Dissimilar rates in molecular evolution

In this work we present an evolutionary tree based on the differences in the physico-chemical properties involved in amino acid substitutions, instead of considering, for its construction, only the number of changes between species. Phylogenetic trees were constructed from the differences in bulkiness, refractivity index, hydrophobicity, polarity and optical rotation of 9 vertebrate calcitonins. A correlation of the form y=a x^b was found between the number of changes (x) and the differences in any given physico-chemical property (y). This correlation implies that the evolutionary time can not be evaluated directly from the number of changes between species.     

Coevolution of life history traits and morphology in female subterranean amphipods

Subterranean species show a distinct morphology, yet the adaptive significance of some traits, like body size and shape, is poorly understood and cannot be explained solely by distinct environmental conditions (darkness, less food). We predicted that in females some morphological changes may have co‐evolved with life history traits, and that co‐evolving life history traits provide at least part of the explanation for evolutionary changes of morphology. Using museum material we tested this prediction on the subterranean amphipod genus Niphargus. We studied six species found in springs and eight species found in cave lakes. We treated them as two ecologically distinct groups, and the major ecological differences between them were the availability of nutrients and the water currents. Cave species were found to be larger and stouter (as inferred from the shape of coxal plates, which are part of the marsupium), they had larger eggs and lower reproductive effort per brood, whereas the egg number and brood volume if corrected for the body size were not different. Using phylogenetic independent contrasts, we found a positive correlation between body shape and egg volume, a positive correlation between body size and egg volume, and a negative correlation between body size and reproductive effort per brood. We tentatively conclude that evolutions of morphology and life histories are functionally connected and that co‐evolving traits contribute to overall selective regime.     

Comparative variation of morphological and molecular evolution through geologic time: 28S ribosomal RNA versus morphology in echinoids.

The comparatively good fossil record of post-Palaeozoic echinoids allows rates of morphological change to be estimated over the past 260 million years and compared with rates of molecular evolution. Parsimony analysis of morphological data, based predominantly on skeletal characteristics, and parsimony, distance and maximum likelihood analyses of molecular data, from the first 380 bases from the 5' end of the 28S rRNA molecule, for 10 species of echinoid produce congruent phylogenies. The molecular sequence chosen is demonstrably far from saturation and sister groups have divergence times ranging from about 15 to 260 Ma. Parsimony analysis allows the great majority of molecular and morphological apomorphies to be placed in one of 18 independent geological time intervals, providing a direct measure of rates of evolution for periods in the geological past. Because most molecular fixed point mutations in our sequences cannot be polarized unambiguously by outgroup comparison (making the outgroup states effectively random), distance and parsimony analyses both tend spuriously to root the echinoid tree on the longest internal branch. A topology identical to that derived from morphological data is, however, obtained using Maximum Likelihood and also parsimony analysis where outgroup rooting is restricted to more conserved regions. This is taken as the correct topology for assessing rates of evolution. Overall, both morphological and molecular changes show a moderately strong correlation with time elapsed, but a weaker correlation with one another. Statistically significant differences in evolutionary rate are found between some, but not all, pair-wise comparisons of sister lineages for both molecular and morphological data. The molecular clock rate for echinaceans is three times faster than that for cidaroids and irregular echinoids. Spearman's rank correlation test, which requires only relative magnitude of changes to be known, suggests that morphological change has a slightly better correlation with time than does molecular change, averaged over all ten species. However, when just echinaceans are considered an extremely good correlation is found between the number of molecular changes and time elapsed, whereas morphological change remains poorly correlated. Thus, molecular rates approximate to a clocklike model within restricted echinoid clades, but vary significantly between clades. Averaging results over all echinoids produces a correlation that is no better than the correlation between morphological change and time elapsed.     

