Character displacement in some Cnemidophorus lizards revisited: A phylogenetic analysis

Ecological studies have demonstrated the role of competition in structuring communities; however, the importance of competition as a vehicle for evolution by natural selection and speciation remains unresolved. Study systems of insular faunas have provided several well known cases where ecological character displacement, coevolution of competitors leading to increased morphological separation, is thought to have occurred (e.g., anoline lizards and geospizine finches). Whiptail lizards (genus Cnemidophorus) from the islands of the Sea of Cortez and the surrounding mainland demonstrate a biogeographic pattern of morphological variation suggestive of character displacement. Two species of Cnemidophorus occur on the Baja peninsula, one relatively large (Cnemidophorus tigris) and one smaller (Cnemidophorus hyperythrus). Oceanic islands in the Sea of Cortez contain only single species, five of six having sizes intermediate to both species found on the Baja peninsula. On mainland Mexico C. hyperythrus is absent, whereas C. tigris is the smaller species in whiptail guilds. Here we construct a phylogeny using nucleotide sequences of the cytochrome b gene to infer the evolutionary history of body size change and historical patterns of colonization in the Cnemidophorus system. The phylogenetic analysis indicates that (i) oceanic islands have been founded at least five times from mainland sources by relatives of either C. tigris or C. hyperythrus, (ii) there have been two separate instances of character relaxation on oceanic islands for C. tigris, and (iii) there has been colonization of the oceanic island Cerralvo with retention of ancestral size for Cnemidophorus ceralbensis, a relative of C. hyperythrus. Finally, the phylogenetic analysis reveals potential cryptic species within mainland populations of C. tigris.

Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences

Homobasidiomycete fungi display many complex fruiting body morphologies, including mushrooms and puffballs, but their anatomical simplicity has confounded efforts to understand the evolution of these forms. We performed a comprehensive phylogenetic analysis of homobasidiomycetes, using sequences from nuclear and mitochondrial ribosomal DNA, with an emphasis on understanding evolutionary relationships of gilled mushrooms and puffballs. Parsimony-based optimization of character states on our phylogenetic trees suggested that strikingly similar gilled mushrooms evolved at least six times, from morphologically diverse precursors. Approximately 87% of gilled mushrooms are in a single lineage, which we call the “euagarics.” Recently discovered 90 million-year-old fossil mushrooms are probably euagarics, suggesting that (i) the origin of this clade must have occurred no later than the mid-Cretaceous and (ii) the gilled mushroom morphology has been maintained in certain lineages for tens of millions of years. Puffballs and other forms with enclosed spore-bearing structures (Gasteromycetes) evolved at least four times. Derivation of Gasteromycetes from forms with exposed spore-bearing structures (Hymenomycetes) is correlated with repeated loss of forcible spore discharge (ballistospory). Diverse fruiting body forms and spore dispersal mechanisms have evolved among Gasteromycetes. Nevertheless, it appears that Hymenomycetes have never been secondarily derived from Gasteromycetes, which suggests that the loss of ballistospory has constrained evolution in these lineages.

Positive selection and rates of evolution in immunodeficiency viruses from humans and chimpanzees.

Evolutionary theory predicts the recent spread of primate immunodeficiency viruses (PIVs) to new human populations to be accompanied by positive selection in response to new host environments and/or by random genetic drift. I assess evidence for positive selection in human and chimpanzee PIVs type I (PIV1s), using ratios of synonymous to nonsynonymous nucleotide change based on branch lengths and outgroup rooting. Ratios are smaller for PIV1s from humans than for PIV1 from a chimpanzee for the pol, gag, and env glycoprotein 120 (gp120) regions, indicating greater effects of positive selection in PIV1s from humans. Parsimony-based relative rate tests for amino acid changes showed significant differences between PIV1s from humans and chimpanzees in 18 of 48 pairwise comparisons, with all 18 showing faster rates of change in PIV1s from humans. This study indicates that in some instances, the recent evolution of human PIV1s follows a speciational pattern, in which increased diversification of taxa is correlated with greater amounts of character change appearing and being maintained through time. This extends the generality of the speciational pattern to a group of organisms (viruses) having the fastest known rates of anagenetic change for nucleotide characters and indicates that comprehensive understanding of PIV1 evolution requires consideration of both anagenetic change within viral lineages and the relative historical success of different viral clades. Phylogenetic analyses show that neither PIV1s infecting humans nor those infecting chimpanzees represent monophyletic groups and suggest multiple host-species shifts for PIV1s.

