Recently, two areas of plant phylogeny have developed in ways that could not have been anticipated, even a few years ago. Among extant seed plants, new phylogenetic hypotheses suggest that Gnetales, a group of nonflowering seed plants widely hypothesized to be the closest extant relatives of angiosperms, may be less closely related to angiosperms than was believed. In addition, recent phylogenetic analyses of angiosperms have, for the first time, clearly identified the earliest lineages of flowering plants: Amborella, Nymphaeales, and a clade that includes Illiciales/Trimeniaceae/Austrobaileyaceae. Together, the new seed plant and angiosperm phylogenetic hypotheses have major implications for interpretation of homology and character evolution associated with the origin and early history of flowering plants. As an example of the complex and often unpredictable interplay of phylogenetic and comparative biology, we analyze the evolution of double fertilization, a process that forms a diploid embryo and a triploid endosperm, the embryo-nourishing tissue unique to flowering plants. We demonstrate how the new phylogenetic hypotheses for seed plants and angiosperms can significantly alter previous interpretations of evolutionary homology and firmly entrenched assumptions about what is synapomorphic of flowering plants. In the case of endosperm, a solution to the century-old question of its potential homology with an embryo or a female gametophyte (the haploid egg-producing generation within the life cycle of a seed plant) remains complex and elusive. Too little is known of the comparative reproductive biology of extant nonflowering seed plants (Gnetales, conifers, cycads, and Ginkgo) to analyze definitively the potential homology of endosperm with antecedent structures. Remarkably, the new angiosperm phylogenies reveal that a second fertilization event to yield a biparental endosperm, long assumed to be an important synapomorphy of flowering plants, cannot be conclusively resolved as ancestral for flowering plants. Although substantive progress has been made in the analysis of phylogenetic relationships of seed plants and angiosperms, these efforts have not been matched by comparable levels of activity in comparative biology. The consequence of inadequate comparative biological information in an age of phylogenetic biology is a severe limitation on the potential to reconstruct key evolutionary historical events.

Development is the process by which genotypes are transformed into phenotypes. Consequently, development determines the relationship between allelic and phenotypic variation in a population and, therefore, the patterns of quantitative genetic variation and covariation of traits. Understanding the developmental basis of quantitative traits may lead to insights into the origin and evolution of quantitative genetic variation, the evolutionary fate of populations, and, more generally, the relationship between development and evolution. Herein, we assume a hierarchical, modular structure of trait development and consider how epigenetic interactions among modules during ontogeny affect patterns of phenotypic and genetic variation. We explore two developmental models, one in which the epigenetic interactions between modules result in additive effects on character expression and a second model in which these epigenetic interactions produce nonadditive effects. Using a phenotype landscape approach, we show how changes in the developmental processes underlying phenotypic expression can alter the magnitude and pattern of quantitative genetic variation. Additive epigenetic effects influence genetic variances and covariances, but allow trait means to evolve independently of the genetic variances and covariances, so that phenotypic evolution can proceed without changing the genetic covariance structure that determines future evolutionary response. Nonadditive epigenetic effects, however, can lead to evolution of genetic variances and covariances as the mean phenotype evolves. Our model suggests that an understanding of multivariate evolution can be considerably enriched by knowledge of the mechanistic basis of character development.

The evolution of dispersal is investigated in a landscape of many patches with fluctuating carrying capacities and spatial heterogeneity in temporal fluctuations. Although asynchronous temporal fluctuations select for dispersal, spatial heterogeneity in the distribution of fluctuating environmental variables selects against it. We find evolutionary branching in dispersal rate leading to the evolutionarily stable coexistence of a high- and a low-dispersal phenotype. We study how the opposing forces of selection for and against dispersal change with the relative size and the environmental qualities of the source and sink habitats. Our results suggest that the evolution of dispersal dimorphism could be a first step towards speciation and local adaptation.

