Molecular data do not support a southern hemisphere base of Nothofagus powdery mildews

Three powdery mildew species present on Nothofagus (viz. Erysiphe magellanica, E. nothofagi and E. patagoniaca) are endemic to South America and have unique ascomatal appendages that are not found in powdery mildews of the northern hemisphere. We determined the nucleotide sequences of the rDNA internal transcribed spacer regions and D1/D2 domains of the 28S rDNA of these three powdery mildew species to reveal their phylogenetic relationships with powdery mildews of the northern hemisphere. Although the molecular phylogenetic analyses indicated that the three Nothofagus powdery mildews are closely related to each other they did not group into one clade in either the ITS or 28S trees. Kishino-Hasegawa, Shimodaira-Hasegawa and Templeton tests could not significantly reject the constrained trees that were constructed based on the assumption that the Nothofagus powdery mildews would form a single clade. Based on this result and the evidence that all Nothofagus powdery mildews are endemic to South America and have similar morphological characteristics, it is likely that these three species diverged from a single ancestor present on Nothofagus. Calibration of evolutionary events with molecular clocks suggested that the Nothofagus powdery mildews split from the northern hemisphere relatives 22-16 million y ago (Ma) in the middle Miocene, and divergence among the Nothofagus powdery mildews occurred 17-13 Ma. These results do not support a southern hemisphere base of the Nothofagus powdery mildews.     

Molecular data from 27 proteins do not support a Precambrian origin of land plants

Heckman et al. (Science 293: 1129-1133) used sequences obtained from GenBank to infer divergence times in fungi and green plants. They estimated that the crown group of land plants originated in the Precambrian, at 703 ± 45 mya, a date much older than dates implied by the fossils, which are no older than about 450 mya. This paper presents an analysis of an entirely different set of sequence data from 27 plastid protein-coding genes in 10 land plants and a green algal outgroup. It uses a calibration point closer to the origin of land plants and inference methods that do not assume a molecular clock. This leads to estimates ranging from 425 to 490 mya, which brackets the age suggested by the fossil record. Possible explanations for the differing conclusions in the two studies include differences in calibration points and use of single-copy plastid genes rather than nuclear gene families.     

Using genomic data to revisit an early example of reproductive character displacement in Haitian Anolis lizards

The pattern of reproductive character displacement (RCD)—in which traits associated with reproductive isolation are more different where two species occur together than where they occur in isolation—is frequently attributed to reinforcement, a process during which natural selection acting against maladaptive mating events leads to enhanced prezygotic isolation between species or incipient species. One of the first studies of RCD to include molecular genetic data was described 40 years ago in a complex of Haitian trunk anole lizards using a small number of allozyme loci. In this example, Anolis caudalis appears to experience divergence in the color and pattern of an extensible throat fan, or dewlap, in areas of contact with closely related species at the northern and southern limits of its range. However, this case study has been largely overlooked for decades; meanwhile, explanations for geographic variation in dewlap color and pattern have focused primarily on adaptation to local signalling environments. We reinvestigate this example using amplified fragment length polymorphism (AFLP) genome scans, mtDNA sequence data, information on dewlap phenotypes and GIS data on environmental variation to test the hypothesis of RCD generated by reinforcement in Haitian trunk anoles. Together, our phenotypic and genetic results are consistent with RCD at the southern and northern limits of the range of A. caudalis. We evaluate the evidence for reinforcement as the explanation for RCD in Haitian trunk anoles, consider alternative explanations and provide suggestions for future work on the relationship between dewlap variation and speciation in Haitian trunk anoles.     

Electromyographic data do not support a progressive recruitment of muscle fibers during exercise exhibiting a VO2 slow component