Fruit production and floral traits: correlated evolution in <Emphasis Type="Italic">Govenia</Emphasis> (Orchidaceae)

The most common estimate of reproductive success in orchids is usually fruit set. Factors such as resource limitation and certain floral traits may influence reproductive success in animal-pollinated plants. Correlated evolution of reproductive success vs. seven floral traits (inflorescence length, flower number, flower distribution along inflorescence, dorsal sepal length, lateral sepal length, flower color, and column position) was studied in eight species of Govenia. Taxa represented three lineages in the genus. Independent contrasts were calculated on a phylogeny inferred from chloroplast (trnL-F IGS) DNA sequences, and a correlation test and multiple regression were then performed. Two data sets were evaluated, one including all eight species and another excluding G. utriculata, which is autogamous. The historical analyses showed that there is a correlation between reproductive success and dorsal sepal length, column position, and flower number, these correlations suggest that changes in these floral traits usually accompany evolutionary shifts in reproductive success. Multiple regression tests suggest that changes in reproductive success can be explained by shifts in flower number, inflorescence length, column position and by dorsal sepal length. When phylogeny is taken into account, our analyses showed that evolutionary shifts in these floral traits were correlated with changes in reproductive success. Evolutionary correlation between reproductive success and floral traits might be explained by the natural selection of certain floral phenotypes by pollinators.     

Xylem function of arid-land shrubs from California, USA: an ecological and evolutionary analysis

Xylem traits were examined among 22 arid-land shrub species, including measures of vessel dimensions and pit area. These structural measures were compared with the xylem functional traits of transport efficiency and safety from cavitation. The influence of evolution on trait relationships was examined using phylogenetic independent contrasts (PICs). A trade-off between xylem safety and efficiency was supported by a negative correlation between vessel dimensions and cavitation resistance. Pit area was correlated with cavitation resistance when cross species data were examined, but PICs suggest that these traits have evolved independently of one another. Differences in cavitation resistance that are not explained by pit area may be related to differences in pit membrane properties or the prevalence of tracheids, the latter of which may alter pit area through the addition of vessel-to-tracheid pits or through changes in xylem conduit connectivity. Some trait relationships were robust regardless of species ecology or evolutionary history. These trait relationships are likely to be the most valuable in predictive models that seek to examine anatomical and functional trait relationships among extant and fossil woods and include the relationship among hydraulic conductivity and vessel diameter, between vessel diameter and vessel length, and between hydraulic conductivity and wood density.     

Comparison of protein and mRNA expression evolution in humans and chimpanzees

Even though mRNA expression levels are commonly used as a proxy for estimating functional differences that occur at the protein level, the relation between mRNA and protein expression is not well established. Further, no study to date has tested whether the evolutionary differences in mRNA expression observed between species reflect those observed in protein expression. Since a large proportion of mRNA expression differences observed between mammalian species appears to have no functional consequences for the phenotype, it is conceivable that many or most mRNA expression differences are not reflected at the protein level. If this is true, then differences in protein expression may largely reflect functional adaptations observed in species phenotypes. In this paper, we present the first direct comparison of mRNA and protein expression differences seen between humans and chimpanzees. We reproducibly find a significant positive correlation between mRNA expression and protein expression differences. This correlation is comparable in magnitude to that found between mRNA and protein expression changes at different developmental stages or in different physiological conditions within one species. Noticeably, this correlation is mainly due to genes with large expression differences between species. Our study opens the door to a new level of understanding of regulatory evolution and poses many new questions that remain to be answered.     

Ascomycota has a faster evolutionary rate and higher species diversity than Basidiomycota

Differences in rates of nucleotide or amino acid substitutions among major groups of organisms are repeatedly found and well documented. A growing body of evidence suggests a link between the rate of neutral molecular change within populations and the evolution of species diversity. More than 98% of terrestrial fungi belong to the phyla Ascomycota or Basidiomycota. The former is considerably richer in number of species than the latter. We obtained DNA sequences of 21 protein-coding genes from the lichenized fungus Rhizoplaca chrysoleuca and used them together with sequences from GenBank for subsequent analyses. Three datasets were used to test rate discrepancies between Ascomycota and Basidiomycota and that within Ascomycota: (i) 13 taxa including 105 protein-coding genes, (ii) nine taxa including 21 protein-coding genes, and (iii) nuclear LSU rDNA of 299 fungal species. Based on analyses of the 105 protein-coding genes and nuclear LSU rDNA datasets, we found that the evolutionary rate was higher in Ascomycota than in Basidiomycota. The differences in substitution rates between Ascomycota and Basidiomycota were significant. Within Ascomycota, the species-rich Sordariomycetes has the fastest evolutionary rate, while Leotiomycetes has the slowest. Our results indicate that the main contribution to the higher substitution rates in Ascomycota does not come from mutualism, ecological conditions, sterility, metabolic rate or shorter generation time, but is possibly caused by the founder effect. This is another example of the correlation between species number and evolutionary rates, which is consistent with the hypothesis that the founder effect is responsible for accelerated substitution rates in diverse clades.     