Gene flow is a key factor in the spatial genetic structure in spatially distributed species. Evolutionary biologists interested in microevolutionary processess and conservation biologists interested in the impact of landscape change require a method that measures the real time process of gene movement. We present a novel two-generation (parent-offspring) approach to the study of genetic structure (TwoGener) that allows us to quantify heterogeneity among the male gamete pools sampled by maternal trees scattered across the landscape and to estimate mean pollination distance and effective neighborhood size. First, we describe the model's elements: genetic distance matrices to estimate intergametic distances, molecular analysis of variance to determine whether pollen profiles differ among mothers, and optimal sampling considerations. Second, we evaluate the model's effectiveness by simulating spatially distributed populations. Spatial heterogeneity in male gametes can be estimated by Φ_FT, a male gametic analogue of Wright's F_ST and an inverse function of mean pollination distance. We illustrate TwoGener in cases where the male gamete can be categorically or ambiguously determined. This approach does not require the high level of genetic resolution needed by parentage analysis, but the ambiguous case is vulnerable to bias in the absence of adequate genetic resolution. Finally, we apply TwoGener to an empirical study of Quercus alba in Missouri Ozark forests. We find that Φ_FT = 0.06, translating into about eight effective pollen donors per female and an effective pollination neighborhood as a circle of radius about 17 m. Effective pollen movement in Q. alba is more restricted than previously realized, even though pollen is capable of moving large distances. This case study illustrates that, with a modest investment in field survey and laboratory analysis, the TwoGener approach permits inferences about landscape-level gene movements.

We present an analysis of Raphanus raphanistrum and simulations illustrating the utility of directly estimating male phenotypic selection gradients using genetic markers. The method offers a much more refined characterization of selection than attempting to assign paternity to individual progeny. Our analysis of R. raphanistrum reveals selection on remarkably fine features of floral morphology, including anther exsertion, that were opaque to previous approaches. The new results also undermine a previous conclusion that selection on wild radish floral morphology acts primarily through female fitness. Simulation results show that selection gradients on the order of β = 0.1–0.2 can be readily detected with allozyme markers in moderate-sized (< 200 paternal individuals) populations. Highly polymorphic (e.g., microsatellite) markers will likely detect fine scale selection (β < 0.1) in larger populations (≥ 400 individuals). Increased progeny sample size, by sampling either additional maternal families or more progeny per maternal parent, partly compensates for low exclusion probability. Increasing the number of possible fathers without changing progeny sample size decreases the ability to detect selection, especially at lower exclusion probabilities. Sampling only some male genotypes reduces the power to detect selection and biases (underestimates) the magnitude of the selection gradient estimate.

The geographic mosaic theory of coevolution posits that the form of selection between interacting species varies across a landscape with coevolution important and active in some locations (i.e., coevolutionary hotspots) but not in others (i.e., coevolutionary coldspots). We tested the hypothesis that the presence of red squirrels (Tamiasciurus hudsonicus) affects the occurrence of coevolution between red crossbills (Loxia curvirostra complex) and Rocky Mountain lodgepole pine (Pinus contorta ssp. latifolia) and thereby provides a mechanism giving rise to a geographic mosaic of selection. Red squirrels are the predominant predispersal seed predator and selective agent on lodgepole pine cones. However, in four isolated mountain ranges east and west of the Rocky Mountains, red squirrels are absent and red crossbills are the main predispersal seed predator. These isolated populations of pine have apparently evolved without Tamiasciurus for about 10,000 to 12,000 years. Based on published morphological, genetic, and paleobotanical studies, we infer that cone traits in these isolated populations that show parallel differences from cones in the Rocky Mountains have changed in parallel. We used data on crossbill and conifer cone morphology and feeding preferences and efficiency to detect whether red crossbills and lodgepole pine exhibit reciprocal adaptations, which would imply coevolution. Cone traits that act to deter Tamiasciurus and result in high ratios of cone mass to seed mass were less developed in the isolated populations. Cone traits that act to deter crossbills include larger and thicker scales and perhaps increased overlap between successive scales and were enhanced in the isolated populations. In the larger, isolated mountain ranges crossbills have evolved deeper, shorter, and therefore more decurved bills to exploit these cones. This provides crossbills with higher feeding rates, and the change in bill shape has improved efficiency by reducing the concomitant increases in body mass and daily energy expenditures that would have resulted if only bill size had increased. These parallel adaptations and counter adaptations in red crossbills and lodgepole pine are interpreted as reciprocal adaptations and imply that these crossbills and pine are in coevolutionary arms races where red squirrels are absent (i.e., coevolutionary hotspots) but not where red squirrels are present (i.e., coevolutionary coldspots).

