing and delimiting integrated subsets of traits and which can be related to standard models of multivariate selection.

Corresponding Editor: M. Zelditch

The importance for fitness of epistatic interactions among mutations is poorly known, yet epistasis can exert important effects on the dynamics of evolving populations. We showed previously that epistatic interactions are common between pairs of random insertion mutations in the bacterium Escherichia coli. In this paper, we examine interactions between these mutations and other mutations by transducing each of twelve insertion mutations into two genetic backgrounds, one ancestral and the other having evolved in, and adapted to, a defined laboratory environment for 10,000 generations. To assess the effect of the mutation on fitness, we allowed each mutant to compete against its unmutated counterpart in that same environment. Overall, there was a strong positive correlation between the mutational effects on the two genetic backgrounds. Nonetheless, three of the twelve mutations had significantly different effects on the two backgrounds, indicating epistasis. There was no significant tendency for the mutations to be less harmful on the derived background. Thus, there is no evidence supporting the hypothesis that the derived bacteria had adapted, in part, by becoming buffered against the harmful effects of mutations.

Corresponding Editor: M. Riley

Understanding the utility and limitations of molecular markers for predicting the evolutionary potential of natural populations is important for both evolutionary and conservation genetics. To address this issue, the distribution of genetic variation for quantitative traits and molecular markers is estimated within and among 14 permanent lake populations of Daphnia pulicaria representing two regional groups from Oregon. Estimates of population subdivision for molecular and quantitative traits are concordant, with Q_ST generally exceeding G_ST. There is no evidence that microsatellites loci are less informative about subdivision for quantitative traits than are allozyme loci. Character-specific comparison of Q_ST and G_ST support divergent selection pressures among populations for the majority of life-history traits in both coast and mountain regions. The level of within-population variation for molecular markers is uninformative as to the genetic variation maintained for quantitative traits. In D. pulicaria, regional differences in the frequency of sex may contribute to variation in the maintenance of expressed within-population quantitative-genetic variation without substantially impacting diversity at the genic level. These data are compared to an identical dataset for 17 populations of the temporary-pond species, D. pulex.

Corresponding Editor: C. López-Fanjul

The extraordinary contemporary species richness and ecological predominance of flowering plants (angiosperms) are even more remarkable when considering the relatively recent onset of their evolutionary diversification. We examine the evolutionary diversification of angiosperms and the observed differential distribution of species in angiosperm clades by estimating the rate of diversification for angiosperms as a whole and for a large set of angiosperm clades. We also identify angiosperm clades with a standing diversity that is either much higher or lower than expected, given the estimated background diversification rate. Recognition of angiosperm clades, the phylogenetic relationships among them, and their taxonomic composition are based on an empirical compilation of primary phylogenetic studies. By making an integrative and critical use of the paleobotanical record, we obtain reasonably secure approximations for the age of a large set of angiosperm clades. Diversification was modeled as a stochastic, time-homogeneous birth-and-death process that depends on the diversification rate (r) and the relative extinction rate (ε). A statistical analysis of the birth and death process was then used to obtain 95% confidence intervals for the expected number of species through time in a clade that diversifies at a rate equal to that of angiosperms as a whole. Confidence intervals were obtained for stem group and for crown group ages in the absence of extinction (ε = 0.0) and under a high relative extinction rate (ε = 0.9). The standing diversity of angiosperm clades was then compared to expected species diversity according to the background rate of diversification, and, depending on their placement with respect to the calculated confidence intervals, exceedingly species-rich or exceedingly species-poor clades were identified. The rate of diversification for angiosperms as a whole ranges from 0.077 (ε = 0.9) to 0.089 (ε = 0.0) net speciation events per million years. Ten clades fall above the confidence intervals of expected species diversity, and 13 clades were found to be unexpectedly species poor. The phylogenetic distribution of clades with an exceedingly high number of species suggests that traits that confer high rates of diversification evolved independently in different instances and do not characterize the angiosperms as a whole.

