Taxic evolutionary paleoecology and the ecological context of macroevolutionary change

Summary A traditional focus of evolutionary paleoecology has been the reconstruction of the selective forces that have affected evolving lineages through time. If the history of those lineages is dominated by stasis and punctuation, however, this is at best an inadequate and at worst a misdirected research strategy for macroevolution, because long-term stasis implies that environmental factors may have less influence on evolving lineages than previously believed. Such reasoning has led some proponents of punctuated views to reject ecological interactions as predominant or even significant forces in evolution. This is not a necessary conclusion. It is possible to accept the empirical predominance of stasis in evolution and at the same time the importance of ecology in affecting the course of evolutionary trends within lineages. If stasis prevails, ecology matters in the evolution of lineages if either (1) stabilizing selection is an important cause of stasis or (2) ecological interactions play an important role in controlling the speciation process. Viewing allopatric speciation explicitly as a three-stage process (consisting of formation, persistence and differentiation of isolated populations) clarifies testing of the role of ecology in speciation and may redirect clade-specific evolutionary paleoecology towards more enlightening interaction with other areas of macroevolutionary study.     

Molecular phylogeny of the entomopathogenic fungi of the genus Cordyceps (Ascomycota:Clavicipitaceae) and its evolutionary implications

Cordyceps is an endoparasite ascomycetous genus containing approximately 450 species with a diversity of insect hosts,traditionally included in the family Clavicipitaceae of Ascomycota.Establishing the relationships among species with a varied range of morphologies and hosts is of importance to our understanding of the phylogeny and co-evolution of parasites and hosts in entomopathogenic ascomycetes.To this end,we used a combination of molecular index and morphological characters from 40 representative species to carry out comprehensive molecular phylogenetic analyses.Based on the phylogenetic tree,we used the program DISCRETE for inferring the rates of evolution and finding ancestral states of morphological character.The phylogenetic analyses revealed two important points.(i) Types of perithecia attached to stroma reflected an evolutionary trend in Cordyceps.The vertically immersed perithecia form was the ancestral state,superficial and obliquely immersed perithecia were derived characters,obliquely immersed was irreversible.Species with obliquely immersed perithecia were in a closely related group and were the derived group.(ii) A strong correlation between fungal relatedness and the microhabitat supported the hypothesis that the host jumps through commingling in soil microhabitats.Based on the results of these analyses,host switching explains the diversity of entomopathogenic fungi of the genus Cordyceps.     

Variation and evolutionary trends in the dentition of late pleistocene Mcrotus pennsylvanicus from three levels in bell cave,Alabama

Dental remains of the meadow vole, Microtus pennsylvanicus, were recovered from three superposed day units (zones) and four excavations (pits) in Bell Cave, Alabama. Bone collagen ¹⁴C dates of 26,500 + 480/ ‐ 500 and 11,800 + 480/‐ 500 yr BP. are associated with the bottom and top units, respectively. Length, width, number of closed triangles (five or six), and a measurement to determine the amount of closure of the sixth triangle were taken on the first lower molar (M₁) from the three zones in Pits 1 and 4. Length and width of the third upper molar (M₃) were also determined for the three zones in Pit 4. Analysis of Variance revealed no effect of pit origin or number of triangles on M₁ length or width. A trend from large to small size in M³ is documented, but is not statistically significant The same trend is evidenced by length and width of M₁. Size changes in length and width of M₁ from Pit 4 are statistically significant, but those from Pit 1 are not Although there is no difference in the lengths or widths of five versus six triangle M¹s from any pit or zone, there may be a trend towards increase in isolation of the sixth triangle from the remainder of the anteroconid complex. This trend is statistically significant for zone when ANOVA is performed on the variable, called closure, including both pit and zone origin, but is not significant when teeth from each pit are tested separately. An independent test of the length of M₁ from additional zones in Pits 2 and 3 confirms the low probability that directional size change is due to accidental sorting of fossil materials. These data demonstrate statistically significant intraspecific differences during a 15,000 year period of the late Pleistocene, and also provide evidence of variation that can be expected due to the combined effects of depositional reorganization, sampling and either stochastic processes or selection. The slight dwarfing recorded, while not particularly supportive of any evolutionary mode, may be correlated with climatic modification during the Wisconsinan glacial period. The evolutionary rate of dwarfing, as measured by mean reduction in length of the first lower molar, is 4.47 darwins. Although faster than many rates for fossil vertebrates and invertebrates calculated over longer periods of time, it is probably not unusual for Quaternary mammals during the time interval represented.     