The origin of the slow component (SC) of oxygen uptake kinetics, presenting during exercise above the ventilatory threshold (VT), remains unclear. Possible physiologic mechanisms include a progressive recruitment of type II muscle fibers. The purpose of this study was to examine alterations in muscle activity through electromyography (EMG) and mean power frequency (MPF) analysis during heavy cycling exercise. Eight trained cyclists (mean +/- S.E.; age = 30 +/- 3 years, height = 1771 +/- 4 cm, weight = 73.8 +/- 6.5 kg, VO2max = 4.33 +/- 0.28 l min(-1)) completed transitions from 20W to a workload equaling 50% of the difference between V(T) and VO2max. VO2 was monitored using a breath-by-breath measurement system, and EMG data were gathered from surface electrodes placed on the gastrocnemius lateralis and vastus lateralis oblique. Breath-by-breath data were time aligned, averaged, interpolated to 1-s intervals, and modeled with non-linear regression. Mean power frequency (MPF) and RMS EMG values were calculated for each minute during the exercise bout. Additionally, MPF was determined using both isolated EMG bursts and complete pedal revolutions. All subjects exhibited a VO2 SC (mean amplitude = 0.98 +/- 0.16 l min(-1)), yet no significant differences were observed during the exercise bout in MPF or RMS EMG data (p > 0.05) using either analysis technique. While it is possible that the sensitivity of EMG may be insufficient to identify changes in muscle activity theorized to affect the VO2 SC, the data indicated no relationship between MPF/EMG and the SC during heavy cycling.     

Existence of a pattern of reproductive character displacement in Homobasidiomycota but not in Ascomycota

Generally, stronger reproductive isolation is expected between sympatric than between allopatric sibling species. Such reproductive character displacement should predominantly affect premating reproductive isolation and can be due to several mechanisms, including population extinction, fusion of insufficiently isolated incipient species and reinforcement of reproductive isolation in response to low hybrid fitness. Experimental data on several taxa have confirmed these theoretical expectations on reproductive character displacement, but they are restricted to animals and a few plants. Using results reported in the literature on crossing experiments in fungi, we compared the degree and the nature of reproductive isolation between allopatric and sympatric species pairs. In accordance with theoretical expectations, we found a pattern of enhanced premating isolation among sympatric sibling species in Homobasidiomycota. By contrast, we did not find evidence for reproductive character displacement in Ascomycota at similar genetic distances. Both allopatric and sympatric species of Ascomycota had similarly low levels of reproductive isolation, being mostly post-zygotic. This suggests that some phylogeny-dependent life-history trait may strongly influence the evolution of reproductive isolation between closely related species. A significant correlation was found between degree of reproductive isolation and genetic divergence among allopatric species of Homobasidiomycota, but not among sympatric ones or among Ascomycota species.     

Reproductive character displacement is not the only possible outcome of reinforcement

We study the form of the clines in a female mating preference and male display trait using simulations of a hybrid zone. Allopatric populations of two species are connected by demes in a stepping stone arrangement. Results show that reproductive character displacement (a pattern of increased prezygotic isolation in sympatry compared with allopatry) may or may not result when there is reinforcement (defined here as the strengthening of prezygotic isolation as a result of selection against hybrids, relative to the amount of prezygotic isolation present when hybrids are not selected against). Further, reproductive character displacement of the preference may or may not occur when it occurs in the male display. We conclude that the absence of reproductive character displacement is not evidence against the operation of reinforcement.     

Sampling bias exaggerates a textbook example of a trophic cascade

Understanding trophic cascades in terrestrial wildlife communities is a major challenge because these systems are difficult to sample properly. We show how a tradition of non-random sampling has confounded this understanding in a textbook system (Yellowstone National Park) where carnivore [Canis lupus (wolf)] recovery is associated with a trophic cascade involving changes in herbivore [Cervus canadensis (elk)] behaviour and density that promote plant regeneration. Long-term data indicate a practice of sampling only the tallest young plants overestimated regeneration of overstory aspen (Populus tremuloides) by a factor of 4–7 compared to random sampling because it favoured plants taller than the preferred browsing height of elk and overlooked non-regenerating aspen stands. Random sampling described a trophic cascade, but it was weaker than the one that non-random sampling described. Our findings highlight the critical importance of basic sampling principles (e.g. randomisation) for achieving an accurate understanding of trophic cascades in terrestrial wildlife systems.     