迁地保护条件下两种沙冬青的开花物候比较研究

沙冬青属(Ammopiptanthus)植物是我国西北荒漠区唯一的常绿阔叶灌木。作者对吐鲁番沙漠植物园迁地保护的两种沙冬青的开花物候进行了详细的比较观察,旨在探讨它们在同一生境条件下开花特性的异同点及其影响因素。主要结果如下:(1)两种植物在开花频率、花序开放顺序、开花振幅曲线及单花寿命等开花参数上相似,但在始花时间、单株花期、花序的开花数及开放持续时间与频率分布、开花振幅等参数上明显不同;(2)在个体和群体水平上,蒙古沙冬青(A.mongolicus)始花时间均比新疆沙冬青(A.nanus)早,蒙古沙冬青开花全过程为20–21d,新疆沙冬青为13–14d;(3)蒙古沙冬青花序的开花数比新疆沙冬青多、开放持续时间长,两者在开花数(F=17.51,P<0.01)和持续时间(F=14.08,P<0.01)上均存在显著差异;(4)花序上的花大多从近基部向两端开放,开花振幅呈单峰曲线,但新疆沙冬青的开花振幅较高;(5)花序开放持续期的频率分布明显不同,新疆沙冬青较蒙古沙冬青更为集中,但两者的单花寿命稳定,均在7d左右;(6)花序上每天的开花数与其座果数呈正相关(蒙古沙冬青,r=0.885,P<0.05;新疆沙冬青,r=0.827,P<0.01),但其开花数和座果数与始花时间存在不同程度的相关关系,这些特点可能与开花对传粉者的吸引以及物种本身的遗传特性有关。对上述观察结果及其影响因素的分析表明,两种植物在开花参数上所表现出的一致性可能是受系统发育限制的,而彼此间的差异可能与其进化历史及所处的环境异质性有关,是在与环境的长期适应过程中分别形成的一些可遗传的变异;而不同年份间两种沙冬青在花序的开花数及开放持续时间上表现出的差异可能与环境温度的变化有关。这些结果对于探讨该属植物的繁殖生物学特性及其保护对策具有重要意义。     

Evolution of development in closely related species of flies and worms

One of the main challenges in evolutionary biology is to identify the molecular changes that underlie phenotypic differences that are of evolutionary significance. Comparative studies of early development have shown that changes in the spatio-temporal use of regulatory genes, as well as changes in the specificity of regulatory proteins, are correlated with important differences in morphology between phylogenetically distant species. However, it is not known how such changes take place in natural populations, and whether they result from a single, or many small, additive events. Extending this approach to the study of development of closely related species promises to enrich this debate.     

Species differences in the regulation of tyrosine hydroxylase in Cnemidophorus whiptail lizards

Evolution of behavioral phenotype involves changes in the underlying neural substrates. Cnemidophorus whiptail lizards enable the study of behavioral and neural evolution because ancestral species involved in producing unisexual, hybrid species still exist. Catecholaminergic systems modulate the expression of social behaviors in a number of vertebrates, including whiptails, and therefore we investigated how changes in catecholamine production correlated with evolutionary changes in behavioral phenotype by measuring the size and number of catecholamine producing (tyrosine hydroxylase-immunoreactive, or TH-ir) cells across the reproductive cycle in females from two related whiptail species. Cnemidophorusuniparens is a triploid, parthenogenetic species that arose from hybridization events involving the diploid, sexual species C. inornatus. Prior to ovulation, females from both species display femalelike receptive behaviors. However, after ovulation, only parthenogenetic individuals display malelike mounting behavior. In all nuclei measured, we found larger TH-ir cells in the parthenogen, a difference consistent with species differences in ploidy. In contrast, species differences in the number of TH-ir cells were nucleus specific. In the preoptic area and anterior hypothalamus, parthenogens had fewer TH-ir cells than females of the sexual species. Reproductive state only affected TH-ir cell number in the substantia nigra pars compacta (SNpc), and C. uniparens individuals had more TH-ir cells after ovulation than when previtellogenic. Thus, species differences over the reproductive cycle in the SNpc are correlated with species differences in behavior, and it appears that the process of speciation may have produced a novel neural and behavioral phenotype in the parthenogen.     

