Using Protistan Examples to Dispel the Myths of Intelligent Design

ABSTRACT. In recent years the teaching of the religiously based philosophy of intelligent design (ID) has been proposed as an alternative to modern evolutionary theory. Advocates of ID are largely motivated by their opposition to naturalistic explanations of biological diversity, in accordance with their goal of challenging the philosophy of scientific materialism. Intelligent design has been embraced by a wide variety of creationists who promote highly questionable claims that purport to show the inadequacy of evolutionary theory, which they consider to be a threat to a theistic worldview. We find that examples from protistan biology are well suited for providing evidence of many key evolutionary concepts, and have often been misrepresented or roundly ignored by ID advocates. These include examples of adaptations and radiations that are said to be statistically impossible, as well as examples of speciation both in the laboratory and as documented in the fossil record. Because many biologists may not be familiar with the richness of the protist evolution dataset or with ID‐based criticisms of evolution, we provide examples of current ID arguments and specific protistan counter‐examples.     

Phylogenetic structure of Brazilian savannas under different fire regimes

Questions: Fire is a strong filter in fire‐prone communities and is expected to assemble closely related species when functional traits are conserved in plant lineages. Do frequent fires assemble savannas with closely related species (phylogenetic clustering)? If so, what are the clades pruned by fire in the phylogenetic trees? Are species of semi‐deciduous seasonal forests, where fires are not frequent, less related than expected by chance (phylogenetic over‐dispersion)? Are life forms conserved in the phylogeny of the species? Location: Central and SE Brazilian savannas (Emas National Park, 18°18′S, 52°54′W; Brasília, 15°56′–15°57′S, 47°53′–47°56′W and Corumbataí‐Itirapina, 22°13′–22°15′S, 47°37′–47°39′W); and close semi‐deciduous seasonal forests (in Pirenópolis, 15°45′S, 49°04′W; Brasília, 15°33′S, 47°51′W; and São Carlos, 21°55′S, 47°48′W). Methods: We recorded woody species in savannas under different fire regimes and in semi‐deciduous seasonal forests. We obtained data from the literature and from field sampling. We compared mean phylogenetic distance of species of savanna and of nearby semi‐deciduous seasonal forest sites. We obtained significance by randomizing the species among the tips of phylogenetic trees. We also assessed whether life forms were evolutionary conserved across phylogeny of the studied plants (phylogenetic signal) with tests based on the variance of phylogenetic independent contrasts. Results: Some sites of savanna under high fire frequency were characterized by phylogenetic over‐dispersion of woody species whereas, in contrast, some sites of semi‐deciduous seasonal forest were characterized by phylogenetic clustering. We found phylogenetic signals in the traits across the phylogeny of the 801 species investigated. Conclusion: Fire may have different roles in assembling plant species in Brazilian savannas than in other fire‐prone communities. We postulate that the absence of phylogenetic clustering in the cerrado is mainly due to the persistence of long‐lived resprouting species from different plant lineages.     

利用氮同位素技术探讨天津地表水氮污染

地表水的氮污染状况与水质、区域景观等密切相连。本文分析了天津地表水的三氮(NO3-N、NH4+-N、NO2-N)组成,以及部分水样NO3-N和NH4+-N的N同位素组成。结果显示:NO3-N的含量为0.01～16.51mg.L-1,均值为2.25mg.L-1,部分样品NO3-的含量超过50mg.L-1(以NO3-N计为11.29mg.L-1);NH4+-N的含量为0～10.60mg.L-1,均值为1.15mg.L-1,有1/4水样超过1.5mg.L-1;另外,在所有样品中有1/12水样有较高的NO2-N。NO3-N为大部分水样无机氮的主要形态,污水等部分水样以NH4+-N为主要形态。NO3-N同位素值的变化范围为-5.5‰～+28.6‰,均值为+9.0‰(n=49),中值为+8.5‰;NH4+-N同位素值的变化范围为-8.8‰～+34.3‰,均值+11.6‰(n=11),中值为+13.6‰。水化学和同位素结果分析表明,该区地表水的氮主要来源为生活污水,而且氮形态转化受硝化作用、挥发作用以及可能的反硝化作用影响明显。     

Phenomorphology and ecomorphological characters of Maytenus senegalensis L. Shrublands in the Iberian Peninsula: A comparison with other Mediterranean plant communities