Rates of phenotypic evolution of ecological characters and sexual traits during the Tanganyikan cichlid adaptive radiation

Theory suggests that sexual traits evolve faster than ecological characters. However, characteristics of a species niche may also influence evolution of sexual traits. Hence, a pending question is whether ecological characters and sexual traits present similar tempo and mode of evolution during periods of rapid ecological divergence, such as adaptive radiation. Here, we use recently developed phylogenetic comparative methods to analyse the temporal dynamics of evolution for ecological and sexual traits in Tanganyikan cichlids. Our results indicate that whereas disparity in ecological characters was concentrated early in the radiation, disparity in sexual traits remained high throughout the radiation. Thus, closely related Tanganyikan cichlids presented higher disparity in sexual traits than ecological characters. Sexual traits were also under stronger selection than ecological characters. In sum, our results suggest that ecological characters and sexual traits present distinct evolutionary patterns, and that sexual traits can evolve faster than ecological characters, even during adaptive radiation.     

昆虫比较线粒体基因组学研究进展

动物线粒体基因组因其基因组成稳定、基因排列相对保守、普遍为母系遗传、极少发生重组等而被广泛应用于进化与系统发育等研究。目前,昆虫中已有356个线粒体基因组序列被测定,代表了33个目中的28个目。大量比较基因组学研究使得我们对昆虫线粒体基因组的特征与进化方式有了较为清晰的认识。本文对昆虫线粒体基因组的测序进展、基因组的结构特征、碱基组成、控制区的特征、基因重排及其机理、进化速率及其在昆虫系统发育研究中的应用等方面的研究进展进行介绍。     

Telling the tree: Narrative representation and the study of evolutionary history

Accounts of the evolutionary past have as much in common with works of narrative history as they do with works of science. Awareness of the narrative character of evolutionary writing leads to the discovery of a host of fascinating and hitherto unrecognized problems in the representation of evolutionary history, problems associated with the writing of narrative. These problems include selective attention, narrative perspective, foregrounding and backgrounding, differential resolution, and the establishment of a canon of important events. The narrative aspects of evolutionary writing, however, which promote linearity and cohesiveness in conventional stories, conflict with the underlying chronicle of evolution, which is not linear, but branched, and which does not cohere, but diverges. The impulse to narrate is so great, however, and is so strongly reinforced by traditional schemes of taxonomic attention, that natural historians have more often abandoned the diverging tree than they have abandoned the narrative mode of representation. If we are to understand the true nature of the evolutionary past then we must adopt tree thinking, and develop new and creative ways, both narrative and non-narrative, of telling the history of life.     

Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins

Understanding the determinants of the rate of protein sequenceevolution is of fundamental importance in evolutionary biology.Many recent studies have focused on the yeast because of theavailability of many genome-wide expressional and functionaldata. Yeast studies revealed a predominant role of gene expressionlevel and a minor role of gene essentiality in determining therate of protein sequence evolution. Whether these rules applyto complex organisms such as mammals is unclear. Here we assemblea list of 1,138 essential and 2,341 nonessential mouse genesbased on targeted gene deletion experiments and report a significantimpact of gene essentiality on the rate of mammalian proteinevolution. Gene expression level has virtually no effect, althoughtissue specificity in expression pattern has a strong influence.Unexpectedly, gene compactness, measured by average intron sizeand untranslated region length, has the greatest influence.Hence, the relative importance of the various factors in determiningthe rate of mammalian protein evolution is gene compactness> gene essentiality tissue specificity > expression level.Our results suggest a considerable variation in rate determinantsbetween unicellular organisms such as the yeast and multicellularorganisms such as mammals.     