A new code for the Hall-driven magnetic evolution of neutron stars

Over the past decade, the numerical modeling of the magnetic field evolution in astrophysical scenarios has become an increasingly important field. In the crystallized crust of neutron stars the evolution of the magnetic field is governed by the Hall induction equation. In this equation the relative contribution of the two terms (Hall term and Ohmic dissipation) varies depending on the local conditions of temperature and magnetic field strength. This results in the transition from the purely parabolic character of the equations to the hyperbolic regime as the magnetic Reynolds number increases, which presents severe numerical problems. Up to now, most attempts to study this problem were based on spectral methods, but they failed in representing the transition to large magnetic Reynolds numbers. We present a new code based on upwind finite differences techniques that can handle situations with arbitrary low magnetic diffusivity and it is suitable for studying the formation of sharp current sheets during the evolution. The code is thoroughly tested in different limits and used to illustrate the evolution of the crustal magnetic field in a neutron star in some representative cases. Our code, coupled to cooling codes, can be used to perform long-term simulations of the magneto-thermal evolution of neutron stars.

Overdeepened glacial basins as archives for the Quaternary landscape evolution of the Alps

The Alps and the Alpine foreland have been shaped by repeated glaciations during Quaternary glacial-interglacial cycles. Extent, timing and impact on landscape evolution of these glaciations are, however, poorly constrained due to the fragmentary character of terrestrial archives. In this context, the sedimentary infills of subglacially eroded, ‘overdeepened’, basins may serve as important archives to complement the Quaternary stratigraphy over several glacial-interglacial cycles. In this thesis, the infills of deep subglacial basins in the Lower Glatt valley (N Switzerland) are explored to better constrain the Middle- to Late Pleistocene environmental change. Five drill cores gave direct insight into to the up to ~200 m thick valley fill at the study site and allowed for detailed analysis of sedimentary facies, age and architecture of the basin fills. A first focus is set on the sedimentology of coarse-grained diamicts with sorted interbeds overlying bedrock in the trough center, which mark the onset of deposition in many glacial bedrock troughs. Evidence from macro- and microsedimentology suggests that these sediments are emplaced subglacially and reflect deposition, reworking and deformation in response to repeated coupling and decoupling of the ice-bed interface promoted by high basal water pressures. Overlying these subglacial sediments, large volumes of sandy glacio-deltaic, fine-grained glacio-lacustrine and lacustrine sediments document sedimentation during glacier retreat from the basins. On these thick valley fill sequences the applicability and reliability of luminescence dating is investigated in a second step on the basis of experiments with several different luminescence signals, protocols and experiments to assess the signal stability. The valley fill of the Lower Glatt valley is then grouped into nine depositional cycles (Formations A-I), which are related to the Birrfeld Glaciation (~MIS2), the Beringen Glaciation (~MIS6), and up to three earlier Middle Pleistocene glaciations, tentatively correlated to the Hagenholz, Habsburg, and Möhlin Glaciations, according to the regional glaciation history. The complex bedrock geometry and valley fill architecture are shown to be the result of multiple erosion and infilling cycles and reflect the interplay of subglacial erosion, glacial to lacustrine infilling of overdeepened basins, and fluvial down-cutting and aggradation in the non-overdeepened valley fill. Evidence suggests that in the study area deep bedrock incision, and/or partial re-excavation, occurred mainly during the Beringen and Hagenholz Glaciation, while older structures may have existed. Together with the observation of minor, ‘inlaid’ glacial basins, dynamic changes in the magnitude and focus of subglacial erosion over time are documented.

The problem of creation, an attempt to define the character and trend of the cosmic process,

pt. 1. Fundamental concepts.--pt. 2. Evolution and creation.--pt. 3. Physical facts.--pt. 4. Life and mind.--pt.5. Moral and spiritual facts.--Appendix A. The new physics.--Appendix B. Matter and energy.--Appendix C. Conservation of mass.--Appendix D. Conservation of energy.