Mouth asymmetry in the textbook example of scale-eating cichlid fish is not a discrete dimorphism after all

Individuals of the scale-eating cichlid fish, Perissodus microlepis, from Lake Tanganyika tend to have remarkably asymmetric heads that are either left-bending or right-bending. The ‘left’ morph opens its mouth markedly towards the left and preferentially feeds on the scales from the right-hand side of its victim fish, and the ‘right’ morph bites scales from the victims’ left-hand side. This striking dimorphism made these fish a textbook example of their astonishing degree of ecological specialization and as one of the few known incidences of negative frequency-dependent selection acting on an asymmetric morphological trait, where left and right forms are equally frequent within a species. We investigated the degree and the shape of the frequency distribution of head asymmetry in P. microlepis to test whether the variation conforms to a discrete dimorphism, as generally assumed. In both adult and juvenile fish, mouth asymmetry appeared to be continuously and unimodally distributed with no clear evidence for a discrete dimorphism. Mixture analyses did not reveal evidence of a discrete or even strong dimorphism. These results raise doubts about previous claims, as reported in textbooks, that head variation in P. microlepis represents a discrete dimorphism of left- and right-bending forms. Based on extensive field sampling that excluded ambiguous (i.e. symmetric or weakly asymmetric) individual adults, we found that left and right morphs occur in equal abundance in five populations. Moreover, mate pairing for 51 wild-caught pairs was random with regard to head laterality, calling into question reports that this laterality is maintained through disassortative mating.     

Molecular clocks do not support the Cambrian explosion

The fossil record has long supported the view that most animal phyla originated during a brief period approximately 520 MYA known as the Cambrian explosion. However, molecular data analyses over the past 3 decades have found deeper divergences among animals (approximately 800 to 1,200 MYA), with and without the assumption of a global molecular clock. Recently, two studies have instead reported time estimates apparently consistent with the fossil record. Here, we demonstrate that methodological problems in these studies cast doubt on the accuracy and interpretations of the results obtained. In the study by Peterson et al., young time estimates were obtained because fossil calibrations were used as maximum limits rather than as minimum limits, and not because invertebrate calibrations were used. In the study by Aris-Brosou and Yang, young time estimates were obtained because of problems with rate models and other methods specific to the study, and not because Bayesian methods were used. This also led to many anomalous findings in their study, including a primate-rodent divergence at 320 MYA. With these results aside, molecular clocks continue to support a long period of animal evolution before the Cambrian explosion of fossils.     

Large-scale genome-wide scans do not support petaloid toenail as a Mendelian trait

正Petaloid toenail,or accessory nail of the fifth toe,is a physical trait characterized by the presence of an additional tiny toenail on the small toe.Since it can occasionally cause disfigurement and tenderness while wearing tight shoes or walking,standard surgical matricectomy is often carried out to repair the petaloid toenail(Chi and Wang,2004).Chinese legends recorded petaloid toenails     

Recent rhinos do not lack character(s): neither do fossil rhinos!

Concepts, methods, and interest of phylogenetic reconstruction are briefly examined. As large data sets are considered and refutable results are proposed, there is no need to use the argument of authority concerning relationships between taxons. Cladistic analysis in vertebrate palaeontology has gained considerable strength in the last decade, based on sets of hundreds of anatomical characters. One example is selected, which concerns the rhino family, i.e. rhinocerotids. Although underrepresented in recent times, these perissodactyl mammals flourished throughout the Cenozoicera (4 recent genera vs. 50 fossil genera). The main results of a recent cladistic analysis of elasmotheriine rhinocerotids, based on 282 anatomical characters, are listed. Such results concern phylogenetics (monophyly of both elasmotheriines and recent rhinos; branching of elasmotheriines among rhinocerotids) and methodology (definition of a "branching group"; location and processing of homoplasy; influence of taxonomic sampling). The implications are both biostratigraphical and palaeobiogeographical (evolution of the diet and spatial distribution; intercontinental dispersals; ghost lineages and heuristic use of the phylogenetic tree). Finally, forthcoming developments of the available data set for rhinocerotids are examined: controversial phylogenetic relationships among recent rhinos will be refined (thanks to close extinct taxa) and an exhaustive phylogeny of fossil and recent rhinocerotids will be reconstructed (54 genera).     

Molecular data do not support the current division of Orthotrichum (Bryophyta) species with immersed stomata

Genetic relationships between 27 Orthotrichum species of the subgenera Orthotrichum and Pulchella were reconstructed using the internal transcribed spacer regions 1 and 2,the chloroplast trnH-psbA regi...     