GEOGRAPHIC VARIATION AND PHENOTYPIC PLASTICITY OF NUMBER OF TRUNK VERTEBRAE IN SLENDER SALAMANDERS,BATRACHOSEPS (CAUDATA: PLETHODONTIDAE)

To understand the evolutionary significance of geographic variation, one must identify the factors that generate phenotypic differences among populations. I examined the causes of geographic variation in and evolutionary history of number of trunk vertebrae in slender salamanders, Batrachoseps (Caudata: Plethodontidae). Number of trunk vertebrae varies at many taxonomic levels within Batrachoseps. Parallel clines in number occur along an environmental gradient in three lineages in the Coast Ranges of California. These parallel clines may signal either adaptation or a shared phenotypically plastic response to the environmental gradient. By raising eggs from 10 populations representing four species of Batrachoseps, I demonstrated that number of trunk vertebrae can be altered by the developmental temperature; however, the degree of plasticity is insufficient to account for geographic variation. Thus, the geographic variation results largely from genetic variation. Number of trunk vertebrae covaries with body size and shape in diverse vertebrate taxa, including Batrachoseps. I hypothesize that selection for different degrees of elongation, possibly related to fossoriality, has led to the extensive evolution of number of trunk vertebrae in Batrachoseps. Analysis of intrapopulational variation revealed sexual dimorphism in both body shape and number of trunk vertebrae, but no correlation between these variables in either sex. Females are more elongate than males, a pattern that has been attributed to fecundity selection in other taxa. Patterns of covariation among different classes of vertebrae suggest that some intrapopulational variation in number results from changes in vertebral identity rather than changes in segmentation.     

Vom Phänotyp zum Genotyp

Forward Genomics – a comparative genomics approach to link phenotype to genotype Despite availability of several sequenced genomes, we know very little about the specific changes in the DNA that underlie phenotypic differences between species. The main reason is that species differ by both numerous genomic and phenotypic changes. A new comparative genomics method addresses this question by for phenotypes with independent evolutionary losses by searching for genomic regions that exhibit an elevated number of mutations in exactly these phenotype‐loss species. The near future sequencing of thousands of novel genomes will make it possible to use comparative genomics to systematically search for such DNA changes that are associated with phenotypic differences.     

Predicting Protein-Protein Interaction by the Mirrortree Method: Possibilities and Limitations

Molecular co-evolution analysis as a sequence-only based method has been used to predict protein-protein interactions. In co-evolution analysis, Pearson''s correlation within the mirrortree method is a well-known way of quantifying the correlation between protein pairs. Here we studied the mirrortree method on both known interacting protein pairs and sets of presumed non-interacting protein pairs, to evaluate the utility of this correlation analysis method for predicting protein-protein interactions within eukaryotes. We varied metrics for computing evolutionary distance and evolutionary span of the species analyzed. We found the differences between co-evolutionary correlation scores of the interacting and non-interacting proteins, normalized for evolutionary span, to be significantly predictive for proteins conserved over a wide range of eukaryotic clades (from mammals to fungi). On the other hand, for narrower ranges of evolutionary span, the predictive power was much weaker.     

Variation in guenon skulls (I): species divergence, ecological and genetic differences