Corresponding Editor: D. Baum

Clonal growth and symbiosis with photosynthetic zooxanthellae typify many genera of marine organisms, suggesting that these traits are usually conserved. However, some, such as Anthopleura, a genus of sea anemones, contain members lacking one or both of these traits. The evolutionary origins of these traits in 13 species of Anthopleura were inferred from a molecular phylogeny derived from 395 bp of the mitochondrial 16S rRNA gene and 410 bp of the mitochondrial cytochrome oxidase subunit III gene. Sequences from these genes were combined and analyzed by maximum-parsimony, maximum-likelihood, and neighbor-joining methods. Best trees from each method indicated a minimum of four changes in growth mode and that symbiosis with zooxanthellae has arisen independently in eastern and western Pacific species. Alternative trees in which species sharing growth modes or the symbiotic condition were constrained to be monophyletic were significantly worse than best trees. Although clade composition was mostly consistent with geographic sympatry, A. artemisia from California was included in the western Pacific clade. Likewise, A. midori from Japan was not placed in a clade containing only other Asian congeners. The history of Anthopleura includes repeated shifts between clonality and solitariness, repeated attainment of symbiosis with zooxanthellae, and intercontinental dispersal.

Corresponding Editor: R. Burton

Much life-history theory assumes that alleles segregating in natural populations pleiotropically affect life-history traits. This assumption, while plausible, has rarely been tested directly. Here we investigate the genetic relationship between two traits often suggested to be connected by pleiotropy: maternal body size and fertility. We carry out a quantitative trait locus (QTL) analysis on two isolates of the free-living nematode Caenorhabditis elegans, and identify two body size and three fertility QTLs. We find that one of the fertility QTLs colocalizes with the two body size QTLs on Chromosome IV. Further analysis, however, shows that these QTLs are genetically separable. Thus, none of the five body size or fertility QTLs identified here shows detectable pleiotropy for the assayed traits. The evolutionary origin of these QTLs, possible candidate loci, and the significance for life-history evolution are discussed.

Corresponding Editor: T. Kawecki

The potential rate of evolution of resistance to natural enemies depends on the genetic variation present in the population and any trade-offs between resistance and other components of fitness. We measured clonal variation and covariation in pea aphids (Acyrthosiphon pisum) for resistance to two parasitoid species (Aphidius ervi and A. eadyi) and a fungal pathogen (Erynia neoaphidis). We found significant clonal variation in resistance to all three natural enemies. We tested the hypothesis that there might be trade-offs (negative covariation) in defensive ability against different natural enemies, but found no evidence for this. All correlations in defensive ability were positive, that between the two parasitoid species significantly so. Defensive ability was not correlated with fecundity. A number of aphid clones were completely resistant to one parasitoid (A. eadyi), but a subset of these failed to reproduce subsequently. We discuss the factors that might maintain clonal variation in natural enemy resistance.

Corresponding Editor: T. Kawecki

The ability of a parasitoid to evolve enhanced counterdefenses against host resistance and its possible costs were studied in a Drosophila-parasitoid system. We reared Asobara tabida (Braconidae, Hymenoptera) exclusively on D. melanogaster to impose artificial selection for improved counterdefenses against cellular encapsulation, the main host defense against parasitism. Controls were reared on D. subobscura, the main host of the population of wasps from which the laboratory culture was derived and a species that never encapsulates parasitoids. We observed improved survival and avoidance of encapsulation in all five selection lines compared to their paired control lines, although there was unexpected variation among pairs. Improved survival was associated with parasitoid eggs becoming embedded in host tissue, where they were protected from circulating haemocytes. There were no differences among lines in average adult size, fat content, egg load, or performance on D. subobscura. However, the duration of the egg stage in selection lines was longer than that of control lines, probably because of reduced nutrient and/or oxygen supply when eggs are embedded in host tissue. We suggest that this delay in hatching reduces the probability of parasitoid survival if another parasitoid egg is laid in the same host (superparasitism or multiparasitism) and hence is a cost of enhanced counterdefenses against host resistance.

