PHYLOGENOMICS REVEALS EXTENSIVE RETICULATE EVOLUTION IN XIPHOPHORUS FISHES

Hybridization is increasingly being recognized as a widespread process, even between ecologically and behaviorally divergent animal species. Determining phylogenetic relationships in the presence of hybridization remains a major challenge for evolutionary biologists, but advances in sequencing technology and phylogenetic techniques are beginning to address these challenges. Here we reconstruct evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by remarkable morphological diversity and behavioral barriers to interspecific mating. Past attempts to reconstruct phylogenetic relationships within Xiphophorus have produced conflicting results. Because many of the 26 species in the genus are interfertile, these conflicts are likely due to hybridization. Using genomic data, we resolve a high‐confidence species tree of Xiphophorus that accounts for both incomplete lineage sorting and hybridization. Our results allow us to reexamine a long‐standing controversy about the evolution of the sexually selected sword in Xiphophorus, and demonstrate that hybridization has been strikingly widespread in the evolutionary history of this genus.     

EVOLUTIONARY IMPLICATIONS OF DIVERGENT CLINES IN AN AVIAN (MANACUS: AVES) HYBRID ZONE

Abstract A previous study of the hybrid zone in western Panama between white‐collared (Manacus candei) and golden‐collared manakins (M. vitellinus) documented the unidirectional introgression of vitellinus male secondary sexual traits across the zone. Here, we examine the hybrid zone in greater genetic and morphological detail. Statistical comparisons of clines are performed using maximum‐likelihood and nonparametric bootstrap methods. Our results demonstrate that an array of six molecular and two morphometric markers agree in cline position and width. Clines for male collar and belly color are similar in width to the first eight clines, but are shifted in position by at least five cline widths. The result is that birds in intervening populations are genetically and morphometrically very like parental candei, but males have the plumage color of parental vitellinus. Neither neutral diffusion nor nonlinearity of color scales appear to be viable explanations for the large cline shifts. Genetic dominance of vitellinus plumage traits is another potential explanation that will require breeding experiments to test. Sexual selection remains a plausible explanation for the observed introgression of vitellinus color traits in these highly dimorphic, polygynous, lek‐mating birds. Two other clines, including a nondiagnostic isozyme locus, are similar in position to the main cluster of clines, but are broader in width. Thus, introgression at some loci is greater than that detected with diagnostic markers. Assuming that narrow clines are maintained by selection, variation in cline width indicates that selection is not uniform throughout the genome and that diagnostic markers are under more intense selective pressure. The traditional focus on diagnostic markers in studies of hybrid zones may therefore lead to underestimates of average introgression. This effect may be more pronounced in organisms with low levels of genetic divergence between hybridizing taxa.     

WEAK CROSSABILITY BARRIER BUT STRONG JUVENILE SELECTION SUPPORTS ECOLOGICAL SPECIATION OF THE HYBRID PINE PINUS DENSATA ON THE TIBETAN PLATEAU

Determining how a new hybrid lineage can achieve reproductive isolation is a key to understanding the process and mechanisms of homoploid hybrid speciation. Here, we evaluated the degree and nature of reproductive isolation between the ecologically successful hybrid species Pinus densata and its parental species P. tabuliformis and P. yunnanensis. We performed interspecific crosses among the three species to assess their crossability. We then conducted reciprocal transplantation experiments to evaluate their fitness differentiation, and to examine how natural populations representing different directions of introgression differ in adaptation. The crossing experiments revealed weak genetic barriers among the species. The transplantation trials showed manifest evidence of local adaptation as the three species all performed best in their native habitats. Pinus densata populations from the western edge of its distribution have evolved a strong local adaptation to the specific habitat in that range; populations representing different directions of introgressants with the two parental species all showed fitness disadvantages in this P. densata habitat. These observations illustrate that premating isolation through selection against immigrants from other habitat types or postzygotic isolation through selection against backcrosses between the three species is strong. Thus, ecological selection in combination with endogenous components and geographic isolation has likely played a significant role in the speciation of P. densata.     

