Taxonomic diversification of normal-marine bivalve mollusks in the Phanerozoic

The dynamics of the taxonomic diversification of normal-marine bivalve mollusks and that of the entire fossil marine skeletal fauna are compared. A major Early Permian turnover has been revealed. The changes in the proportions of the bivalve mollusks to the entire marine fauna during the Phanerozoic are studied.     

Parasites and sexual selection: a macroevolutionary perspective.

The Hamilton-Zuk hypothesis postulates a causal link between parasitism and the evolution of epigamic traits by intersexual selection. Oversimplified assumptions about basic parasite biology, ambiguous formulation of the hypothesis, and poor communication between ethologists and parasitologists have hampered its testing. The hypothesis is supported at the microevolutionary level if females show significant preference for lightly or uninfected males, if intensity of infection reflects host resistance to parasites that depress host fitness by causing disease, and if intensity of infection is related to the degree of epigamic development. It must be shown that particular parasites cause disease, that the host population is polymorphic for resistance to infection by those species, and that female hosts are capable of distinguishing male hosts with low parasite loads due to heritable aspects of host resistance from males that are uninfected due to chance. The macroevolutionary prediction of the hypothesis, that species displaying strongly developed epigamic characters should host "more parasites" than species with weakly developed epigamic traits, contradicts the microevolutionary dynamic of the hypothesis, and is too ambiguous. We propose a macroevolutionary prediction based on understanding the evolutionary origin of epigamic traits and the evolutionary origin of each host-parasite association. Associations originating in the ancestor in which the epigamic trait appeared corroborate the hypothesis most strongly; those originating prior to the evolution of the epigamic trait corroborate it weakly; those beginning after the origin of the epigamic trait could not have been involved in the origin and spread of the epigamic trait.     

Coevolution: a history of the macroevolutionary approach to studying host-parasite associations.

The year 1991 marked 100 yr of coevolution research. I have reviewed the first 90 yr of this history. Three chronological phases are apparent: recognition of predictable associations among hosts and their parasites; search for patterns of association and their underlying causes, emphasizing either correlated biogeographic patterns or correlated phylogenies; and development of objective and repeatable methodologies for reconstructing and interpreting these patterns of association. Von Ihering, an outspoken anti-Darwinian, was undoubtedly the first to recognize and make use of predictable host-parasite associations. Kellogg and Fahrenholz, however, had more profound influence on subsequent generations, but in different directions. Kellogg attempted to meld natural selection with speciation by isolation. He also considered host specificity a component of coevolution, important but variable. His work laid the foundation for future research concentrated on biogeographic interpretations of host-parasite relationships. This emphasis and Metcalf's failed attempts to provide adequate mechanisms for reconstructing phylogenies reduced the biogeographic approach to an empirical research program in the hands of Manter. Fahrenholz, on the other hand, exposed to a strong anti-Darwinian sentiment, emphasized the importance of strict host specificity. This led to Eichler's formulation of the first 3 coevolutionary rules and the conclusion that host specificity was not a component but the cause of coevolution and ultimately the tautology inherent in the phylogenetic approach. All had to rely on 1 assumption, that host and parasite phylogenies were reflected in the taxonomic hierarchy. Hennig criticized this assumption and provided a method whereby phylogenies are reconstructed independently. Brooks melded this new phylogenetic method (cladistics) with an equally new biogeographic method (vicariance biogeography), providing the foundations for the modern macroevolutionary approach to studying host-parasite associations.     

Modeling genetic architecture: a multilinear theory of gene interaction

The map from genotype to phenotype is an exceedingly complex function of central importance in biology. In this work we derive and analyze a mathematically tractable model of the genotype-phenotype map that allows for any order of gene interaction. By assuming that the alterations of the effect of a gene substitution due to changes in the genetic background can be described as a linear transformation, we show that the genotype-phenotype map is a sum of linear and multilinear terms of operationally defined "reference" effects at each locus. The "multilinear" model is used to study the effect of epistasis on quantitative genetic variation, on the response to selection, and on genetic canalization. It is shown how the model can be used to estimate the strength of "functional" epistasis from a variety of genetic experiments.     