Corresponding Editor: T. Kawecki

The evolutionary explanation of senescence proposes that selection against alleles with deleterious effects manifested only late in life is weak because most individuals die earlier for extrinsic reasons. This argument also applies to alleles whose deleterious effects are nongenetically transmitted from mother to progeny, that is, that affect the performance of progeny produced at late ages rather than of the aging individuals themselves. We studied the effect of maternal age on offspring viability (egg hatching success and larva-to-adult survival) in two sets of Drosophila melanogaster lines (HAM/LAM and YOUNG/OLD), originating from two long-term selection experiments. In each set, some lines (HAM and YOUNG, respectively) have been selected for early reproduction, whereas later reproduction was favored in their counterparts (LAM and OLD). In the HAM and LAM lines, both egg hatching success and larval viability declined with mother's age and did so with accelerating rates. The hatching success declined significantly faster with maternal age in HAM than in LAM lines, according to one of two statistical approaches used. Egg hatching success also declined with maternal age in YOUNG and OLD lines, with no difference between the selection regimes. However, the relationship between mother's age and offspring larva-to-adult viability differed significantly between these two selection regimes: a decline of larval viability with maternal age occurred in YOUNG lines but not in OLD lines. This suggests that the rate with which offspring viability declines with mother's age responded to selection for early versus late reproduction. We suggest broadening the evolutionary concept of senescence to include intrinsically caused declines in offspring quality with maternal age.

Corresponding Editor: T. Mousseau

A hybrid zone between the grasshoppers Chorthippus brunneus and C. jacobsi (Orthoptera: Acrididae) in northern Spain has been analyzed for variation in morphology and ecology. These species are readily distinguished by the number of stridulatory pegs on the hind femur. Both sexes are fully winged and inhabit disturbed habitats throughout the study area. We develop a maximum-likelihood approach to fitting a two-dimensional cline to geographical variation in quantitative traits and for estimating associations of population mean with local habitat. This method reveals a cline in peg number approximately 30 km south of the Picos de Europa Mountains that shows substantial deviations in population mean compared with the expectations of simple tension zone models. The inclusion of variation in local vegetation in the model explains a significant proportion of the residual variation in peg number, indicating that habitat-genotype associations contribute to the observed spatial pattern. However, this association is weak, and a number of populations continue to show strong deviations in mean even after habitat is included in the final model. These outliers may be the result of long-distance colonization of sites distant from the cline center or may be due to a patchy pattern of initial contact during postglacial expansion. As well as contrasting with the smooth hybrid zones described for Chorthippus parallelus, this situation also contrasts with the mosaic hybrid zones observed in Gryllus crickets and in parts of the hybrid zone between Bombina toad species, where habitat-genotype associations account for substantial amounts of among-site variation.

Corresponding Editor: M. Noor

We used DNA analysis of the freshwater Galaxias vulgaris complex (Pisces: Galaxiidae) to test a geological hypothesis of drainage evolution in South Island, New Zealand. Geological evidence suggests that the presently north-flowing Nevis River branch of the Clutha/Kawarau River system (Otago) once flowed south into the Nokomai branch of the Mataura system (Southland). The flow reversal is thought to have resulted from fault and fold activity associated with post-Miocene uplift. Mitochondrial DNA sequence data (control region and cytochrome b genes; 76 individuals; maximum divergence 7.1%) corroborate this geomorphological hypothesis: The Nevis River retains a freshwater fish species (Galaxias gollumoides; five sites; 10 haplotypes) that is otherwise restricted to Southland (nine sites; 15 haplotypes). There is no indication that the Nevis River lineage of G. gollumoides lives elsewhere in the Clutha/Kawarau system (> 30 sites). Likewise, two widespread Clutha lineages (G. ‘sp D’; G. anomalus–G. pullus) are apparently absent from the Nevis (> 30 sites). In particular, G. ‘sp D’ lives throughout much of the Clutha (12 sites, 23 haplotypes), including a tributary of the Kawarau, but is absent from the Nevis itself. Conventional molecular clock calibrations (based on a minimum Nevis-Mataura haplotype divergence of 3.0%) indicate that the Nevis flow reversal may have occurred in the early-mid Pleistocene, which is roughly consistent with geological data. The broad phylogeographic structure evident in the Clutha system is consistent with the sedentary nature of nonmigratory galaxiids. Our study reinforces the value of combining biological and geological data for the formulation and testing of historical hypotheses.