Exceptional among-lineage variation in diversification rates during the radiation of Australia's most diverse vertebrate clade

The disparity in species richness among groups of organisms is one of the most pervasive features of life on earth. A number of studies have addressed this pattern across higher taxa (e.g. 'beetles'), but we know much less about the generality and causal basis of the variation in diversity within evolutionary radiations at lower taxonomic scales. Here, we address the causes of variation in species richness among major lineages of Australia's most diverse vertebrate radiation, a clade of at least 232 species of scincid lizards. We use new mitochondrial and nuclear intron DNA sequences to test the extent of diversification rate variation in this group. We present an improved likelihood-based method for estimating per-lineage diversification rates from combined phylogenetic and taxonomic (species richness) data, and use the method in a hypothesis-testing framework to localize diversification rate shifts on phylogenetic trees. We soundly reject homogeneity of diversification rates among members of this radiation, and find evidence for a dramatic rate increase in the common ancestor of the genera Ctenotus and Lerista. Our results suggest that the evolution of traits associated with climate tolerance may have had a role in shaping patterns of diversity in this group.     

Accelerated evolution and coevolution drove the evolutionary history of AGPase sub-units during angiosperm radiation

Background and Aims

ADP-glucose pyrophosphorylase (AGPase) is a key enzyme of starch biosynthesis. In the green plant lineage, it is composed of two large (LSU) and two small (SSU) sub-units encoded by paralogous genes, as a consequence of several rounds of duplication. First, our aim was to detect specific patterns of molecular evolution following duplication events and the divergence between monocotyledons and dicotyledons. Secondly, we investigated coevolution between amino acids both within and between sub-units.

Methods

A phylogeny of each AGPase sub-unit was built using all gymnosperm and angiosperm sequences available in databases. Accelerated evolution along specific branches was tested using the ratio of the non-synonymous to the synonymous substitution rate. Coevolution between amino acids was investigated taking into account compensatory changes between co-substitutions.

Key Results

We showed that SSU paralogues evolved under high functional constraints during angiosperm radiation, with a significant level of coevolution between amino acids that participate in SSU major functions. In contrast, in the LSU paralogues, we identified residues under positive selection (1) following the first LSU duplication that gave rise to two paralogues mainly expressed in angiosperm source and sink tissues, respectively; and (2) following the emergence of grass-specific paralogues expressed in the endosperm. Finally, we found coevolution between residues that belong to the interaction domains of both sub-units.

Conclusions

Our results support the view that coevolution among amino acid residues, especially those lying in the interaction domain of each sub-unit, played an important role in AGPase evolution. First, within SSU, coevolution allowed compensating mutations in a highly constrained context. Secondly, the LSU paralogues probably acquired tissue-specific expression and regulatory properties via the coevolution between sub-unit interacting domains. Finally, the pattern we observed during LSU evolution is consistent with repeated sub-functionalization under ‘Escape from Adaptive Conflict’, a model rarely illustrated in the literature.     

Bayesian inference of evolutionary history from chloroplast microsatellites in the cosmopolitan weed Capsella bursa-pastoris (Brassicaceae)

Besides showing an extraordinary degree of phenotypic variability, Capsella bursa-pastoris (Brassicaceae) is also one of the world's most common plant species and a serious weed in many countries. We have employed a coalescent-based Bayesian analysis of chloroplast microsatellite data to infer demographic and evolutionary parameters of this species. Two different demographic models applied to data from seven chloroplast microsatellite loci among 59 accessions show that the effective population size of C. bursa-pastoris is very small indicating a rapid expansion of the species, a result that is in accordance with fossil and historical data. Against this background, analysis of flowering time variation among accessions suggests that ecotypic differentiation in flowering time has occurred recently in the species' history. Finally, our results also indicate that mononucleotide repeat loci in the chloroplast genome can deteriorate in relatively short periods of evolutionary time.     