The effect of a bacteriophage on diversification of the opportunistic bacterial pathogen, Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic human pathogen that colonizes the lungs of cystic fibrosis (CF) patients. CF lungs often contain a diverse range of P. aeruginosa phenotypes, some of which are likely to contribute to the persistence of infection, yet the causes of diversity are unclear. While the ecological heterogeneity of the lung environment and therapeutic regimes are probable factors, a role for parasitic bacteriophage cannot be ruled out. Parasites have been implicated as a key ecological variable driving the evolution of diversity in host populations. PP7 drove cycles of morphological diversification in host populations of P. aeruginosa due to the de novo evolution of small-rough colony variants that coexisted with large diffuse colony morph bacteria. In the absence of phage, bacteria only displayed the large diffuse colony morphology of the wild-type. Further assays revealed there to be two distinct types of resistant bacteria; these had very different ecological phenotypes, yet each carried a cost of resistance.     

Molecular evolution across the Asteraceae: micro- and macroevolutionary processes

The Asteraceae (Compositae) is a large family of over 20,000 wild, weedy, and domesticated species that comprise approximately 10% of all angiosperms, including annual and perennial herbs, shrubs and trees, and species on every continent except Antarctica. As a result, the Asteraceae provide a unique opportunity to understand the evolutionary genomics of lineage radiation and diversification at numerous phylogenetic scales. Using publicly available expressed sequence tags from 22 species representing four of the major Asteraceae lineages, we assessed neutral and nonneutral evolutionary processes across this diverse plant family. We used bioinformatic tools to identify candidate genes under selection in each species. Evolution at silent and coding sites were assessed for different Gene Ontology functional categories to compare rates of evolution over both short and long evolutionary timescales. Our results indicate that patterns of molecular change across the family are surprisingly consistent on a macroevolutionary timescale and much more so more than would be predicted from the analysis of one (or many) examples of microevolution. These analyses also point to particular classes of genes that may be crucial in shaping the radiation of this diverse plant family. Similar analyses of nuclear and chloroplast genes in six other plant families confirm that many of these patterns are common features of the plant kingdom.     

Modeling the temperature effect on the specific growth rate of phytoplankton: a review

Phytoplankton are key components of ecosystems. Their growth is deeply influenced by temperature. In a context of global change, it is important to precisely estimate the impact of temperature on these organisms at different spatial and temporal scales. Here, we review the existing deterministic models used to represent the effect of temperature on microbial growth that can be applied to phytoplankton. We first describe and provide a brief mathematical analysis of the models used in constant conditions to reproduce the thermal growth curve. We present the mechanistic assumptions concerning the effect of temperature on the cell growth and mortality, and discuss their limits. The coupling effect of temperature and other environmental factors such as light are then shown. Finally, we introduce the models taking into account the acclimation needed to thrive with temperature variations. The need for new thermal models, coupled with experimental validation, is argued.     

Historical diversification of a terra-firme forest bird superspecies: a phylogeographic perspective on the role of different hypotheses of Amazonian diversification

Among those few hypotheses of Amazonian diversification amenable to falsification by phylogenetic and population genetics methods, three can be singled out because of their general application to vertebrates: the riverine barrier, the refuge, and the Miocene marine incursion hypotheses. I used phylogenetic and population genetics methods to reconstruct the diversification history of the upland (terra-firme) forest superspecies Xiphorhynchus spixii/elegans (Aves: Dendrocolaptidae) in Amazonia, and to evaluate predictions of the riverine barrier, refuge, and Miocene marine incursion hypotheses. Phylogeographic and population genetics analyses of the X. spixiilelegans superspecies indicated that the main prediction of the riverine barrier hypothesis (that sister lineages occur across major rivers) hold only for populations separated by "clear-water" rivers located on the Brazilian shield, in central and eastern Amazonia; in contrast, "white-water" rivers located in western Amazonia did not represent areas of primary divergence for populations of this superspecies. The main prediction derived from the refuge hypothesis (that populations of the X. spixii/elegans superspecies would show signs of past population bottlenecks and recent demographic expansions) was supported only for populations found in western Amazonia, where paleoecological data have failed to support past rainforest fragmentation and expansion of open vegetation types; conversely, populations from the eastern and central parts of Amazonia, where paleoecological data are consistent with an historical interplay between rainforest and open vegetation types, did not show population genetics attributes expected under the refuge hypothesis. Phylogeographic and population genetics data were consistent with the prediction made by the Miocene marine incursion hypothesis that populations of the X. spixii/elegans superspecies found on the Brazilian shield were older than populations from other parts of Amazonia. In contrast, the phylogeny obtained for lineages of this superspecies falsified the predicted monophyly of Brazilian shield populations, as postulated by the Miocene marine incursion hypothesis. In general, important predictions of both riverine barrier and Miocene marine incursion hypotheses were supported, indicating that they are not mutually exclusive; in fact, the data presented herein suggest that an interaction among geology, sea level changes, and hydrography created opportunities for cladogenesis in the X. spixii/elegans superspecies at different temporal and geographical scales.     