基因组基因定位(基因DNA酶解图谱技术)的计算机方法研究

本文提出基于酶解图谱技术的基因组基因定位的计算机方法,用于连接定位从克隆分析得到的数据．我们选择了若干例子作为研究对象,尝试了该方法的有效性．结果表明,计算机方法性能良好,可望成为大基因组基因定位的有用工具．     

PATTERNS OF HYBRIDIZATION IN THE PIRIQUETA CAROLINIANA COMPLEX IN CENTRAL FLORIDA: EVIDENCE FOR AN EXPANDING HYBRID ZONE

We have identified a broad zone of hybridization between two morphologically and ecologically distinct herbaceous perennial taxa (morphotypes) within the Piriqueta caroliniana complex, which extends more than 300 km across the central Florida peninsula. Phylogeographic analyses indicate that the caroliniana morphotype has been present in north and central Florida since the early Pleistocene and that the viridis morphotype has immigrated into southern Florida much more recently. We examine the distribution of diagnostic morphological characters and nuclear genetic markers to assess the extent and patterns of introgression in this system. The results are consistent with the hypothesis that this hybrid zone has expanded north in recent history as viridis alleles have introgressed into regions that were previously occupied by populations of caroliniana. Genetic markers diagnostic for caroliniana have consistently high frequencies across the hybrid zone, whereas markers for viridis are extremely variable among populations with frequency reversals in adjacent populations. The latter pattern is probably the result of the combined stochastic effects of dispersal and drift on viridis alleles as they introgressed northward. Additional evidence for the recent expansion of this hybrid zone comes from patterns of variation for morphological and genetic markers. As expected for an expanding hybrid zone, within-population morphological variation was greatest toward the advancing front of introgression and levels of genetic variation for neutral diagnostic markers were greatest in the region of initial contact and lower in areas of recent expansion. The observed patterns of variation suggest that at least some hybrid genotypes have high fitnesses, which has led to the expansion of the hybrid zone via the displacement of parental genotypes in central Florida.     

UNIFICATION OF REGRESSION‐BASED METHODS FOR THE ANALYSIS OF NATURAL SELECTION

Regression analyses are central to characterization of the form and strength of natural selection in nature. Two common analyses that are currently used to characterize selection are (1) least squares–based approximation of the individual relative fitness surface for the purpose of obtaining quantitatively useful selection gradients, and (2) spline‐based estimation of (absolute) fitness functions to obtain flexible inference of the shape of functions by which fitness and phenotype are related. These two sets of methodologies are often implemented in parallel to provide complementary inferences of the form of natural selection. We unify these two analyses, providing a method whereby selection gradients can be obtained for a given observed distribution of phenotype and characterization of a function relating phenotype to fitness. The method allows quantitatively useful selection gradients to be obtained from analyses of selection that adequately model nonnormal distributions of fitness, and provides unification of the two previously separate regression‐based fitness analyses. We demonstrate the method by calculating directional and quadratic selection gradients associated with a smooth regression‐based generalized additive model of the relationship between neonatal survival and the phenotypic traits of gestation length and birth mass in humans.     

SUPPORT FOR THE IMMUNOCOMPETENCE HANDICAP HYPOTHESIS IN THE WILD: HORMONAL MANIPULATION DECREASES SURVIVAL IN SICK DAMSELFLIES

The immunocompetence handicap hypothesis (ICHH) states that hormones enhance sexual trait expression but impair immunity. Previous tests of the ICHH have been hampered by experimental design problems. Here, we report on an experimental test of the ICHH that includes manipulations of both hormones and infections in males of the territorial damselfly, Hetaerina americana, with accurate survival measurements. We conducted a fully factorial experiment subjecting each individual to one of three topical treatments: methoprene (a juvenile hormone analog), acetone, or control, and one of three injection treatments: bacteria, PBS, or control. We measured survival of manipulated males in both the wild and in captivity. As predicted, survival was most heavily impaired in methoprene‐bacteria males than in the other groups in the wild, and no survival differences emerged in captive animals. This result confirms that survival is one cost an animal pays for increased hormonal levels. This corroborates theoretical predictions of the ICHH.     