Diversification in a fluctuating island setting: rapid radiation of Ohomopterus ground beetles in the Japanese Islands

The Japanese Islands have been largely isolated from the East Asian mainland since the Early Pleistocene, allowing the diversification of endemic lineages. Here, we explore speciation rates and historical biogeography of the ground beetles of the subgenus Ohomopterus (genus Carabus) based on nuclear and mitochondrial gene sequences. Ohomopterus diverged into 15 species during the Pleistocene. The speciation rate was 1.92 Ma(-1) and was particularly fast (2.37 Ma(-1)) in a group with highly divergent genitalia. Speciation occurred almost solely within Honshu, the largest island with complex geography. Species diversity is highest in central Honshu, where closely related species occur parapatrically and different-sized species co-occur. Range expansion of some species in the past has resulted in such species assemblages. Introgressive hybridization, at least for mitochondrial DNA, has occurred repeatedly between species in contact, but has not greatly disturbed species distinctness. Small-island populations of some species were separated from main-island populations only after the last glacial (or the last interglacial) period, indicating that island isolation had little role in speciation. Thus, the speciation and formation of the Ohomopterus assemblage occurred despite frequent opportunities for secondary contact and hybridization and the lack of persistent isolation. This radiation was achieved without substantial ecological differentiation, but with marked differentiation in mechanical agents of reproductive isolation (body size and genital morphology).     

Red Queens and ESS: the coevolution of evolutionary rates

Summary The Red Queen principle states that a set of interacting species reaches an evolutionary equilibrium at which all their rates of coevolution exactly balance each other. The lag-load model, which is one way of searching for Red Queens, has, by itself, previously predicted that they do not exist. But this model has assumed that infinite maladaptedness is possible. The lag-load model is improved by assuming that once the lag load of all but one species is determined, so is that of the final species. This assumption eliminates the possibility of infinite maladaptedness. Its result is to allow the lag-load model to yield Red Queen coevolution. It does this whether or not speciation and extinction rates are included. Thus the lag-load model is harmonized with the earlier Red Queen model derived from studies of predation.Because of the intercorrelation of phenotypic traits, the predatory model concluded that the eventual stable rate of coevolution must be zero (except for intermittent bursts after some correlation or compromise is successfully broken). Another model that predicts stable coevolutionary rates of zero is that of evolutionarily stable strategies (ESS).Red Queen assumes that the more extreme a phenotypic trait is, the better it is, and that there are no constraints on the growth of such a phenotypic trait value. Such traits are the key to the Red Queen prediction of progressive coevolution. ESS models make no such assumptions. Eliminating unbounded traits from the model of predator-victim evolution changed its prediction from progressive coevolution to stasis. Before this paper, no model had dealt simultaneously with both unbounded and constrained traits.To handle both sorts of phenotypic traits at the same time in the same model, we abandoned lag load as a measure of evolutionary rate (lag loads do not uniquely determine phenotype). Instead, we used the traditional assumption that rate is proportional to the slope of the adaptive landscape. A model, relying on continuous evolutionary game theory, was developed and simulated under various conditions in two or three species sets, with up to five independent traits coevolving simultaneously. The results were: (1) there was always a set of equilibrium densities eventually achieved by coevolution; if the population interaction represented by this stable coevolutionary state is also stable, then the system should persist whether it evolves further or not; (2) whenever traits were present which were unbounded and best at their most extreme values, then a Red Queen emerged; (3) whenever traits were present which were correlated with each other or constrained below infinity, then an ESS emerged; (4) if both types were present, both results occurred: Red Queen in the unbounded traits and ESS in the constrained ones.Because unbounded traits may not exist, the Red Queen may have no domain. But the domain of ESS is real. ESS should lead to the evolutionary pattern called punctuated equilibrium. The changes in design rules which punctuate stasis should lead to an ever-expanding independence of traits from each other, i.e. to more and more refined differentiation. A single set of design rules which governs a set of species is called a fitness-generating function. Such functions may help to define the concepts of adaptive zone and ecological guild.     

Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: Rapid evolution in warm-blooded vertebrates

Summary By using complete sequence data of mitochondrial DNAs, three Markov models (Day-hoff, Proportional, and Poisson models) for amino acid substitutions during evolution were applied in maximum likelihood analyses of mitochondrially encoded proteins to estimate a phylogenetic tree depicting human, cow, whale, and murids (mouse and rat), with chicken, frog, and carp as outgroups. A cow/whale clade was confirmed with a more than 99.8% confidence level by any of the three models, but the branching order among human, murids, and the cow/whale clade remained uncertain. It turned out that the Dayhoff model is by far the most appropriate model among the alternatives in approximating the amino acid substitutions of mitochondrially encoded proteins, which is consistent with a previous analysis of a more limited data set. It was shown that the substitution rate of mitochondrially encoded proteins has increased in the order of fishes, amphibians, birds, and mammals and that the rate in mammals is at least six times, probably an order of magnitude, higher than that in fishes. The higher evolutionary rate in birds and mammals than in amphibians and fishes was attributed to relaxation of selective constraints operating on proteins in warm-blooded vertebrates and to high mutation rate of bird and mammalian mitochondrial DNAs.Offprint requests to: M. Hasegawa     

Testing the island effect in adaptive radiation: rates and patterns of morphological diversification in Caribbean and mainland Anolis lizards

Many of the classic examples of adaptive radiation, including Caribbean Anolis lizards, are found on islands. However, Anolis also exhibits substantial species richness and ecomorphological disparity on mainland Central and South America. We compared patterns and rates of morphological evolution to investigate whether, in fact, island Anolis are exceptionally diverse relative to their mainland counterparts. Quite the contrary, we found that rates and extent of diversification were comparable--Anolis adaptive radiation is not an island phenomenon. However, mainland and Caribbean anoles occupy different parts of morphological space; in independent colonizations of both island and mainland habitats, island anoles have evolved shorter limbs and better-developed toe pads. These patterns suggest that the two areas are on different evolutionary trajectories. The ecological causes of these differences are unknown, but may relate to differences in predation or competition among mainland and island communities.     

Functional specificity lies within the properties and evolutionary changes of amino acids

The rapid increase in the amount of protein sequence data has created a need for automated identification of sites that determine functional specificity among related subfamilies of proteins. A significant fraction of subfamily specific sites are only marginally conserved, which makes it extremely challenging to detect those amino acid changes that lead to functional diversification. To address this critical problem we developed a method named SPEER (specificity prediction using amino acids' properties, entropy and evolution rate) to distinguish specificity determining sites from others. SPEER encodes the conservation patterns of amino acid types using their physico-chemical properties and the heterogeneity of evolutionary changes between and within the subfamilies. To test the method, we compiled a test set containing 13 protein families with known specificity determining sites. Extensive benchmarking by comparing the performance of SPEER with other specificity site prediction algorithms has shown that it performs better in predicting several categories of subfamily specific sites.     

The influence of environmental factors, the pollen : ovule ratio and seed bank persistence on molecular evolutionary rates in plants

One of the main goals of molecular evolutionary biology is to determine the factors that influence the evolutionary rate of selectively neutral DNA, but much remains unknown, especially for plants. Key factors that could alter the mutation rate include environmental tolerances (because they reflect a plants vulnerability to changes in habitat), the pollen:ovule ratio (as it is associated with the number of mitotic divisions) and seed longevity (because this influences the number of generations per unit time in plants). This is the first study to demonstrate that seed bank persistence and drought tolerance are positively associated with molecular evolutionary rates in plants and that pollen:ovule ratio, shade tolerance and salinity tolerance have no detectable relationship. The implications of the findings to our understanding of the impact of environmental agents, the number of cell divisions and cell aging on neutral DNA sequence evolution are discussed.     