Processes generating macroevolutionary patterns of morphological variation in birds: a simulation study

Multivariate patterns of morphological variation in birds are analysed. In general, there are strong allometric patterns among characters such that most of the variation is confined to a major “size” axis. To analyse the possible evolutionary processes behind this pattern I employed a computer simulation of cladogenesis and anagenesis based on a genetic and a random walk model (drift). All runs started with one species and speciation occurred to generate 100 species. Three levels of correlations were allowed. The results from the simulations were compared with the pattern of variation in finches (Fringillidae). The simulations showed two things. First, the univariate drift model was inappropriate in terms of the level of variation; the observed level was lower than expected by drift. Univariate drift was also unable to create tight correlations among characters as observed in several taxa. Second, to create the pattern observed, either relatively strong genetic correlations (r_g ≈ 0.5), or alternatively strong correlated selection, was needed. This suggests that morphological change in birds in general consists of changes in growth such that species become larger or smaller than their ancestors but retain their ancestral shape. The results stress the importance of stabilising selection in shaping the macroevolutionary patterns of morphological variation in birds.     

Microevolutionary dynamics of a macroevolutionary key innovation in a Lepidopteran herbivore

Background  

A molecular population genetics understanding is central to the study of ecological and evolutionary functional genomics. Population genetics identifies genetic variation and its distribution within and among populations, it reveals the demographic history of the populations studied, and can provide indirect insights into historical selection dynamics. Here we use this approach to examine the demographic and selective dynamics acting of a candidate gene involved in plant-insect interactions. Previous work documents the macroevolutionary and historical ecological importance of the nitrile-specifier protein (Nsp), which facilitated the host shift of Pieridae butterflies onto Brassicales host plants ~80 Myr ago.     

Rhabdoviruses and the cellular ubiquitin-proteasome system: a budding interaction

The matrix (M) proteins of vesicular stomatitis virus (VSV) and rabies virus (RV) play a key role in both assembly and budding of progeny virions. A PPPY motif (PY motif or late-budding domain) is conserved in the M proteins of VSV and RV. These PY motifs are important for virus budding and for mediating interactions with specific cellular proteins containing WW domains. The PY motif and flanking sequences of the M protein of VSV were used as bait to screen a mouse embryo cDNA library for cellular interactors. The mouse Nedd4 protein, a membrane-localized ubiquitin ligase containing multiple WW domains, was identified from this screen. Ubiquitin ligase Rsp5, the yeast homolog of Nedd4, was able to interact both physically and functionally with full-length VSV M protein in a PY-dependent manner. Indeed, the VSV M protein was multiubiquitinated by Rsp5 in an in vitro ubiquitination assay. To demonstrate further that ubiquitin may be involved in the budding process of rhabdoviruses, proteasome inhibitors (e.g., MG132) were used to decrease the level of free ubiquitin in VSV- and RV-infected cells. Viral titers measured from MG132-treated cells were reproducibly 10- to 20-fold lower than those measured from untreated control cells, suggesting that free ubiquitin is important for efficient virus budding. Last, release of a VSV PY mutant was not inhibited in the presence of MG132, signifying that the functional L domain of VSV is required for the inhibitory effect exhibited by MG132. These data suggest that the cellular ubiquitin-proteasome machinery is involved in the budding process of VSV and RV.     

