Lansing man: a half century later

One of the major fossil man finds from the Plains Area of the United States and one of the few from Kansas are the “Lansing Man” skeletons. The discovery was in February 1902 on the west bank of the Missouri River, south of Leavenworth near the town of Lansing, Kansas. Much was written about this skeleton following its discovery and Ale? Hrdli?ka's only trip to Kansas in October 1902 was to observe the skeletons and the site of its discovery. Numerous articles were written suggesting that “Lansing Man” was many thousands of years old. Geologists could not agree on an age of the skeletons, an adult male and a six to seven year old child, because they were discovered in deposits of slumped loess, confusing the geological picture. Hrdli?ka states that the skeletons were physically identical to Indians of that region at the period of historical contact. William Holmes had the skull sent to the U. S. National Museum and the remaining bones were placed in the Museum of Natural History at the University of Kansas. While on the staff of the University of Kansas, I had Carbon-14 tests conducted on bones from the lower limbs by three separate laboratories. These dates range from 2660 to 5020 B.C. with an average date of four samples (1 each from Geochron Laboratories and the University of Michigan and two from the Smithsonian Institution) of 3579 B.C. This suggests that the “Lansing Man” skeletons are Early Middle Archaic and not Paleoindian. They do, however, represent the oldest known human skeletons from Kansas.     

Development of the human cerebral cortex: Boulder Committee revisited

In 1970 the Boulder Committee described the basic principles of the development of the CNS, derived from observations on the human embryonic cerebrum. Since then, numerous studies have significantly advanced our knowledge of the timing, sequence and complexity of developmental events, and revealed important inter-species differences. We review current data on the development of the human cerebral cortex and update the classical model of how the structure that makes us human is formed.     

The rust genus Frommeella revisited: a later synonym of Phragmidium after all

Fromme?lla (Phragmidiaceae, Pucciniales, Basidiomycota), which currently includes two species and is typified by F. tormentillae, causes rust on members of tribe Potentilleae (Rosaceae). The genus has been distinguished from Phragmidium on the basis of having only one germ pore per teliospore cell rather than two or three and by aecial characters. Phylogenetic analyses of both currently accepted Fromme?lla spp. with nLSU rDNA data suggest that Fromme?lla was derived from within a clade representing Phragmidium. Thus Fromme?lla should be considered to be a later generic synonym of Phragmidium. Analyses also indicate that Fromme?lla tormentillae on Potentilla species includes two taxa recognized herein as Phragmidium potentillae-canadensis and P. tormentillae. Fromme?lla mexicana on Potentilla spp. formerly classified in Duchesnea, is distinct from but sister to the other two species. Based on data regarding type specimens that were presented in a study by McCain and Hennen, the new combination Phragmidium mexicanum is proposed as the correct name for this species. Necessary studies of original material were made, and Phragmidium potentillae-canadensis is lectotpyified and epitypified. Although considered and expanded here, further examination of species boundaries and host ranges of the fungi formerly classified in Fromme?lla is warranted.     

Evaluation of species distribution models by resampling of sites surveyed a century ago by Joseph Grinnell

Species distribution models (SDMs) are commonly applied to predict species’ responses to anticipated global change, but lack of data from future time periods precludes assessment of their reliability. Instead, performance against test data in the same era is assumed to correlate with accuracy in the future. Moreover, high‐confidence absence data is required for testing model accuracy but is often unavailable since a species may be present when undetected. Here we evaluate the performance of eight SDMs trained with historic (1900–1939) or modern (1970–2009) climate data and occurrence records for 18 mammalian species. Models were projected to the same or the opposing time period and evaluated with data obtained from surveys conducted by Joseph Grinnell and his colleagues in the Sierra Nevada of California from 1900 to 1939 and modern resurveys from 2003 to 2011. Occupancy modeling was used to confidently assign absences at test sites where species were undetected. SDMs were evaluated using species’ presences combined with this high‐confidence absence (HCA) set, a low‐confidence set in which non‐detections were assumed to indicate absence (LCA), and randomly located ‘pseudoabsences’ (PSA). Model performance increased significantly with the quality of absences (mean AUC ± SE: 0.76 ± 0.01 for PSA, 0.79 ± 0.01 for LCA, and 0.81 ± 0.01 for HCA), and apparent differences between SDMs declined as the quality of test absences increased. Models projecting across time performed as well as when projecting within the same time period when assessed with threshold‐independent metrics. However, accuracy of presence and absence predictions sometimes declined in cross‐era projections. Although most variation in performance occurred among species, autecological traits were only weakly correlated with model accuracy. Our study indicates that a) the quality of evaluation data affects assessments of model performance; b) within‐era performance correlates positively but unreliably with cross‐era performance; and c) SDMs can be reliably but cautiously projected across time.     