In many nonclonal, benthic marine species, geographic distribution is mediated by the dispersal of their larvae. The dispersal and recruitment of marine larvae may be limited by temperature gradients that can affect mortality or by ocean currents that can directly affect the movements of pelagic larvae. We focus on Point Conception, a well-known biogeographic boundary between the Californian and Oregonian biogeographic provinces, to investigate whether ocean currents affect patterns of gene flow in intertidal marine invertebrates. The predominance of pelagically dispersing species with northern range limits at Point Conception suggests that ocean currents can affect species distributions by erecting barriers to the dispersal of planktonic larvae. In this paper, we investigate whether the predominantly southward currents have left a recognizable genetic signature in species with pelagically dispersing larvae whose ranges span Point Conception. We use patterns of genetic diversity and a new method for inferring cladistic migration events to test the hypothesis that southward currents increase southward gene flow for species with pelagically dispersing larvae. We collected mitochondrial DNA (mtDNA) sequence data for the barnacles Balanus glandula and Chthamalus fissus and also reanalyzed a previously published mtDNA dataset (Strongylocentrotus purpuratus, Edmands et al. 1996). For all three species, our cladistic approach identified an excess of southward migration events across Point Conception. In data from a fourth species with nondispersing larvae (Nucella emarginata, Marko 1998), our method suggests that ocean currents have not played a role in generating genetic structure.

Colony and population structure of the obligate slavemaker ant Protomognathus americanus was analyzed via four nuclear microsatellite loci and mitochondrial DNA (mtDNA) markers. Colonies of P. americanus usually contain a single queen, and here we show that she is singly inseminated. Nestmate workers are generally full sisters and their relatedness does not deviate from the expected value of 0.75. Even though colonies were strictly monogynous, we were able to infer that colony takeover by related queens was common and queen replacement by unrelated queens was rare. Polydomy is widespread, with neighboring nests having the same genetic composition. Although we found no evidence of population viscosity or inbreeding from nuclear markers, mtDNA markers provided evidence for small-scale genetic structuring. Haplotype structuring and takeover by related queens suggest philopatry of newly mated queens. In this species, workers reproduce in queenright and queenless nests and worker reproduction accounts for more than 70% of all males. Although sex-ratio theory points to slavemaking ants as important systems for studying queen-worker conflict, our results indicate no basis for such conflict in P. americanus, because extensive worker reproduction generates shifts in relatedness values. Rather, the dual effects of independent polydomous nest units and local resource competition among queens produce male-biased allocation ratios in this species.

The parasite pressure exerted by the slavemaker ant Protomognathus americanus on its host species Leptothorax longispinosus was analyzed demographically and genetically. The origin of slaves found in colonies of the obligate slavemaker was examined with nuclear and mitochondrial DNA markers to make inferences about the frequency and severity of slave raids. Relatedness of enslaved L. longispinosus workers in the same nest was very low, and our data suggest that, on average, each slavemaker nest raids six host colonies per season. Therefore, the influence of slavemaker species on their hosts is much stronger than simple numerical ratios suggest. We also found that slave relatedness was higher in small than in large slavemaker nests; thus, larger nests wield a much stronger influence on the host. We estimated that in the study population, on average, a host nest has a 50% chance of being attacked by a slavemaker colony per year. Free-living Leptothorax colonies in the vicinity of slavemaker nests did not represent the source of slaves working in P. americanus colonies, which suggests that raided nests either do not survive or migrate after being raided. Colony composition and intranest relatedness of free-living L. longispinosus colonies differed markedly between areas with slavemakers and those that are parasite-free. In the presence of slavemakers, host colonies were less likely to be polygynous and had fewer workers and a higher relatedness among worker brood. Host nests with slavemaker neighbors allocated more resources into sexuals, possibly caused by these shifts in nest demography. Finally, enslaved Leptothorax workers in P. americanus nests appeared to be less efficient than their counterparts in free-living colonies. Thus, slavemakers exert a much stronger impact on their hosts than had previously been suspected and represent an unique system to study parasite-host coevolution.