Allometric space and allometric disparity: a developmental perspective in the macroevolutionary analysis of morphological disparity

Here, we advance novel uses of allometric spaces--multidimensional spaces specifically defined by allometric coefficients--with the goal of investigating the focal role of development in shaping the evolution of morphological disparity. From their examination, operational measures of allometric disparity can be derived, complementing standard signals of morphological disparity through an intuitive and process-oriented refinement of established analytical protocols used in disparity studies. Allometric spaces thereby become a promising context to reveal different patterns of evolutionary developmental changes and to assess their relative prevalence and importance. Such spaces offer a novel domain of investigation of phenotypic variation and should help in detecting large-scale trends, thus placing various macroevolutionary phenomena in an explicitly developmental context. Ammonoidea (Cephalopoda) at the Lower-Middle Jurassic transition were chosen as a case study to illustrate this methodological approach. We constructed two phenotypic spaces: a static, adult one (adult morphospace) and a dynamic, developmental one (allometric space). Comparative disparity analyses show a strikingly stable occupation in both spaces, despite extensive change in taxonomic composition. In contrast, disparity analyses of subclades reveal clearly distinct morphological and allometric disparity dynamics. Allometric approaches allow developmental insights into morphological diversification otherwise intractable from the analysis of adult morphospace alone.     

Modeling the effect of sleep regulation on a neural mass model

In mammals, sleep is categorized by two main sleep stages, rapid eye movement (REM) and non-REM (NREM) sleep that are known to fulfill different functional roles, the most notable being the consolidation of memory. While REM sleep is characterized by brain activity similar to wakefulness, the EEG activity changes drastically with the emergence of K-complexes, sleep spindles and slow oscillations during NREM sleep. These changes are regulated by circadian and ultradian rhythms, which emerge from an intricate interplay between multiple neuronal populations in the brainstem, forebrain and hypothalamus and the resulting varying levels of neuromodulators. Recently, there has been progress in the understanding of those rhythms both from a physiological as well as theoretical perspective. However, how these neuromodulators affect the generation of the different EEG patterns and their temporal dynamics is poorly understood. Here, we build upon previous work on a neural mass model of the sleeping cortex and investigate the effect of those neuromodulators on the dynamics of the cortex and the corresponding transition between wakefulness and the different sleep stages. We show that our simplified model is sufficient to generate the essential features of human EEG over a full day. This approach builds a bridge between sleep regulatory networks and EEG generating neural mass models and provides a valuable tool for model validation.     

megB1, a novel macroevolutionary genomic marker of the fungal phylum Basidiomycota

Molecular studies on the evolution and systematics of fungi have been established primarily based on the neutral theory by analyzing neutral mutations in some defined segments of housekeeping genes as genetic markers. Such an approach is, however, hardly applicable for analyzing ancient evolutionary radiations. In the present study, we looked for DNA sequences characterizing higher taxa, and discovered a unique macroevolutionary genomic marker, megB1, that specifies the phylum Basidiomycota. megB1 is an approximately 500-bp DNA element, which is defined by terminal sequences and five internal segments conserved throughout the phylum. megB1 resides on the rDNA intergenic spacer 1 (IGS1) from 27 species of 10 Basidiomycota genera examined. While megB1 was not found in IGS1 from the other 92 species of the 27 Basidiomycota genera, several genera representing them carry megB1 in some other genomic regions. No known taxonomic criteria fit into the classification on the basis of whether megB1 resides on rDNA. Neighbor-joining analysis of the megB1 sequence, however, properly assigned species to their respective genera. Thus far, megB1 has not been found in any genomic or genetic databases currently available for other phyla. These results suggest that megB1 may have emerged upon the occurrence of Basidiomycota, and that this phylum evolved thereafter leaving this element conserved throughout their further differentiation. megB1 may be a novel genomic marker useful in the analysis of ancient through the latest evolutionary radiation in Basidiomycota.     