Photosynthesis and associated metabolism during development of a Theobroma cacao hybrid with the lethal factor Luteus-Pa

The recessive lethal character Luteus-Pa, expressed as a yellowing of leaves of young seedlings and followed by death approximately 60 d after emergence, presents a 3:1 segregation in crosses and/or selfpollinated plants. We evaluated quantitatively the fluorescence emission of chlorophyll (Chl), gas exchange, and chemical composition of normal and recessive homozygous cacao seedlings of the cross Pa 121×Pa 169. The characteristics of Chl fluorescence kinetics were studied in stages B2, B3, C, D, and E of leaf development, corresponding to plant ages of 9 to 12, 13 to 15, 16 to 20, 21 to 30, and >30 d, respectively. Gas exchanges were measured in mature leaves of both seedlings. In regular intervals of 3 d beginning at 33 d after emergence, the seedlings were separated into roots, stems, leaves, and cotyledons to determine the contents of saccharides (SAC) and free amino acids (FAA) and variation of the leaf Chl content. The Chl distribution in complexes of the photosynthetic apparatus was analysed by SDS-PAGE in mature leaves of both normal and recessive 32-d-old seedlings. There were variations in Chl fluorescence, gas exchanges and chemical composition of different parts of both types of seedlings. However, no significant differences were found in the Chl distribution through photosynthetic complexes of 32-d-old normal and recessive homozygous seedlings. After that period a decrease in the Chl concentration was observed in the recessive seedlings, and only minimum fluorescence (F0) was found. The F0 values were higher in the recessive seedlings than in the normal ones. The net photosynthetic rate of mature leaves was negative in agreement with low conductance, transpiration rate, and high internal CO2 concentration. These factors might have contributed to a depletion in SAC in different plant parts. Although F0 partially reflects the Chl concentration in leaf tissue, the increase in its value was probably due to a damage in reaction centres of photosystem 2. Therefore, the growth and development of recessive homozygous seedlings depended exclusively on cotyledon reserves, the depletion of which leads to death.     

Sea level and faunal change during the late Wenlock and earliest Ludlow (Silurian): A point of view from the Algerian Sahara

A late Wenlock transgression (C. rigidus zone) affecting a large area of the Algerian Sahara has been known for the last thirty years; in this case there is no break at the Wenlock‐Ludlow boundary and the sedimentation is continuous to the earliest Ludlow. But in many other areas of Sahara a late Wenlock regression is observed. This regression may or may not be followed by a latest Wenlock or an early Ludlow transgression. A sedimentary model is proposed in despite of several problems. In order to compare what happens in each region a schematic diagram is used showing the tendencies to shallowing and deepening. Differences observed between the North Sahara basin and the other parts of the Algerian Sahara and comparison between local sea‐level curves and the global sea‐level curve proposed by Johnson et al. (1991) lead to reconsider the evidence of an eustatic early Ludlow event. To end the problem of the disappearance of nearly all graptolites at the end of Wenlock is discussed. The influence of land emergence in the evolution of marine fossil groups in the disturbance that it can bring to the development of the microplankton and the chemistry of the sea seems to have been too neglected.     

Pollen analysis of the ship site of Pisa San Rossore,Tuscany, Italy: the implications for catastrophic hydrological events and climatic change during the late Holocene

In 1998, an ancient shipping wharf was brought to light in Pisa, Italy. The shipwrecks found there showed human activity from the Etruscan to the late Roman Empire periods. Sandy sediments burying the ships and related materials show four main periods of catastrophic floods separated by thin muddy layers pointing to phases between flooding episodes. Pollen analyses in these fine grained deposits showed: 1) significant percentages of Abies and Fagus during the pre-Roman period; 2) elements of mixed oak woodland together with hygrophilous plants in pollen spectra dominated by herbs, in the Roman interflood deposits. On the whole, the pollen data show a vegetational change which may be attributed to different climatic conditions, supporting the hypothesis that the Roman period was warmer, even though a significant human influence cannot be excluded. Numerous fresh water genera suggest that the area was a poorly drained alluvial plain. Integration between pollen and sedimentological analyses allows some inferences on the dynamics of the warm Roman period and indicates that the warm climate was punctuated by century-scale hydro-climatic crises triggering catastrophic floods. Communicated by J.-L. de Beaulieu