Mating success in the western harvester ant, Pogonomyrmex occidentalis, increases with male size. We tested the hypothesis that increased mating success increases male fitness and the fitness of colonies that make large males by comparing the sperm content of males prior to and at the conclusion of the mating swarm. The number of sperm a male initially possesses is a function of male size, and large males transfer a greater proportion of their sperm than do small males. For colonies, the payoff per unit of investment is an increasing function of male size, and investment in large males is not equivalent to investing in a larger number of small males. Allocation ratios in species that show size variation in reproductives may need to be modified by the individual fitness functions.

Variation in ontogeny can produce phenotypic variation both within and among species. I investigated whether changes in timing and rate of growth were a source of phenotypic variation in a putative incipient species group of pupfish (Cyprinodon spp.). On San Salvador Island, Bahamas, sympatric forms of pupfish differ in morphology but show only partial reproductive isolation in the laboratory. Offspring from two forms and two geographical areas and their hybrids were bred in the laboratory, and ontogenetic trajectories of their feeding morphology were followed until maturity. In the Bahamian pupfish the two forms grow along similar size but not shape trajectories. Two heterochronic parameters, onset and rate of growth, alter shape trajectories in the Bahamian pupfish. Similar forms from different geographical areas (Florida and the Bahamas) grow along parallel shape trajectories, differing only in one heterochronic parameter, the onset shape. Hybrids within and between the pupfish forms produced intermediate feeding morphologies that were influenced by their maternal phenotype, suggesting that maternal effects may be a source of phenotypic variation in shape that can persist to maturity. In Cyprinodon, small changes in multiple heterochronic parameters translate into large phenotypic differences in feeding morphology.

Drainage systems of the Great Plains and western Gulf Slope underwent substantial changes through diversions and stream captures during the Pleistocene, either as the result of the glacial advances or through independent geologic processes. The distributions of a variety of fishes that range across west-central North America, such as the plains killifish (Fundulus zebrinus), are thought to be the product of this Pleistocene influence. We examined the geographic pattern of genetic variation in F. zebrinus using three allozyme loci (n = 793), mitochondrial DNA restriction fragment length polymorphisms (RFLPs, n = 352), and sequencing of the mitochondrial cytochrome oxidase I (COI, n = 23) in an attempt to understand the roles of dispersal and vicariance. The phylogeographic patterns were concordant between the allozyme and mitochondrial data with the exception of the population in the North Canadian River. The populations fell into three geographic assemblages, which we designated as northern, central, and southern. A large phylogenetic break (average Roger's D = 0.702; average sequence divergence in RFLPs = 4.6%; average sequence divergence in COI = 5.5%) separated the northern/central and southern assemblages. The northern region was likely colonized sometime during the mid-Pleistocene. Fish in the Brazos and Pecos Rivers probably reached these drainages through stream captures of the Red River. The large phylogenetic break between the northern/central and southern clades supports previous attempts to recognize two species of plains killifish: F. zebrinus and F. kansae.

Phylogeographic, nested clade, and mismatch analyses of mitochondrial DNA (mtDNA) variation were used to infer the temporal dynamics of distributional and demographic history of brown trout (Salmo trutta). Both new and previously published data were analyzed for 1794 trout from 174 populations. This combined analysis improved our knowledge of the complex evolutionary history of brown trout throughout its native Eurasian and North African range of distribution in many ways. It confirmed the existence of five major evolutionary lineages that evolved in geographic isolation during the Pleistocene and have remained largely allopatric since then. These should be recognized as the basic evolutionarily significant units within brown trout. Finer phylogeographic structuring was also resolved within major lineages. Contrasting temporal juxtaposition of different evolutionary factors and timing of major demographic expansions were observed among lineages. These unique evolutionary histories have been shaped both by the differential latitudinal impact of glaciations on habitat loss and potential for dispersal, as well as climatic impacts and landscape heterogeneity that translated in a longitudinal pattern of genetic diversity and population structuring at more southern latitudes. This study also provided evidence for the role of biological factors in addition to that of physical isolation in limiting introgressive hybridization among major trout lineages.