A refined solution to Earth's hidden niobium: implications for evolution of continental crust and mode of core formation

New high-precision niobium (Nb) and tantalum (Ta) concentration data are presented for early Archaean metabasalts, metabasaltic komatiites and their erosion products (mafic metapelites) from SW Greenland and the Acasta gneiss complex, Canada. Individual datasets consistently show sub-chondritic Nb/Ta ratios averaging 15.1+/-11.6. This finding is discussed with regard to two competing models for the solution of the Nb-deficit that characterises the accessible Earth. Firstly, we test whether Nb could have sequestered into the core due to its slightly siderophile (or chalcophile) character under very reducing conditions, as recently proposed from experimental evidence. We demonstrate that troilite inclusions of the Canyon Diablo iron meteorite have Nb and V concentrations in excess of typical chondrites but that the metal phase of the Grant, Toluca and Canyon Diablo iron meteorites do not have significant concentrations of these lithophile elements. We find that if the entire accessible Earth Nb-deficit were explained by Nb in the core, only ca. 17% of the mantle could be depleted and that by 3.7 Ga, continental crust would have already achieved ca. 50% of its present mass. Nb/Ta systematics of late Archaean metabasalts compiled from the literature would further require that by 2.5 Ga, 90% of the present mass of continental crust was already in existence. As an alternative to this explanation, we propose that the average Nb/Ta ratio (15.1+/-11.6) of Earth's oldest mafic rocks is a valid approximation for bulk silicate Earth. This would require that ca. 13% of the terrestrial Nb resided in the Ta-free core. Since the partitioning of Nb between silicate and metal melts depends largely on oxygen fugacity and pressure, this finding could mean that metal/silicate segregation did not occur at the base of a deep magma ocean or that the early mantle was slightly less reducing than generally assumed. A bulk silicate Earth Nb/Ta ratio of 15.1 allows for depletion of up to 40% of the total mantle. This could indicate that in addition to the upper mantle, a portion of the lower mantle is depleted also, or if only the upper mantle were depleted, an additional hidden high Nb/Ta reservoir must exist. Comparison of Nb/Ta systematics between early and late Archaean metabasalts supports the latter idea and indicates deeply subducted high Nb/Ta eclogite slabs could reside in the mantle transition zone or the lower mantle. Accumulation of such slabs appears to have commenced between 2.5 and 2.0 Ga. Regardless of these complexities of terrestrial Nb/Ta systematics, it is shown that the depleted mantle Nb/Th ratio is a very robust proxy for the amount of extracted continental crust, because the temporal evolution of this ratio is dominated by Th-loss to the continents and not Nb-retention in the mantle. We present a new parameterisation of the continental crust volume versus age curve that specifically explores the possibility of lithophile element loss to the core and storage of eclogite slabs in the transition zone. (C) 2003 Elsevier Science B.V. All rights reserved.

Parallel evolution of sexual isolation in sticklebacks

Mechanisms of speciation are not well understood, despite decades of study. Recent work has focused on how natural and sexual selection cause sexual isolation. Here, we investigate the roles of divergent natural and sexual selection in the evolution of sexual isolation between sympatric species of threespine sticklebacks. We test the importance of morphological and behavioral traits in conferring sexual isolation and examine to what extent these traits have diverged in parallel between multiple, independently evolved species pairs. We use the patterns of evolution in ecological and mating traits to infer the likely nature of selection on sexual isolation. Strong parallel evolution implicates ecologically based divergent natural and/or sexual selection, whereas arbitrary directionality implicates nonecological sexual selection or drift. In multiple pairs we find that sexual isolation arises in the same way: assortative mating on body size and asymmetric isolation due to male nuptial color. Body size and color have diverged in a strongly parallel manner, similar to ecological traits. The data implicate ecologically based divergent natural and sexual selection as engines of speciation in this group.

Animal visual systems and the evolution of color patterns: Sensory processing illuminates signal evolution

Animal color pattern phenotypes evolve rapidly. What influences their evolution? Because color patterns are used in communication, selection for signal efficacy, relative to the intended receiver's visual system, may explain and predict the direction of evolution. We investigated this in bowerbirds, whose color patterns consist of plumage, bower structure, and ornaments and whose visual displays are presented under predictable visual conditions. We used data on avian vision, environmental conditions, color pattern properties, and an estimate of the bowerbird phylogeny to test hypotheses about evolutionary effects of visual processing. Different components of the color pattern evolve differently. Plumage sexual dimorphism increased and then decreased, while overall (plumage plus bower) visual contrast increased. The use of bowers allows relative crypsis of the bird but increased efficacy of the signal as a whole. Ornaments do not elaborate existing plumage features but instead are innovations (new color schemes) that increase signal efficacy. Isolation between species could be facilitated by plumage but not ornaments, because we observed character displacement only in plumage. Bowerbird color pattern evolution is at least partially predictable from the function of the visual system and from knowledge of different functions of different components of the color patterns. This provides clues to how more constrained visual signaling systems may evolve.