Prediction error estimation: a comparison of resampling methods

MOTIVATION: In genomic studies, thousands of features are collected on relatively few samples. One of the goals of these studies is to build classifiers to predict the outcome of future observations. There are three inherent steps to this process: feature selection, model selection and prediction assessment. With a focus on prediction assessment, we compare several methods for estimating the 'true' prediction error of a prediction model in the presence of feature selection. RESULTS: For small studies where features are selected from thousands of candidates, the resubstitution and simple split-sample estimates are seriously biased. In these small samples, leave-one-out cross-validation (LOOCV), 10-fold cross-validation (CV) and the .632+ bootstrap have the smallest bias for diagonal discriminant analysis, nearest neighbor and classification trees. LOOCV and 10-fold CV have the smallest bias for linear discriminant analysis. Additionally, LOOCV, 5- and 10-fold CV, and the .632+ bootstrap have the lowest mean square error. The .632+ bootstrap is quite biased in small sample sizes with strong signal-to-noise ratios. Differences in performance among resampling methods are reduced as the number of specimens available increase. SUPPLEMENTARY INFORMATION: A complete compilation of results and R code for simulations and analyses are available in Molinaro et al. (2005) (http://linus.nci.nih.gov/brb/TechReport.htm).     

Recent changes in mountain grasslands: a vegetation resampling study

Understanding how land‐use changes affect different facets of plant biodiversity in seminatural European grasslands is of particular importance for biodiversity conservation. As conclusions of previous experimental or synchronic observational studies did not converge toward a general agreement, assessing the recent trends in vegetation change in various grassland systems using a diachronic approach is needed. In this resurvey study, we investigated the recent changes in grassland vegetation of the French Jura Mountains, a region with a long tradition of pastoralism. We compared the floristic composition of 150 grassland plots recorded between 1990 and 2000 with new relevés made in 2012 on the same plots. We considered taxonomic, phylogenetic and functional diversity as well as ecological characteristics of the plant communities derived from ecological indicator values and life strategies of the species. PCA of the floristic composition revealed a significant general trend linked to the sampling year. Wilcoxon paired tests showed that contemporary communities were generally more dominated by grass species and presented a higher tolerance to defoliation, a higher pastoral value, and a higher nutrient indicator value. Comparisons revealed a decrease in phylogenetic and functional diversity. By contrast, local species richness has slightly increased. The intensity of change in species composition, measured by Hellinger distance between pairs of relevés, was dependent on neither the time lag between the two surveys, the author of the first relevé nor its location or elevation. The most important changes were observed in grasslands that previously presented low pastoral value, low grass cover, low tolerance to defoliation, and high proportion of stress‐tolerant species. This trend was likely linked to the intensification of grassland management reported in the region, with a parallel increase in mowing frequency, grazing pressure, and fertilization level. More restrictive specifications should be applied to agricultural practices to avoid overexploitation of mountain species‐rich grasslands and its negative consequences on their biodiversity and resilience.     

Smallpox diagnosed 400 years later: results of skin lesions examination of 16th century Italian mummy

Results are presented on virological examination conducted on WHO request of a Naples infant mummy with smallpox-like lesions. Electron microscopy of lesions confirmed the findings of Italian researchers: well-preserved virus-like structures, whose size and morphology were identical to those of orthopoxviruses have been revealed. It was shown that the virus in mummy skin had lost its viability. Viral antigenic activity could not be detected in EIA or RPHA, nor was determined its DNA in the test of DNA molecular hybridization.     