This work sets out to establish ecomorphological and phenomorphological patterns in the constituent flora of an Iberian Maytenus senegalensis plant community in order to relate it with or separate it from other types of Mediterranean vegetation. This plant community contains tall shrubs, scrubs, palms and vines of a variety of families. Typical ecomorphological adaptations to the Mediterranean climate were observed in the community studied: an abundance of thorny species or species with tomentose leaves and photosynthetic stems, small leaves and a high presence of species with organs capable of post-fire regeneration. However, the community also showed hybrid characteristics between scrubland (predominantly malacophyllous leaves lasting 9 months on average and low biomass) and tall shrubland communities (predominance of phanerophytes up to 3 m in height, predominantly smooth bark, periodical reposition of leaves, mean lifespan of plants 25 years and mainly fleshy fruit). The community also presents an outstanding quantity of amphiphytes (29%). From a phenological point of view, the formation of buds in winter, flowering in spring, summer–autumn seed dispersal and leaf shedding in summer are typical of other Mediterranean communities, while fructification and growth lasting three seasons, as in the case of Maytenus shrubland, is not. The RVA phenophasic index (balance between reproductive and vegetative phenophases) with values of 0.4–2 shows an intermediate value between typical shrubland (0.3–1) and forest community (1–2) values. The APC index (period of phenophasic activity of the community) differentiates it from others, since it remains at 100% for seven months, three of which are winter months. Phenophasic patterns (overlapping, or not, of flower bud formation, flowering and growth) show how similar M. senegalensis shrubland is to forests because of the absence of phenophase pattern type A (characteristic in open-scrublands); in addition, we have detected a new pattern (type G), still regarded as exclusive to M. senegalensis. As regards the existence of coenomorphs (group of species with similar morpho-functional strategies), the studied community showed much greater diversity than other communities studied to date, with an Strategies Richness index (SRi) of 0.79 (11 groups covering the 14 species existing), pointing to the co-existence of a great variety of eco-phenomorphological strategies, each with a successful response to the same ecological conditions. Finally, some of the species in the community, e.g. Asparagus horridus, Chamaerops humilis and M. senegalensis, stand out because of their unique ecomorphological and phenological characteristics.     

Water use efficiency of twenty-five co-existing Patagonian species growing under different soil water availability

The variation of plant water use efficiency (WUE) with water availability has two interacting components: a plastic response, evident when individuals of the same genotype are compared (e.g. wet versus dry years), and an interspecific response, evident when different species living in habitats with different water availability are compared. We analysed the WUE of 25 Patagonian species that belong to four life forms (grasses, shrubs, annual herbs and perennial herbs) in relation to the climatic conditions of 2 years and the mean historic water availability experienced by each species. To estimate water availability, we calculated the effective soil water potential (EWP) of each species, based on available information about soil water dynamics, phenology and root system structure. To estimate WUE, we used isotopic discrimination of leaf C (Δ¹³C) and mean annual water vapour difference between leaves and atmosphere (Δe) measured in situ. For the plastic response, for every species and life form, WUE increased from the dry to the wet year. We hypothesize that photosynthesis was less nutrient limited in the wet than in the dry year, facilitating higher net photosynthesis rates per unit of stomatal conductance in the wet year. For the interspecific response, WUE was lower in species native to drier habitats than in species native to wetter habitats. This response was mostly accounted for by a decrease in Δe with EWP. Annual herbs, which avoid drought in time (they have the earliest growth cycle), and shrubs, which avoid drought in space (they have the deepest roots), showed the highest EWP and WUE. We conclude that the conventional wisdom which states that the highest WUE occurs within a species during the driest years, and among species in the driest habitats, does not always hold true, and that co-existing life forms drastically differ in water availability and water economy.     

The N-terminal region of the starch-branching enzyme from Phaseolus vulgaris L. is essential for optimal catalysis and structural stability