THE DESIGN OF A BEAUTIFUL WEAPON: COMPENSATION FOR OPPOSING SEXUAL SELECTION ON A TRAIT WITH TWO FUNCTIONS

Male fiddler crabs, genus Uca, have one greatly enlarged claw with which they court females and threaten and fight other males. Longer claws are more effective signals but are thought to be less effective weapons because the relative closing force at the tip of the claw decreases with claw length. We studied claw morphology and fighting in Uca terpsichores and Uca beebei and found a mechanism that may resolve opposing selection for signaling and fighting ability. When males fought they delivered gripping forces not at the tips but at the tubercles on the inner margins of their claws’ fingers. As claws grow, these tubercles remain relatively close to the apex of the gape. Consequently, the mechanical advantage that governs the forces that can be delivered at these tubercles decreases only slightly with increasing claw length allowing the claw to be an effective signal and a powerful weapon. Animal weapons are exceptionally diverse in form and detail of armature and the causes of this diversity are poorly understood. We suggest that the designs of weapons may often reflect compensatory patterns of growth and placement of armature that enhances the weapon's overall utility for multiple uses in competition for mates.     

AN EMPIRICAL TEST OF PREDICTIONS OF TWO COMPETING MODELS FOR THE MAINTENANCE AND FATE OF HYBRID ZONES: BOTH MODELS ARE SUPPORTED IN A HARD-CLAM HYBRID ZONE

Two models developed to discern the mode of selection in hybrid zones differ in some predictions. The tension-zone model predicts that selection acts against hybrids and independently of the environment (endogenous selection) and that selection is invariant throughout the hybrid zone. The ecological selection-gradient, or ecotone, model maintains that fitness of different genotypes varies in response to environmental variation (exogenous selection) and thus, that in a region of the zone, fitness of hybrids is at least equal to that of the parental species. Therefore, to assess the predominant mode of selection operating in a hybrid zone, it is fundamental to evaluate whether selection is acting specifically against hybrid individuals, that is, whether hybridity alone is the basis for deficiencies of hybrids, and to evaluate whether the relative fitness of hybrids versus that of pure species varies across the zone. In a hardclam (genus Mercenaria) hybrid zone located in a polyhaline lagoon in east-central Florida, we used age-specific and location-specific analyses to determine that a hybrid deficit occurrs, that the deficit seems to be due to selection against hybrids, and that selection varies across the zone. Various measures of deviation from Hardy-Weinberg equilibrium, linkage disequilibrium analyses, and shifts in allele frequencies at semidiagnostic loci support the idea that selection is strongest in the northern region of the lagoon, the zone of sympatry and hybridization. Southward, into the range of M. mercenaria (the numerically predominant species), the percentage of hybrids remains relatively high and selection against hybrids decreases. For some genetic linkage groups, selection for M. mercenaria alleles seems to be occurring, but selection seems to be acting principally against alleles characteristic of M. mercenaria and, to a lesser degree, for alleles characteristic of M. campechiensis (the rarer species). These findings and others from previous analyses we have done on this hybrid zone demonstrate that selection in the zone is complex, and that characteristics of both the tension-zone and ecotone models are present. Supporting the tension-zone model, selection against hybrids per se clearly occurs, but specific genotypes seem to be at a selective disadvantage, whereas others have a selective advantage, and selection operates differentially on the two parental species within the zone. Supporting the ecotone model, the strength of overall selection varies throughout the zone, and environmentally mediated selection in which each species and hybrids have an advantage in specific habitats occurs, but some selection against hybrids is invariant throughout the zone. Thus, the structure and genetic architecture of this hybrid zone appear to be products of a complicated interaction between both types of selective forces cited in the two competing models.     

FEMALE CHOICE FOR AN INDICATOR OF MALE SIZE IN THE SONG OF THE BLACK-HORNED TREE CRICKET,OECANTHUS NIGRICORNIS (ORTHOPTERA: GRYLLIDAE: OECANTHINAE)

The calling song of male crickets, including Oecanthus nigricornis (Walker), attracts females for mating and provides a model system of sexual communication. We give the first conclusive identification of a feature of cricket song that is both attractive to females and indicates a phenotypic feature (body size) that determines male mating success and female reproductive benefits. We do this by first testing for correlations between song characteristics and aspects of male phenotype that are hypothesized to indicate male quality. We show that song is a reliable indicator of male size and male age, and that large male size is associated with increased female fecundity. We then use playbacks of synthetic songs that mimic natural variation in song parameters to study song preferences and we compare preferences under different presentation regimes to determine whether choices are based on relative song quality or some fixed criterion. Females show a preference for the lower frequency songs produced by large males, but only during simultaneous playbacks. Thus female choice is based on the relative quality of calls that can be sampled simultaneously. These results provide strong support for the hypothesis that females use variation in calling song to assess male mate quality.     