The genetic equidistance result: misreading by the molecular clock and neutral theory and reinterpretation nearly half of a century later

In 1963,Margoliash discovered the unexpected genetic equidistance result after comparing cytochrome c sequences from different species.This finding,together with the hemoglobin analyses of Zuckerkandl and Pauling in 1962,directly inspired the ad hoc molecular clock hypothesis.Unfortunately,however,many biologists have since mistakenly viewed the molecular clock as a genuine reality,which in turn inspired Kimura,King,and Jukes to propose the neutral theory of molecular evolution.Many years of studies have found numerous contradictions to the theory,and few today believe in a universal constant clock.What is being neglected,however,is that the failure of the molecular clock hypothesis has left the original equidistance result an unsolved mystery.In recent years,we fortuitously rediscovered the equidistance result,which remains unknown to nearly all researchers.Incorporating the proven virtues of existing evolutionary theories and introducing the novel concept of maximum genetic diversity,we proposed a more complete hypothesis of evolutionary genetics and reinterpreted the equidistance result and other major evolutionary phenomena.The hypothesis may rewrite molecular phylogeny and population genetics and solve major biomedical problems that challenge the existing framework of evolutionary biology.     

Quaking aspen (Populus tremuloides Michx.) at treeline: a century of change in the San Juan Mountains, Colorado, USA

During a repeat photography study quaking aspen (Populus tremuloides Michx.) was observed invading conifer stands at treeline in the San Juan Mountains of south‐western Colorado. Aspen tree core samples were collected from nine plots ranging in elevation from 3192 to 3547 m, and estimated dates of establishment of aspen were grouped into 10‐year intervals for analysis. Estimated periods of establishment were compared with century‐long climate data records to derive any correlations with aspen invasion. Other disturbance agents, such as fire and livestock grazing were also considered. Quantitative analysis of climate variables suggests that decreased mean spring precipitation and increased mean summer maximum temperature provide optimal conditions for aspen establishment. Episodes of invasion were non‐synchronous, but all occurred after 1900, and are likely from seed germination, considered unusual in aspen. Different climate variables explain stand initiation from seed and subsequent peak establishment from vegetative reproduction. Long‐term climate records indicate a general warming since the beginning of the 20th century and explain the continued invasion and persistence of aspen at treeline, resulting from asexual reproduction. Short‐term climate records identify anomalously cool, moist years that explain rarely observed sexual reproduction in aspen.     

Boulder ALignment Editor (ALE): a web-based RNA alignment tool

SUMMARY: The explosion of interest in non-coding RNAs, together with improvements in RNA X-ray crystallography, has led to a rapid increase in RNA structures at atomic resolution from 847 in 2005 to 1900 in 2010. The success of whole-genome sequencing has led to an explosive growth of unaligned homologous sequences. Consequently, there is a compelling and urgent need for user-friendly tools for producing structure-informed RNA alignments. Most alignment software considers the primary sequence alone; some specialized alignment software can also include Watson-Crick base pairs, but none adequately addresses the needs introduced by the rapid influx of both sequence and structural data. Therefore, we have developed the Boulder ALignment Editor (ALE), which is a web-based RNA alignment editor, designed for editing and assessing alignments using structural information. Some features of BoulderALE include the annotation and evaluation of an alignment based on isostericity of Watson-Crick and non-Watson-Crick base pairs, along with the collapsing (horizontally and vertically) of the alignment, while maintaining the ability to edit the alignment. AVAILABILITY: http://www.microbio.me/boulderale.     

Birth of a prion: spontaneous generation revisited

The proposal that the transmissible agent in prion diseases can be a conformationally altered host protein that multiplies by autocatalytic conversion has gained wide acceptance. Recent work shows that the agent, the prion, can be replicated in a cell-free system, that it can be generated de novo, and that the strain-specific properties of prions are encoded by conformational variations of the underlying protein.     