Corresponding Editor: B. Bowen

Have the warm tropical waters and currents of the southern Gulf of California, Mexico (also known as the Sea of Cortez), formed a barrier to gene flow, resulting in disjunct populations in the upper gulf that are isolated from the outer Pacific Coast? Phylogeographic and genetic divergences of the spotted sand bass, Paralabrax maculatofasciatus, from three Gulf of California and two outer Pacific coastal locations were tested using mitochondrial DNA (mtDNA) control region sequences. Sequence data from two congeners that are sympatrically distributed along the outer Pacific Coast, the barred sand bass, P. nebulifer, and the kelp bass, P. clathratus, were used to gauge the levels of genetic divergences. Differences among the three species and between the northern gulf and outer Pacific coastal populations of P. maculatofasciatus also were analyzed using 40 allozymic presumptive gene loci. Allozyme and mtDNA analyses each revealed many fixed differences among the species. Three significant allozymic frequency differences and two fixed mtDNA substitutions differentiated the gulf and outer Pacific coastal populations of P. maculatofasciatus. Three unique mtDNA haplotypes and three unique allozyme alleles were identified from the outer Pacific coastal population. The gulf sites contained four unique mtDNA haplotypes and six unique allozyme alleles. Partitioning of the mtDNA variation revealed that 72% of the variance occurred between the gulf and outer Pacific Coast, 20% between sampling sites in the two regions, and 8% within the sites. There appears to be little gene flow across the waters of the southern Baja Penninsula, producing divergence estimated as 120,000 to 600,000 years between the outer Pacific coastal and the Gulf of California populations. This separation level may date to a hypothesized seaway closure near La Paz, Mexico, during the mid-Pleistocene, and characterizes other fish populations. A second pattern of deeper allopatric species-level divergences in some other fishes may date to a Pliocene closure of a mid–Baja Penninsular seaway. Significant differences also were discerned in P. maculatofasciatus between the San Diego and central Baja California coastal sites and between the upper/central and the lower gulf locations. Variation between locations in the two regions may be indicative of larval retention and low adult migration, which needs to be tested further.

Corresponding Editor: S. Karl

Latitudinal populations of the Atlantic silverside, Menidia menidia, show substantial genetic variation in rates of energy acquistion and allocation. Reared in common environments, silversides from northern latitudes consume more food, grow faster and more efficiently, store more energy, and produce greater quantities of eggs than their southern conspecifics. The persistence of seemingly inferior southern genotypes in the face of ostensibly superior northern genotypes suggest that there are hidden evolutionary trade-offs associated with these elevated acquisition and allocation rates. We tested the hypothesis that rapid growth and high levels of food consumption trade-off against locomotory performance in M. menidia. We compared both aerobic (prolonged and endurance) and anaerobic (burst) swimming capacities between intrinsically fast-growing fish from the north (Nova Scotia, NS) and intrinsically slow-growing fish from the south (South Carolina, SC) and between growth-manipulated phenotypes within each population. We also compared swimming speeds and endurance between fasted and recently fed fish within populations. Maximum prolonged and burst swimming speeds of NS fish were significantly lower than those of SC fish, and swimming speeds of fast-growing phenotypes were lower than those of slow-growing phenotypes within populations. Fed fish had lower burst speeds and less endurance than fasted fish from the same population. Thus, high rates of growth and the consumption of large meals clearly diminish swimming performance, which likely increases vulnerability to predation and decreases survival and relative fitness. The submaximal growth rate of southern M. menidia appears to be adaptive, resulting from balancing selection on rates of somatic growth.

Corresponding Editor: D. Roff

The Atlantic silverside (Menidia menidia) exhibits countergradient latitudinal variation in somatic growth rate along the East Coast of North America. Larvae and juveniles from high-latitude populations display higher intrinsic rates of energy consumption and growth than genotypes from low-latitude populations. The existence of submaximal growth in some environments suggests that trade-offs must counter the oft-cited theoretical benefits of energy and growth maximization (e.g., “bigger is better,” “faster is better”) in the immature life stages. We hypothesized that energy and growth maximization trades off against investment in defense from predators. We conducted laboratory selection experiments to compare vulnerability to predation of silversides from: (1) fast-growing northern (Nova Scotia, NS) versus slow-growing southern (South Carolina, SC) source populations; (2) phenotypically manipulated fast-growing versus moderately-growing NS fish; and (3) recently fed versus unfed NS and SC fish. Tests involved fish drawn from common-garden environments and were conducted by subjecting mixed-treatment schools of size-matched silversides to natural, common piscine predators. NS silversides suffered significantly higher predation mortality than SC silversides. Parallel results were found in phenotypic manipulation of growth: NS silversides reared on a fast-growth trajectory (∼1.0 mm/day) were significantly more vulnerable to predation than those growing at a moderate rate (∼0.5 mm/day). Food consumption also affected vulnerability to predators: Silversides with large meals in their stomachs suffered significantly higher predation mortality than unfed silversides. Differences in predation vulnerability were likely due to swimming performance, not attractiveness to predators. Our findings demonstrate that maximization of energy intake and growth rate engenders fitness costs in the form of increased vulnerability to predation.