MEASURING THE EFFECTS OF PAIRING SUCCESS,EXTRA-PAIR COPULATIONS AND MATE QUALITY ON THE OPPORTUNITY FOR SEXUAL SELECTION

Sexual selection can act through variation in the number of social mates obtained, variation in mate quality, or variation in success at obtaining extra-pair fertilizations. Because within-pair fertilizations (WPF) and extra-pair fertilizations (EPF) are alternate routes of reproduction, they are additive, rather than multiplicative, components of fitness. We present a method for partitioning total variance in reproductive success (a measure of the opportunity for selection) when fitness components are both additive and multiplicative and use it to partition the variance into components that correspond to each mechanism of sexual selection. Computer simulations show that extra-pair fertilizations can either increase or decrease total variance, depending on the covariance between within-pair and extra-pair success. Simulations also suggest that for socially monogamous species, extra-pair fertilizations have a greater effect than variation in mate quality or pairing status on the opportunity for selection. Application of our model to data gathered for a population of red-winged blackbirds (Agelaius phoeniceus) indicates that most of the variance in male reproductive success was attributable to within-pair sources of variance. Nevertheless, extra-pair copulations increased the opportunity for selection because males varied both in the proportion of their social young that they sired and in the number of extra-pair mates that they obtained. Furthermore, large and positive covariances existed between the number of extra-pair mates a male obtained and both social pairing success and within-pair paternity, indicating that, in this population, males preferred as social mates also were preferred as extra-pair mates.     

SEXUAL SIZE DIMORPHISM AS A CORRELATED RESPONSE TO SELECTION ON BODY SIZE: AN EMPIRICAL TEST OF THE QUANTITATIVE GENETIC MODEL

We artificially selected for body size in Drosophila melanogaster to test Lande's quantitative genetic model for the evolution of sexual size dimorphism. Thorax width was used as an estimator of body size. Selection was maintained for 21 generations in both directions on males only, females only, or both sexes simultaneously. The correlated response of sexual size dimorphism in each selection regime was compared to the response predicted by four variants of the model, each of which differed only in assumptions about input parameters. Body size responded well to selection, but the correlated response of sexual size dimorphism was weaker than that predicted by any of the variants. Dimorphism decreased in most selection lines, contrary to the model predictions. We suggest that selection on body size acts primarily on growth trajectories. Changes in dimorphism are caused by the fact that male and female growth trajectories are not parallel and termination of growth at different points along the curves results in dimorphism levels that are difficult to predict without detailed knowledge of growth parameters. This may also explain many of the inconsistent results in dimorphism changes seen in earlier selection experiments.     

小型啮齿动物种群系统调节复合因子理论的野外实验研究：食物可利用性和捕食对根田鼠种群动态作用的分析

本研究在野外围栏条件下采用析因实验设计,测定营养、捕食及空间行为对根田鼠（Ｍｉ－ｃｒｏｔｕｓｏｅｃｏｎｏｍｕｓ）种群统计特征的影响。本文旨在检验下述特定假设：高质量食物可利用性和捕食对限制小型啮齿动物种群密度具有独立的和累加的效应。３年期间,４种野外实验处理６个重复的研究结果表明,附加食物并预防捕食者处理的种群具有最高密度;未附加食物及不预防捕食者处理（对照）的种群密度最低;而单一处理的种群,其密度居中。不同处理条件下,新生个体在种群的补充模式以及种群瞬时增长率的变化均与种群密度的变动相应一致。双因素ＡＮＯＶＡ的结果证明,附加高质量食物能明显地提高根田鼠的种群密度,而对种群补充量的作用则较弱,仅接近显著水平;预防捕食者不仅能显著地作用于种群密度,更能强烈地影响种群补充量。高质量食物和捕食者的作用具有累加的性质,两者的交互作用对种群密度和补充量均无显著影响。     