Genetically distinct anadromous (sockeye) and nonanadromous (kokanee) morphs of the Pacific salmon, Oncorhynchus nerka, develop identical, brilliant red color at maturity during sympatric breeding in freshwater streams. The marine and lacustrine environments they occupy prior to maturity, however, appear to differ in the availability of dietary carotenoid pigments necessary to produce red coloration. We tested the hypothesis that kokanee, which occupy carotenoid-poor lakes, are more efficient at using the dietary pigments than are sockeye, which occupy the more productive North Pacific Ocean. In a 2-year controlled breeding study, flesh and skin color of mature and immature crosses fed a low-carotenoid diet were quantified with both a chromameter and by chemical extraction of carotenoid pigments. Results revealed striking countergradient variation in carotenoid use, with kokanee approximately three times more efficient at sequestering the pigments to the flesh musculature than similar age sockeye. This difference translated into virtually nonoverlapping differences between pure crosses in secondary sexual color at maturity, when the pigments are mobilized and transported to the skin. Kokanee crosses turned pinkish red over most of their body, whereas sockeye turned olive green. The olive green was similar to the breeding color of residuals in the wild, the progeny of anadromous sockeye that remain in fresh water and are believed to have given rise to kokanee on numerous independent occasions. Reciprocal hybrids were similar to each other and intermediate to the pure crosses, indicating additive genetic inheritance. Mate choice trials with sockeye males in the wild showed the ancestral morph strongly preferred red over green models. These results suggest a preference for red mates maintained in nonanadromous breeding populations drove the reevolution of the red phenotype in kokanee via more efficient use of dietary carotenoid pigments. This is a novel, yet hidden, mechanism by which sexual selection promotes the genetic differentiation of these sympatric populations.

Correlation between intraspecific phenotypic variability and variation of environmental conditions could reflect adaptation. Different phenotypes may result from differential expression of a genotype in different environments (phenotypic plasticity) or from expression of different genotypes (genetic diversity). Populations of Lacerta vivipara exhibit larger adult body length, lower age at maturity, higher fecundity, and smaller neonatal size in humid habitats compared to dry habitats. We conducted reciprocal transplants of juvenile L. vivipara to test for the genetic or plastic origin of this variation. We captured gravid females from four populations that differed in the relative humidity of their habitats, and during the last 2 to 4 weeks of gestation, we manipulated heat and water availability under laboratory conditions. Juveniles were released into the different populations and families were divided to compare growth rate and survival of half-sibs in two environments. Growth rate and survival were assessed using capture-recapture techniques. Growth rate was plastic in response to postnatal conditions and did not differ between populations of origin. Survival differed between populations of origin, partially because of differences in neonatal body length. The response of juvenile body length and body condition to selection in the different habitats was affected by the population of origin. This result cannot be simply interpreted in terms of adaptation; however, phenotypic plasticity of fecundity or juvenile size most probably resulted in adaptive reproductive strategies. Adaptation to the habitat by means of genetic specialization was not detected. Further investigation is needed to discriminate between genetic and long-term maternal effects.