Guenons are the most diverse clade of African monkeys. They have varied ecologies, include arboreal and terrestrial species, and can be found in nearly every region of sub-Saharan Africa. Species boundaries are often uncertain, with a variable number of species and subspecies mostly recognised on the basis of their geographic distribution and pelage. If guenon soft tissue patterns show high variability, the same does not seem to hold for skull morphology. Guenon skulls are traditionally considered relatively undifferentiated and homogeneous. However, patterns of variation in skulls have never been examined using a large number of specimens sampled across the breadth of species diversity. Thus, in the present study, skulls of adult guenons and two outgroup species are analysed using three-dimensional geometric morphometrics. Three-dimensional coordinates of 86 anatomical landmarks were measured on 1,315 adult specimens belonging to all living guenon species except Cercopithecus dryas. Species are well-discriminated using shape but the best discrimination occurs when species have either a long evolutionary history (e.g., Allenopithecus nigroviridis) or represent extremes of size variation (Miopithecus sp. and Erythrocebus patas). Interspecific phenetic relationships reflect size differences. Four main clusters are found that mainly correspond to four size groups: the smallest species (Miopithecus sp.), the largest species (E. patas plus the study outgroups), a group of medium-small arboreal guenons, and a group of medium-large arboreal and terrestrial guenons. Correlations between interspecific shape distances and interspecific differences in size are higher than between shape distances and genetic distances. However, if only the component of interspecific shape variation which is not correlated to evolutionary allometry is used in the comparison with genetic distances, correlations are up to 1.4 times larger than those including allometric shape. The smallest correlations are those between shape and ecological distances, which is consistent with the lack of clusters clearly reflecting broad ecological specialisations (e.g., arboreality versus terrestriality). Thus, size, which is generally considered more evolutionarily labile than shape, seems to have played a major role in the evolution of the guenons. The incongruence between interspecific shape differences and phylogeny might be explained by a large proportion of shape changes having occurred along allometric trajectories that tend to be conserved within this clade.     

An interspecific comparison between morphology and swimming performance in cyprinids

Flow regimes are believed to be of major evolutionary significance in fish. The flow regimes inhabited by cyprinids vary extensively from still flow regimes to riptide flow regimes. To test (i) whether flow‐driven swimming performance and relevant morphological differentiation are present among fish species and (ii) whether evolutionary shifts between high‐flow and low‐flow habitats in cyprinids are associated with evolutionary trade‐offs in locomotor performance, we obtained data on both steady and unsteady swimming performance and external body shape for 19 species of cyprinids that typically occur in different flow regimes (still, intermediate and riptide). We also measured the routine energy expenditure (RMR) and maximum metabolic rate (MMR) and calculated the optimal swimming speed. Our results showed that fish species from riptide groups tend to have a higher critical swimming speed (U_crit), maximum linear velocity (V_max) and fineness ratio (FR) than fish from the other two groups. However, there was no correlation between the reconstructed changes in the steady and unsteady swimming performance of the 19 species. According to the phylogenetically independent contrast (PIC) method, the U_crit was actively correlated with the MMR. These results indicated that selection will favour both higher steady and unsteady swimming performance and a more streamlined body shape in environments with high water velocities. The results suggested that steady swimming performance was more sensitive to the flow regime and that for this reason, changes in body shape resulted more from selective pressure on steady swimming performance than on unsteady swimming performance. No evolutionary trade‐off was observed between steady and unsteady swimming performance, although U_crit and MMR were found to have coevolved. However, a further analysis within each typically occurring habitat group suggested that the trade‐off that may exist between steady and unsteady swimming performance may be concealed by the effect of habitat.     

Evolutionary diversification of the auditory organ sensilla in Neoconocephalus katydids (Orthoptera: Tettigoniidae) correlates with acoustic signal diversification over phylogenetic relatedness and life history

Neoconocephalus Tettigoniidae are a model for the evolution of acoustic signals as male calls have diversified in temporal structure during the radiation of the genus. The call divergence and phylogeny in Neoconocephalus are established, but in tettigoniids in general, accompanying evolutionary changes in hearing organs are not studied. We investigated anatomical changes of the tympanal hearing organs during the evolutionary radiation and divergence of intraspecific acoustic signals. We compared the neuroanatomy of auditory sensilla (crista acustica) from nine Neoconocephalus species for the number of auditory sensilla and the crista acustica length. These parameters were correlated with differences in temporal call features, body size, life histories and different phylogenetic positions. By this, adaptive responses to shifting frequencies of male calls and changes in their temporal patterns can be evaluated against phylogenetic constraints and allometry. All species showed well‐developed auditory sensilla, on average 32–35 between species. Crista acustica length and sensillum numbers correlated with body size, but not with phylogenetic position or life history. Statistically significant correlations existed also with specific call patterns: a higher number of auditory sensilla occurred in species with continuous calls or slow pulse rates, and a longer crista acustica occurred in species with double pulses or slow pulse rates. The auditory sensilla show significant differences between species despite their recent radiation, and morphological and ecological similarities. This indicates the responses to natural and sexual selection, including divergence of temporal and spectral signal properties. Phylogenetic constraints are unlikely to limit these changes of the auditory systems.     