GAPE‐LIMITED PREDATORS AS AGENTS OF SELECTION ON THE DEFENSIVE MORPHOLOGY OF AN INVASIVE INVERTEBRATE

Invasive species have widespread and pronounced effects on ecosystems and adaptive evolution of invaders is often considered responsible for their success. Despite the potential importance of adaptation to invasion, we still have limited knowledge of the agents of natural selection on invasive species. Bythotrephes longimanus, a cladoceran zooplankton, invaded multiple Canadian Shield lakes over the past several decades. Bythotrephes have a conspicuous caudal process (tail spine) that provides a morphological defense against fish predation. We measured viability selection on the longest component of the Bythotrephes spine, the distal spine segment, through a comparison of the lengths of first and second instar Bythotrephes collected from lakes differing in the dominance of gape‐limited predation (GLP) and nongape‐limited predation (NGLP) by fish. We found that natural selection varied by predator gape‐limitation, with strong selection (selection intensity: 0.20–0.79) for increased distal spine length in lakes dominated by GLP, and no significant selection in lakes dominated by NGLP. Further, distal spine length was 17% longer in lakes dominated by GLP, suggesting the possibility of local adaptation. As all study lakes were invaded less than 20 years prior to our collections, our results suggest rapid divergence in defensive morphology in response to selection from fish predators.     

CLASSIFICATION OF THE GENUS ISHIGE (ISHIGEALES,PHAEOPHYCEAE) IN THE NORTH PACIFIC OCEAN WITH RECOGNITION OF ISHIGE FOLIACEA BASED ON PLASTID rbcl AND MITOCHONDRIAL cox3 GENE SEQUENCES1

The taxonomy and biogeography of a genus with species that occur in geographically isolated regions is interesting. The brown algal genus Ishige Yendo is a good example, with species that apparently inhabit warm regions of both the northwestern and northeastern Pacific Ocean. We determined the sequences of mitochondrial cox3 and plastid rbcL genes from specimens of the genus collected over its distributional range. Analyses of the 86 cox3 and 97 rbcL sequences resulted in congruent trees in which Ishige sinicola (Setch. et N. L. Gardner) Chihara consisted of two distinct clades: one comprising samples from Korea and Japan, and the other comprising samples from the Gulf of California. Additional observations of the morphology and anatomy of the specimens agree with the molecular data. On the basis of results, we reinstated Ishige foliacea S. Okamura (considered a synonym of I. sinicola from the Gulf of California) for plants from the northwest Pacific region and designated a specimen in the Yendo Herbarium (SAP) as the lectotype. I. foliacea is distinguished by large (up to 20 cm) and wide (up to 20 mm) thalli, with a cortex of 4–7 cells, and a medulla composed of long, tangled hyphal cells. Both cox3 and rbcL sequence data strongly support the sister‐area relationship between the northwest Pacific region and the Gulf of California. A likely explanation for this pattern would be the presence of a species ancestral to contemporary species of Ishige in both regions during the paleogeological period, with descendants later isolated by distance.     

THE RESPONSE TO SELECTION FOR FAST LARVAL DEVELOPMENT IN DROSOPHILA MELANOGASTER AND ITS EFFECT ON ADULT WEIGHT: AN EXAMPLE OF A FITNESS TRADE-OFF

A selection experiment using Drosophila melanogaster revealed a strong trade-off between adult weight and larval development time (LDT), supporting the view that antagonistic pleiotropy for these two fitness traits determines mean adult size. Two experimental lines of flies were selected for a shorter LDT (measured from egg laying to pupation). After 15 generations LDT was reduced by an average of 7.9%. The response appeared to be controlled primarily by autosomal loci. A correlated response to the selection was a reduction in adult dry weight: individuals from the selected populations were on average 15.1% lighter than the controls. The lighter females of the selected lines showed a 35% drop in fecundity, but no change in longevity. Thus, there is no direct relationship between LDT and adult longevity. The genetic correlation between weight and LDT, as measured from their joint response to selection, was 0.86. Although there was weak evidence for dominance in LDT, there was none for weight, making it unlikely that selection acting on this antagonistic pleiotropy could lead to a stable polymorphism. In all lines, sex differences in weight violated expectations based on intrasex genetic correlations: Females, being larger than males, ought to require a longer LDT, whereas there was a slight trend in the opposite direction. Because the sexual dimorphism in size was not significantly altered by selection, it appears that the controlling loci are either invariant or have very limited pleiotropic effect on developmental time. It is suggested that they probably control some intrinsic, energy-intensive developmental process in males.