The European Patterns of "Homo Academicus“ and The Chances of Its Evolution In Current Hungarian Higher Education

In the recent four or five years, there have been abrupt and radical changes in the governance of Hungarian higher education. It can then be interesting to assess the state of “homo academicus“ as it looks currently in Hungary. The notion of “homo academicus“ is obvious: it concerns participants in the system of a country’s higher education. The paper as follows still comes back to the definition of “homo academicus“ by referring first to it as occupation, or rather as a profession that can be interpreted in terms of sociology. Secondly, some historic patterns can also be mobilised, based on the assumption that university is a very European institutions that is even rooted in the tradition of the Middle Ages. The elbow-room of seeking for identity and the role to be filled by academics are limited by the effective system of the governance of higher education. It is a key to the chances of academics of meeting the historically corroborated professional standards that they exercise academic freedom. As it cannot be done individually, but in cooperation (through a collegial system), academic freedom is always combined with collective action. The field where this freedom can be exercised can be specified through university autonomy, the lack of which makes a serious barrier to the full development of a character of “homo academicus“. This is now the case in Hungary, the paper suggests. The paper seeks to gain deeper understanding of the character of academics, their vocation and professional roles, and the governance of higher education, serving as the environment for academic activity, by creating a conceptual framework. The paper is established on the results of sociological research and the experience of legal management, although it remains to be of theoretical nature. It criticises the current Hungarian situation of the governance of higher education, arguing for the reconstruction of university autonomy and financial stability. It also emphasises the importance of predictable regulations.

Origin, colonization, adaptive radiation, intrainsular evolution snd species substitution processes in the fossil and living lizards of the Canary Islands

[EN] The Canary lsland lizards constitute a monophyletic group which separated from the rest of the family shortly after the first islands of the archipelago emerged. Five living and at least one recently extinct species belong to the genus Gallotia. In addition, two of the living species, Gallotia simonyi and Gallotia stehlini have become extinct on Gomera and Tenerife, respectively. Juveniles of all species present tricuspid teeth. This character is preserved in the adults with changes to one degree or another in G. galloti, G. caesaris, G. simonyi and G. goliath. In G. atlantica there are only two cuspids and G. stehlini has 4 or more.

Selection and Floral Evolution in Platanthera bifolia and P. chlorantha (Orchidaceae)

Natural selection mediated by pollinators has influenced the evolution of floral diversity of the flowering plants (angiosperms). The scope of this thesis was to study: 1) phenotypic selection, 2) mating systems, and 3) floral shifts involved in plant speciation. Model plant species were Platanthera bifolia and P. chlorantha (Orchidaceae). These orchids are moth-pollinated, strictly co-sexual (bisexual flowers), and produce a spike that displays 10-20 white flowers. I explored the influence of characters on plant fitness by using multiple linear regressions. Pollen removal (male fitness) and fruit set (female fitness) increased with more flowers per plant in three P. bifolia populations. There was selection towards longer spurs in a dry year when average spur length was shorter than in normal-wet years. Female function was sensitive to drought, which enabled an application of the male function hypothesis of floral evolution (Bateman's principle). The results show that selection may vary between populations, years, and sex-functions. I examined inbreeding by estimating levels of geitonogamy (self-pollination between flowers of an individual) with an emasculation method in two P. bifolia populations. Geitonogamy did not vary with inflorescence size. Levels of geitonogamy was 20-40% in the smaller, but non-significant in the larger population. This may relate to lower number of possible mates and pollinator activity in the smaller population. Platanthera bifolia exhibits the ancestral character state of tongue-attachment of pollinia on the pollinator. Its close relative P. chlorantha attaches its pollinia onto the pollinator's eyes. To explore the mechanism of a floral shift, pollination efficiency and speed was compared between the two species. The results showed no differences in pollination efficiency, but P. chlorantha had faster pollen export and import. Efficiency of pollination in terms of speed may cause floral shifts, and thus speciation.

Information and the evolution of codon bias

The informational properties of biological systems are the subject of much debate and research. I present a general argument in favor of the existence and central importance of information in organisms, followed by a case study of the genetic code (specifically, codon bias) and the translation system from the perspective of information. The codon biases of 831 Bacteria and Archeae are analyzed and modeled as points in a 64-dimensional statistical space. The major results are that (1) codon bias evolution does not follow canonical patterns, and (2) the use of coding space in organsims is a subset of the total possible coding space. These findings imply that codon bias is a unique adaptive mechanism that owes its existence to organisms' use of information in representing genes, and that there is a particularly biological character to the resulting biased coding and information use.