Starch-branching enzymes (SBEs) play a pivotal role in determining the fine structure of starch by catalyzing the syntheses of alpha-1,6-branch points. They are the members of the alpha-amylase family and have four conserved regions in a central (beta/alpha)8 barrel, including the catalytic sites. Although the role of the catalytic barrel domain of an SBE is known, that of its N- and C-terminal regions remain unclear. We have previously shown that the C-terminal regions of the two SBE isozymes (designated as PvSBE1 and PvSBE2) from kidney bean (Phaseolus vulgaris L.) have different roles in branching enzyme activity. To understand the contribution of the N-terminal region to catalysis, six chimeric enzymes were constructed between PvSBE1 and PvSBE2. Only one enzyme (1Na/2Nb)-II, in which a portion of the N-terminal region of PvSBE2 was substituted by the corresponding region of PvSBE1, retained 6% of the PvSBE2 activity. The N-terminal truncated form (DeltaN46-PvSBE2), lacking 46 N-terminal residues of PvSBE2, lost enzyme activity and stability to proteolysis. To investigate the possible function of this region, three residues (Asp-15, His-24, and Arg-28) among these 46 residues were subjected to site-directed mutagenesis. The purified mutant enzymes showed nearly the same K(m) values as PvSBE2 but had lower V(max) values and heat stabilities than PvSBE2. These results suggest that the N-terminal region of the kidney bean SBE is essential for maximum enzyme activity and thermostability.     

有机磷农药对滇池微囊藻生长和摄磷效应的影响

采集滇池水体作为铜绿微囊藻培养基,研究了两种有机磷农药(甲胺磷和辛硫磷)对微囊藻生长和摄磷效应的动力学规律。结果表明,在滇池水体中添加较低浓度的甲胺磷(0.8、1.6、3.2mg/L)和辛硫磷(0.02、0.06、0.1mg/L)均能不同程度地促进微囊藻的生长,且在HGZ培养基中抑制微囊藻生长的浓度在滇池水体中却能促进微囊藻的生长。微囊藻的生长取决于细胞内磷的浓度且对磷的吸收利用存在积累性,在微囊藻生长初期,摄取各形态磷的速率较快;随后微囊藻摄取各形态磷的速率较慢。总溶解磷(TSP)和溶解反应磷(SRP)是微囊藻优先摄取的磷形态,在生长过程中微囊藻利用了大量的溶解有机磷(DOP)作为磷源加速生长。这一特点对于微囊藻成为淡水湖泊富营养化发展过程中的一种重要优势种具有极为重要的作用。     

Insertion polymorphism of transposable elements and population structure of Anopheles gambiae M and S molecular forms in Cameroon

The insertion polymorphism of five transposable element (TE) families was studied by Southern blots in several populations of the M and S molecular forms of the mosquito Anopheles gambiae sensu stricto from southern Cameroon. We showed that the mean TE insertion site number and the within-population insertion site polymorphism globally differed between the M and S molecular forms. The comparison of the TE insertion profiles of the populations revealed a significant differentiation between these two molecular forms (0.163 < Phi(ST) < 0.371). We cloned several insertions of a non-LTR retrotransposon (Aara8) that were fixed in one form and absent in the other one. The only insertion that could be clearly located on a chromosome arm mapped to cytological division 6 of chromosome X, confirming the importance of this region in the ongoing speciation between the M and S molecular forms.     

Pleistocene refugia in an arid landscape: analysis of a widely distributed Australian passerine

While many studies have documented the effect that glacial cycles have had on northern hemisphere species, few have attempted to study the associated effect of aridification at low latitudes in the southern hemisphere. We investigated the past effects that cyclic aridification may have had on the population structure and history of a widespread endemic Australian bird species, the Australian magpie (Gymnorhina tibicen). One thousand one hundred and sixty-six samples from across its native range were analysed for mitochondrial control region sequence variation and variation at six microsatellite loci. Analysis of mitochondrial control region sequence data indicated monophyletic clades that were geographically congruent with an eastern and western region. The contemporary distribution of east and west clades is nonoverlapping but in close proximity. Populations were estimated to have diverged in the Pleistocene around 36,000 years ago. The putative Carpentarian and Nullarbor arid barriers appear to be associated with the divergence between east and west mainland populations. Nested clade analysis indicated a signature of range expansion in the eastern region suggesting movement possibly inland and northward subsequent to the last period of aridity. The island population of Tasmania was of very recent origin, possibly since sea levels rose 16,000 years ago. Given the east-west structure, there was no congruence between morphology and recent history of this species indicating a lack of support for morphological taxa. Overall mitochondrial DNA and microsatellite variation suggest that increasing aridity and Pleistocene refugia played a role in structuring populations of the Australian magpie; however, the dispersal ability and generalist habitat requirements may have facilitated the movement of magpies into an almost contiguous modern distribution across the continent. This study supports the idea that Pleistocene aridification played an important role in structuring intraspecific variation in low latitudinal southern hemisphere avian species.