We analyze variation in phenotypes and mitochondrial DNA (mtDNA) haplotypes over the breeding ranges of hermit and Townsend's warblers and across two of their three hybrid zones. Within these two hybrid zones, we demonstrate that the placement, shape, and width of transitions in seven plumage characters are remarkably similar, suggesting that a balance between dispersal and sexual selection keeps these hybrid zones narrow. A consistent asymmetry in these character transition curves suggests that Townsend's warblers have a selective advantage over hermit warblers, which is presumably due to the aggressive superiority of Townsend's over hermit males (Pearson and Rohwer 2000). An association between plumage and mtDNA haplotypes shows that pure Townsend's warblers, but not pure hermit warblers, immigrate into these hybrid zones, further supporting the competitive superiority of Townsend's warblers over hermit warblers. The mitochondrial haplotype transitions across these hybrid zones are much wider than the phenotypic transitions and provide no indication that the mtDNA haplotypes representing these two warblers are selectively maintained. More importantly, the phenotypically pure populations of Townsend's warblers throughout a 2000-km coastal strip north of the Washington hybrid zones contain a preponderance of hermit warbler mtDNA haplotypes. This result suggests massive movement of the hybrid zone between these warblers during the 5000 years since their most recent interglacial contact. We develop a model to explain the phenotypic and genetic divergence between these warblers and the evolution of their dramatic differences in aggressiveness; we also show how differences in male aggression, in combination with biased pairing patterns, can explain the haplotype footprint recording the historical movement of this hybrid zone.

Whether contemporary human populations are still evolving as a result of natural selection has been hotly debated. For natural selection to cause evolutionary change in a trait, variation in the trait must be correlated with fitness and be genetically heritable and there must be no genetic constraints to evolution. These conditions have rarely been tested in human populations. In this study, data from a large twin cohort were used to assess whether selection will cause a change among women in a contemporary Western population for three life-history traits: age at menarche, age at first reproduction, and age at menopause. We control for temporal variation in fecundity (the “baby boom” phenomenon) and differences between women in educational background and religious affiliation. University-educated women have 35% lower fitness than those with less than seven years education, and Roman Catholic women have about 20% higher fitness than those of other religions. Although these differences were significant, education and religion only accounted for 2% and 1% of variance in fitness, respectively. Using structural equation modeling, we reveal significant genetic influences for all three life-history traits, with heritability estimates of 0.50, 0.23, and 0.45, respectively. However, strong genetic covariation with reproductive fitness could only be demonstrated for age at first reproduction, with much weaker covariation for age at menopause and no significant covariation for age at menarche. Selection may, therefore, lead to the evolution of earlier age at first reproduction in this population. We also estimate substantial heritable variation in fitness itself, with approximately 39% of the variance attributable to additive genetic effects, the remainder consisting of unique environmental effects and small effects from education and religion. We discuss mechanisms that could be maintaining such a high heritability for fitness. Most likely is that selection is now acting on different traits from which it did in pre-industrial human populations.

We investigate changes in resistance to desiccation and starvation during adaptation of Drosophila melanogaster to laboratory culture. We test the hypothesis that resistance to environmental stresses is lost under laboratory adaptation. For both traits, there was a rapid loss of resistance over a three-year period. The rapidity of the response suggested that mutation accumulation could not account for it. Rather, resistance to environmental stresses appeared to be lost as a correlated response to selection on another trait, such as early fertility, with which stress resistance is negatively genetically correlated. These results suggest that caution is needed when extrapolating from evolution of stress resistance in long-established laboratory stocks to patterns of responses and correlated responses in natural populations.

We measured the egg size of six geographic populations of the pitcher-plant mosquito, Wyeomyia smithii, from Florida (30°N) to Ontario (49°N). Populations from northern latitudes produced larger eggs than populations from southern latitudes. Egg size increased with increasing latitude more rapidly when larvae were reared under low rather than high density. One southern (30°N) and one northern (49°N) population of W. smithii that persisted through 10 generations of selection for increased persistence under conditions of chronic thermal- and nutrient-limiting stress (conditions similar to southern rather than northern habitats) produced smaller eggs more rapidly than unselected control lines. However, there were no differences in lifetime fecundity or fertility between control and selected lines. Thus, laboratory evolution in an environment representative of extreme southern latitudes caused evolutionary changes consistent with geographic patterns of egg size. These results implicate temperature as a selective factor influencing the geographic variation of egg size in W. smithii, and demonstrate a novel trade-off in reproductive allocation between egg size and egg maturation time.