Prognostic Value Of Dna And Mrna E6/e7 Of Human Papillomavirus In The Evolution Of Cervical Intraepithelial Neoplasia Grade 2.

This study aimed at evaluating whether human papillomavirus (HPV) groups and E6/E7 mRNA of HPV 16, 18, 31, 33, and 45 are prognostic of cervical intraepithelial neoplasia (CIN) 2 outcome in women with a cervical smear showing a low-grade squamous intraepithelial lesion (LSIL). This cohort study included women with biopsy-confirmed CIN 2 who were followed up for 12 months, with cervical smear and colposcopy performed every three months. Women with a negative or low-risk HPV status showed 100% CIN 2 regression. The CIN 2 regression rates at the 12-month follow-up were 69.4% for women with alpha-9 HPV versus 91.7% for other HPV species or HPV-negative status (P < 0.05). For women with HPV 16, the CIN 2 regression rate at the 12-month follow-up was 61.4% versus 89.5% for other HPV types or HPV-negative status (P < 0.05). The CIN 2 regression rate was 68.3% for women who tested positive for HPV E6/E7 mRNA versus 82.0% for the negative results, but this difference was not statistically significant. The expectant management for women with biopsy-confirmed CIN 2 and previous cytological tests showing LSIL exhibited a very high rate of spontaneous regression. HPV 16 is associated with a higher CIN 2 progression rate than other HPV infections. HPV E6/E7 mRNA is not a prognostic marker of the CIN 2 clinical outcome, although this analysis cannot be considered conclusive. Given the small sample size, this study could be considered a pilot for future larger studies on the role of predictive markers of CIN 2 evolution.

Effects Of Therapeutic Approach On The Neonatal Evolution Of Very Low Birth Weight Infants With Patent Ductus Arteriosus.

To analyze the effects of treatment approach on the outcomes of newborns (birth weight [BW] < 1,000 g) with patent ductus arteriosus (PDA), from the Brazilian Neonatal Research Network (BNRN) on: death, bronchopulmonary dysplasia (BPD), severe intraventricular hemorrhage (IVH III/IV), retinopathy of prematurity requiring surgical (ROPsur), necrotizing enterocolitis requiring surgery (NECsur), and death/BPD. This was a multicentric, cohort study, retrospective data collection, including newborns (BW < 1000 g) with gestational age (GA) < 33 weeks and echocardiographic diagnosis of PDA, from 16 neonatal units of the BNRN from January 1, 2010 to Dec 31, 2011. Newborns who died or were transferred until the third day of life, and those with presence of congenital malformation or infection were excluded. Groups: G1 - conservative approach (without treatment), G2 - pharmacologic (indomethacin or ibuprofen), G3 - surgical ligation (independent of previous treatment). Factors analyzed: antenatal corticosteroid, cesarean section, BW, GA, 5 min. Apgar score < 4, male gender, Score for Neonatal Acute Physiology Perinatal Extension (SNAPPE II), respiratory distress syndrome (RDS), late sepsis (LS), mechanical ventilation (MV), surfactant (< 2 h of life), and time of MV. death, O2 dependence at 36 weeks (BPD36wks), IVH III/IV, ROPsur, NECsur, and death/BPD36wks. Student's t-test, chi-squared test, or Fisher's exact test; Odds ratio (95% CI); logistic binary regression and backward stepwise multiple regression. Software: MedCalc (Medical Calculator) software, version 12.1.4.0. p-values < 0.05 were considered statistically significant. 1,097 newborns were selected and 494 newborns were included: G1 - 187 (37.8%), G2 - 205 (41.5%), and G3 - 102 (20.6%). The highest mortality was observed in G1 (51.3%) and the lowest in G3 (14.7%). The highest frequencies of BPD36wks (70.6%) and ROPsur were observed in G3 (23.5%). The lowest occurrence of death/BPD36wks occurred in G2 (58.0%). Pharmacological (OR 0.29; 95% CI: 0.14-0.62) and conservative (OR 0.34; 95% CI: 0.14-0.79) treatments were protective for the outcome death/BPD36wks. The conservative approach of PDA was associated to high mortality, the surgical approach to the occurrence of BPD36wks and ROPsur, and the pharmacological treatment was protective for the outcome death/BPD36wks.