Corresponding Editor: D. Roff

Populations of the Asian elephant (Elephas maximus) have been reduced in size and become highly fragmented during the past 3000 to 4000 years. Historical records reveal elephant dispersal by humans via trade and war. How have these anthropogenic impacts affected genetic variation and structure of Asian elephant populations? We sequenced mitochondrial DNA (mtDNA) to assay genetic variation and phylogeography across much of the Asian elephant's range. Initially we compare cytochrome b sequences (cyt b) between nine Asian and five African elephants and use the fossil-based age of their separation (∼5 million years ago) to obtain a rate of about 0.013 (95% CI = 0.011–0.018) corrected sequence divergence per million years. We also assess variation in part of the mtDNA control region (CR) and adjacent tRNA genes in 57 Asian elephants from seven countries (Sri Lanka, India, Nepal, Myanmar, Thailand, Malaysia, and Indonesia). Asian elephants have typical levels of mtDNA variation, and coalescence analyses suggest their populations were growing in the late Pleistocene. Reconstructed phylogenies reveal two major clades (A and B) differing on average by HKY85/Γ-corrected distances of 0.020 for cyt b and 0.050 for the CR segment (corresponding to a coalescence time based on our cyt b rate of ∼1.2 million years). Individuals of both major clades exist in all locations but Indonesia and Malaysia. Most elephants from Malaysia and all from Indonesia are in well-supported, basal clades within clade A, thus supporting their status as evolutionarily significant units (ESUs). The proportion of clade A individuals decreases to the north, which could result from retention and subsequent loss of ancient lineages in long-term stable populations or, perhaps more likely, via recent mixing of two expanding populations that were isolated in the mid-Pleistocene. The distribution of clade A individuals appears to have been impacted by human trade in elephants among Myanmar, Sri Lanka, and India, and the subspecies and ESU statuses of Sri Lankan elephants are not supported by molecular data.

Corresponding Editor: B. Bowen

The common occurrence of polyandry continues to puzzle evolutionary biologists, as female reproductive success is thought to be limited mostly by her fecundity. Here we test whether females of the bulb mite, a species in which the females are highly promiscuous, benefit from polyandry in terms of increased fitness of their progeny. Females were given opportunity to mate with either one or six males, but the experiment was designed to allow the same number of matings per female in both groups, that is, irrespective of the number of males. We found that daughters of females mated to six males had significantly higher fecundity than daughters of females mated to one male, whereas other fitness components of progeny (male virility and longevity of both sexes) were not affected. These findings appear to support hypotheses proposing that multi-male mating enables females to exercise postcopulatory mate-choice (direct or indirect, via sperm competition) and thus accrue genetic benefits.

Corresponding Editor: D. Wheeler

Corresponding Editor: D. Waller

Corresponding Editor: D. Waller

A publication by Shanley and Kirkwood (2000) attempts to explain data on caloric restriction (CR) and life extension in the context of the Disposable Soma (DS) theory for the evolution of senescence. As the authors concede, this juxtaposition appears at first to offend intuition: According to the DS theory, senescence is the result of a tight budget for caloric energy, such that repair and maintenance functions are shortchanged; yet, in CR experiments, it is found that longevity decreases smoothly as the total caloric budget is increased. In the Shanley-Kirkwood model, an optimized allocation of resources causes energy to be diverted away from somatic maintenance at a greater rate than caloric intake increases, with the net result that more total energy is associated with less energy available for maintenance. In the present critique, the limitations of this model are detailed and its special assumptions reviewed. While the CR experiments find comparable life extension for males and females, measured relative to nonbreeding controls, the Shanley-Kirkwood model draws its energy budget from data on breeding females. In addition, the success in reproducing the observed relationship between feeding and longevity depends crucially on a mathematical relationship between food availability and the probability of reproductive success which may be difficult to justify.

Corresponding Editor: T. Mousseau

Corresponding Editor: T. Mousseau