Surfing on the seascape: Adaptation in a changing environment

The environment changes constantly at various time scales and, in order to survive, species need to keep adapting. Whether these species succeed in avoiding extinction is a major evolutionary question. Using a multilocus evolutionary model of a mutation‐limited population adapting under strong selection, we investigate the effects of the frequency of environmental fluctuations on adaptation. Our results rely on an “adaptive‐walk” approximation and use mathematical methods from evolutionary computation theory to investigate the interplay between fluctuation frequency, the similarity of environments, and the number of loci contributing to adaptation. First, we assume a linear additive fitness function, but later generalize our results to include several types of epistasis. We show that frequent environmental changes prevent populations from reaching a fitness peak, but they may also prevent the large fitness loss that occurs after a single environmental change. Thus, the population can survive, although not thrive, in a wide range of conditions. Furthermore, we show that in a frequently changing environment, the similarity of threats that a population faces affects the level of adaptation that it is able to achieve. We check and supplement our analytical results with simulations.     

Relationships between ecological interaction modifications and diffuse coevolution: similarities, differences, and causal links

A major empirical approach in community ecology is to describe the dynamics of a community by examining small subsets of species. Unfortunately, interaction modifications, which cause pair-wise interaction coefficients to depend on the presence or absence of additional species, can make it difficult to predict the overall dynamics of species within a community from experiments with pairs of species. In a similar fashion, one of the major approaches in evolutionary ecology has been to describe the likely evolutionary dynamics of a single species by focusing on the selection imposed by a limited number of other species within the community. However, recent work on diffuse coevolution indicates that selection pressures due to one species can change in the presence of other species. The magnitude of the difficulty that interaction modifications and diffuse coevolution present for predicting ecological and evolutionary dynamics is an unresolved question. Here we outline the similarities and differences between the two topics, discuss experimental and statistical approaches to studying them, and make predictions about when ecological interaction modifications are likely to cause diffuse coevolution. Since the currencies for interaction modifications are usually fitness components such as growth, fecundity, or survival, is it likely that these will translate into corresponding differences in the relative fitness of individuals or genotypes, and thus in general these two phenomena will occur together. We argue that community ecologists and evolutionary ecologists will both benefit from experiments that test for the effects of interaction modifications, and that studies of the mechanisms driving interaction modifications and diffuse coevolution (e.g., changes in behavior, nonlinear effects on shared resources, genetic covariances) will aid our progress in understanding the ecological and evolutionary dynamics of communities.     

Growth trajectories of some major ammonoid sub‐clades revealed by serial grinding tomography data

Molluscs such as ammonoids record their growth in their accretionary shells, making them ideal for the study of evolutionary changes in ontogeny through time. Standard methods usually focus on two‐dimensional data and do not quantify empirical changes in shell and chamber volumes through ontogeny, which can possibly be important to disentangle phylogeny, interspecific variation and palaeobiology of these extinct cephalopods. Tomographic and computational methods offer the opportunity to empirically study volumetric changes in shell and chamber volumes through ontogeny of major ammonoid sub‐clades in three dimensions (3‐D). Here, we document (1) the growth of chamber and septal volumes through ontogeny and (2) differences in ontogenetic changes between species from each of three major sub‐clades of Palaeozoic ammonoids throughout their early phylogeny. The data used are three‐dimensional reconstructions of specimens that have been subjected to grinding tomography. The following species were studied: the agoniatitid Fidelites clariondi and anarcestid Diallagites lenticulifer (Middle Devonian) and the Early Carboniferous goniatitid Goniatites multiliratus. Chamber and septum volumes were plotted against the septum number and the shell diameter (proxies for growth) in the three species; although differences are small, the trajectories are more similar among the most derived Diallagites and Goniatites compared with the more widely umbilicate Fidelites. Our comparisons show a good correlation between the 3‐D and the 2‐D measurements. In all three species, both volumes follow exponential trends with deviations in very early ontogeny (resolution artefacts) and near maturity (mature modifications in shell growth). Additionally, we analyse the intraspecific differences in the volume data between two specimens of Normannites (Middle Jurassic).