The theory of increasing autonomy in evolution: a proposal for understanding macroevolutionary innovations

Attempts to explain the origin of macroevolutionary innovations have been only partially successful. Here it is proposed that the patterns of major evolutionary transitions have to be understood first, before it is possible to further analyse the forces behind the process. The hypothesis is that major evolutionary innovations are characterized by an increase in organismal autonomy, in the sense of emancipation from the environment. After a brief overview of the literature on this subject, increasing autonomy is defined as the evolutionary shift in the individual system–environment relationship, such that the direct influences of the environment are gradually reduced and a stabilization of self-referential, intrinsic functions within the system is generated. This is described as relative autonomy because numerous interconnections with the environment and dependencies upon it are retained. Features of increasing autonomy are spatial separations, an increase in homeostatic functions and in body size, internalizations and an increase in physiological and behavioral flexibility. It is described how these features are present in different combinations in the major evolutionary transitions of metazoans and, consequently, how they should be taken into consideration when evolutionary innovations are studied. The hypothesis contributes to a reconsideration of the relationship between organisms and their environment.     

Biotic diversification in the Guayana Highlands: a proposal

Until recently, the high degree of diversity and endemism of the Guayana Highlands was explained within the frame of the refuge theory. Although this hypothesis is unsupported by recent palaeoecological evidence, no new diversification model has been proposed. This paper is a proposal based on the latest palynological findings that indicate a downward biotic migration of c. 1100 m altitude during glacials, and the subsequent interglacial upward shift, in response to colder and warmer climates, respectively. Therefore, during glacials, biotic mixing is expected in the lowlands, thus promoting sympatric speciation, hybridization and polyploidy. At the mountaintops, unknown cold‐adapted taxa and páramo‐like(?) communities are expected to have occurred, and vicariance prevailed. In the interglacials, many taxa have had the opportunity for ascending to the mountains again, allowing genetic interchange among their slopes and summits, while others would have been adapted to lowlands. The interglacial highland communities, where vicariance still predominated, experienced some extinction owing to habitat loss by upland displacement. According to this model, the successive alternation of glacials and interglacials resulted in a net increase of diversity and endemism, favoured by the complex topography and habitat heterogeneity, which allowed high niche diversification. This model has some similarities with the Andean and Amazon modes of diversification, but the special topographical characteristics of the Guayana region made it different in other fundamental aspects. The Guayana Highlands would have acted as a ‘biodiversity pump’ for the surrounding inner and coastal lowlands, due to the repeated speciation and further spreading events, as a response to climate. Several working hypotheses are suggested in relation to the proposed model. The use of coordinated international multiproxy projects combining palaeoecology and genetic analysis of modern taxa is strongly encouraged for exploring these ideas.     

Correction to: Reef-associated fishes have more maneuverable body shapes at a macroevolutionary scale

Coral Reefs - This erratum has been initiated as several formatting errors were overlooked during proofing stage by vendor.     

The fossil record and macroevolutionary history of the beetles

Coleoptera (beetles) is the most species-rich metazoan order, with approximately 380 000 species. To understand how they came to be such a diverse group, we compile a database of global fossil beetle occurrences to study their macroevolutionary history. Our database includes 5553 beetle occurrences from 221 fossil localities. Amber and lacustrine deposits preserve most of the beetle diversity and abundance. All four extant suborders are found in the fossil record, with 69% of all beetle families and 63% of extant beetle families preserved. Considerable focus has been placed on beetle diversification overall, however, for much of their evolutionary history it is the clade Polyphaga that is most responsible for their taxonomic richness. Polyphaga had an increase in diversification rate in the Early Cretaceous, but instead of being due to the radiation of the angiosperms, this was probably due to the first occurrences of beetle-bearing amber deposits in the record. Perhaps, most significant is that polyphagan beetles had a family-level extinction rate of zero for most of their evolutionary history, including across the Cretaceous–Palaeogene boundary. Therefore, focusing on the factors that have inhibited beetle extinction, as opposed to solely studying mechanisms that may promote speciation, should be examined as important determinants of their great diversity today.