Circular codes revisited: a statistical approach

In 1996 Arquès and Michel [1996. A complementary circular code in the protein coding genes. J. Theor. Biol. 182, 45-58] discovered the existence of a common circular code in eukaryote and prokaryote genomes. Since then, circular code theory has provoked great interest and underwent a rapid development. In this paper we discuss some theoretical issues related to the synchronization properties of coding sequences and circular codes with particular emphasis on the problem of retrieval and maintenance of the reading frame. Motivated by the theoretical discussion, we adopt a rigorous statistical approach in order to try to answer different questions. First, we investigate the covering capability of the whole class of 216 self-complementary, C³ maximal codes with respect to a large set of coding sequences. The results indicate that, on average, the code proposed by Arquès and Michel has the best covering capability but, still, there exists a great variability among sequences. Second, we focus on such code and explore the role played by the proportion of the bases by means of a hierarchy of permutation tests. The results show the existence of a sort of optimization mechanism such that coding sequences are tailored as to maximize or minimize the coverage of circular codes on specific reading frames. Such optimization clearly relates the function of circular codes with reading frame synchronization.     

The Gomphidiaceae revisited: a worldwide perspective

Recent studies in the Gomphidiaceae have clearly delimited two genera, Gomphidius and Chroogomphus, both of which are mycorrhizal associates only with the Pinaceae. Ecological studies show Chroogomphus as a mycorrhizal associate of Pinus (Pinoideae), while Gomphidius is associated with the other three gymnosperm subfamilies Piceoideae, Lariceideae, and Abietoideae. The genus Brauniellula, which is based upon the secotioid habit and the presence of orthotropic, statismosporic basidia, falls within Chroogomphus in a clade with ballistosporic species. Brauniellula is, therefore, placed in synonymy with Chroogomphus. Molecular and morphological studies of new material from Nepal, Russia, Korea, and the United States have delimited two new species in each genus. The morphologically identical Chroogomphus rutilus clades are separate, one European and one North American. The relationship of the two genera in the Gomphidiaceae, with their mycorrhizal associates, is related to similar host relationships within other genera in the Suilloid Clade.     

Myrtaceae revisited: a reassessment of infrafamilial groups

Cladistic analyses are presented of matK sequence data as well as a nonmolecular database for an identical set of exemplar species chosen to represent the core genera or groups of genera in Myrtaceae. Eleven robust clades are recognized on the molecular data. Polyphyly of the previously recognized Metrosideros and Leptospermum alliances is confirmed, and several smaller informal taxonomic groupings are recognized from among the members of the former alliance, i.e., the Tristania, Tristaniopsis, Metrosideros, and Lophostemon groups. The nonmolecular analysis provides only limited resolution of relationships. A degree of congruence exists between the two analyses in that two separate fleshy-fruited clades, the Acmena and Myrtoid groups, are identified, as are the Eucalypt and Tristania groups, and Psiloxylon and Heteropyxis are the first lineages to diverge in both analyses. A combined analysis recognized all 11 clades that received strong support from the molecular data. A high level of homoplasy is revealed in many of the nonmolecular characters when they are examined against the combined estimate of phylogeny.     

Bees explain floral variation in a recent radiation of Linaria

The role of pollinators in floral divergence has long attracted the attention of evolutionary biologists. Although abundant studies have reported the effect of pollinators on flower‐shape variation and plant speciation, the influence of pollinators on plant species differentiation during rapid radiations and the specific consequences of shifts among similar pollinators are not well understood. Here, we evaluate the association between pollinators and floral morphology in a closely related and recently diversifying clade of Linaria species (sect. Supinae subsect. Supinae). Our approach combined pollinator observations, functional floral morphometric measures and phylogenetic comparative analyses. The fauna visiting Linaria species was determined by extensive surveys and categorized by a modularity algorithm, and the size and shape of flowers were analysed by means of standard and geometric morphometric measures. Standard measures failed to find relationships between the sizes of representative pollinators and flowers. However, discriminant function analyses of geometric morphometric data revealed that pollination niches are finer predictors of flower morphologies in Linaria if compared with phylogenetic relationships. Species with the most restrictive flowers displayed the most slender spurs and were pollinated by bees with larger proboscides. These restrictive flower shapes likely appeared more than once during the evolutionary history of the study group. We show that floral variation can be driven by shifts between pollinators that have been traditionally included in a single functional group, and discuss the consequences of such transitions for plant species differentiation during rapid radiations.