Protists – A textbook example for a paraphyletic taxon

Protists constitute a paraphyletic taxon since the latter is based on the plesiomorphic character of unicellularity and does not contain all descendants of the stem species. Multicellularity evolved several times independently in metazoans, higher fungi, heterokonts, red and green algae. Various hypotheses have been developed on the evolution and nature of the eukaryotic cell, considering the accumulating data on the chimeric nature of the eukaryote genome. Subsequent evolution of the protists was further complicated by primary, secondary, and even tertiary intertaxonic recombinations. However, multi-gene sequence comparisons and structural data point to a managable number of such events. Several putative monophyletic lineages and a gross picture of eukaryote phylogeny are emerging on the basis of those data. The Chromalveolata comprise Chromista and Alveolata (Dinoflagellata, Apicomplexa, Ciliophora, Perkinsozoa, and Haplospora). Major lineages of the former ‘amoebae’ group within the Heterolobosa, Cercozoa, and Amoebozoa. Cercozoa, including filose testate amoebae, chlorarachnids, and plasmodiophoreans seem to be affiliated with foraminiferans. Amoebozoa consistently form the sister group of the Opisthokonta (including fungi, and with choanoflagellates as sister group of metazoans). A clade of ‘plants’ comprises glaucocystophytes, red algae, green algae, and land vascular plants. The controversial debate on the root of the eukaryote tree has been accelerated by the interpretation of gene fusions as apomorphic characters. In the more traditional view, based on sequence comparisons using archaebacteria as outgroup representatives, parabasaleans and diplomonads branch off first, rendering the biflagellate eukaryotes paraphyletic. In sharp contrast, the root is placed between Bikonta and Opisthokonta plus Amoebozoa on the argument of a single enzyme gene fusion which is postulated to have occurred in the stem species of the Bikonta, and of a double enzyme gene fusion weighed as a synapomorphy of the Opisthokonta and Amoebozoa. We conclude that the paraphyletic taxon ‘protists’ may be maintained for practical reasons. However, introduction of new, clearly recognizable paraphyletic taxa should be avoided.     

Leg-attached data loggers do not modify the diving performances of a foot-propelled seabird

Global location sensors (GLS) are increasingly being used to determine animal position at sea. Their small size and weight means that they can be attached to the leg of volant birds with supposedly little impact on the flight ability. However, very few studies have investigated the impact that foot-attached devices may have on the diving ability of foot-propelled seabirds. We compared the diving activity of two groups of free-ranging great cormorants Phalacrocorax carbo carbo , both groups carrying identical time-depth recorders attached to the tail, and one group also having leg-attached GLS. Our results showed that there were no differences between the two groups in any of the diving parameters investigated, at least over the short term. Caution should be exercised when extrapolating to other species, especially those smaller than great cormorants, and also when deploying GLS over longer periods.     

Population regulation and character displacement in a seasonal environment

Competition has negative effects on population size and also drives ecological character displacement, that is, evolutionary divergence to utilize different portions of the resource spectrum. Many species undergo an annual cycle composed of a lean season of intense competition for resources and a breeding season. We use a quantitative genetic model to study the effects of differential reproductive output in the summer or breeding season on character displacement in the winter or nonbreeding season. The model is developed with reference to the avian family of Old World leaf warblers (Phylloscopidae), which breed in the temperate regions of Eurasia and winter in tropical and subtropical regions. Empirical evidence implicates strong winter density-dependent regulation driven by food shortage, but paradoxically, the relative abundance of each species appears to be determined by conditions in the summer. We show how population regulation in the two seasons becomes linked, with higher reproductive output by one species in the summer resulting in its evolution to occupy a larger portion of niche space in the winter. We find short-term ecological processes and longer-term evolutionary processes to have comparable effects on a species population size. This modeling approach can also be applied to other differential effects of productivity across seasons.     

Some protein interaction data do not exhibit power law statistics

It has been claimed that protein-protein interaction (PPI) networks are scale-free, and that identifying high-degree "hub" proteins reveals important features of PPI networks. In this paper, we evaluate the claims that PPI node degree sequences follow a power law, a necessary condition for networks to be scale-free. We provide two PPI network examples which clearly do not have power laws when analyzed correctly, and thus at least these PPI networks are not scale-free. We also show that these PPI networks do appear to have power laws according to methods that have become standard in the existing literature. We explain the source of this error using numerically generated data from analytic formulas, where there are no sampling or noise ambiguities.