Pre-Darwinian Taxonomy and Essentialism – A Reply to MaryWinsor

Mary Winsor (2003) argues against the received view that pre-Darwinian taxonomy was characterized mainly by essentialism. She argues, instead, that the methods of pre-Darwinian taxonomists, in spite of whatever their beliefs, were that of clusterists, so that the received view, propagated mainly by certain modern biologists and philosophers of biology, should at last be put to rest as a myth. I argue that shes right when it comes to higher taxa, but wrong when it comes the most important category of all, the species category.     

A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter

Obesity is an important and intractable public health problem. In addition to the well-known risk factors of behavior, diet, and genetics, gut microbial communities were recently identified as another possible source of risk and a potential therapeutic target. However, human and animal-model studies have yielded conflicting results about the precise nature of associations between microbiome composition and obesity. In this paper, we use publicly available data from the Human Microbiome Project (HMP) and MetaHIT, both surveys of healthy adults that include obese individuals, plus two smaller studies that specifically examined lean versus obese adults. We find that inter-study variability in the taxonomic composition of stool microbiomes far exceeds differences between lean and obese individuals within studies. Our analyses further reveal a high degree of variability in stool microbiome composition and diversity across individuals. While we confirm the previously published small, but statistically significant, differences in phylum-level taxonomic composition between lean and obese individuals in several cohorts, we find no association between BMI and taxonomic composition of stool microbiomes in the larger HMP and MetaHIT datasets. We explore a range of different statistical techniques and show that this result is robust to the choice of methodology. Differences between studies are likely due to a combination of technical and clinical factors. We conclude that there is no simple taxonomic signature of obesity in the microbiota of the human gut.     

On the Value of Taxonomy,Phylogeny, and Systematics to Orchid Conservation: Implications for China’s Yachang Orchid Reserve

Orchid classification has undergone a series of significant changes during the past decade as molecular phylogenetic studies have examined relationships at all taxonomic levels in the family. Today, the 750 genera and 25,000 species of Orchidaceae are organized into five subfamilies, the two largest of which (Epidendroideae and Orchidoideae) are further divided into 19 tribes and 43 subtribes. Whereas some of these groups are relatively small in terms of total species numbers, and may be of little horticultural or medicinal value, they are especially important for understanding orchid evolution and may deserve to be conserved for this reason alone. The question of which orchids to conserve is a complex one, but the science of systematics, including taxonomy and phylogenetics, has an undeniable role to play in answering that question. Among the many ways that phylogenetic trees can assist biologists in setting conservation priorities are by: 1) guiding taxonomists in naming species, which is essential for creating checklists within floras, monographs, and inventories; 2) discovering overlooked, rare or cryptic species that deserve recognition and protection; 3) determining whether or not a taxon is actually a species or simply a variant or hybrid; 4) predicting species that may be of value to humans for economic value; 5) identifying species that may have particularly important scientific value for better understanding the biology of plants. In the same way that we cannot protect all habitats, we may not be able to save every orchid species. Priorities must be established. The Yachang Orchid Reserve has been recognized as important not only because of the number of individual orchid plants that grow there, but also because of its great orchid diversity. Diversity is a product of evolution by natural selection, and the science of phylogenetics has a role to play in better understanding that process.     

Taxonomic and nomenclatural notes on the?genera Themus Motschulsky and Lycocerus Gorham (Coleoptera,Cantharidae)

The following taxonomic or nomenclatural changes are proposed: Themus (s.str.) regalis (Gorham, 1889), nom. rest.; Themus (s.str.) scutulatus Wittmer, 1983 = Themus (s.str.) hmong Kazantsev, 2007, syn. n.; Themus (Telephorops) coelestis (Gorham, 1889) = Themus violetipennis Wang & Yang, 1992, syn. n.; Themus (Telephorops) uniformis Wittmer, 1983, stat. n. = Themus (Telephorops) cribripennis Wittmer, 1983, syn. n.; Themus (Haplothemus) licenti Pic, 1938, stat. rev., resurrected from synonymy with Themus coriaceipennis (Fairmaire, 1889); Lycocerus aenescens (Fairmaire, 1889) = Lycocerus tcheonanus (Pic, 1922), syn. n.; Lycocerus asperipennis (Fairmaire, 1891) = Lycocerus wangi (Švihla, 2004), syn. n.; Lycocerus borneoensis nom. n. for Athemellus atricolor (Wittmer, 1972); Lycocerus bilineatus (Wittmer, 1995) = Lycocerus amplus (Wittmer, 1995), syn. n.; Lycocerus fairmairei nom. n. et stat. rev. for Athemus dimidiaticrus (Fairmaire, 1889), originally in Telephorus, resurrected from synonymy with Lycocerus orientalis (Gorham, 1889); Lycocerus confossicollis (Fairmaire, 1891), comb. n. hereby transferred from Cantharis = Lycocerus multiimpressus (Wittmer, 1997), syn. n.; Lycocerus inopaciceps (Pic, 1926) = Athemus (Athemellus) bimaculicollis (Švihla, 2005), syn. n.; Lycocerus nigratus nom. n. for Lycocerus nigricolor (Wittmer, 1972), originally in Podabrinus; Lycocerus plebejus (Kiesenwetter, 1874) = Lycocerus brunneonotaticeps (Pic, 1922), syn. n. = Cantharis rufonotaticeps Pic, 1921 syn. n.; Lycocerus swampingatus (Pic, 1916), comb. n., hereby transferred from Cantharis. The neotypes of Themus violetipennis Wang & Yang, 1992 and Athemus (s.str.) maculithorax Wang & Yang, 1992 are designated respectively.     

Extinct or still out there? Disentangling influences on extinction and rediscovery helps to clarify the fate of species on the edge

Each year, two or three species that had been considered to be extinct are rediscovered. Uncertainty about whether or not a species is extinct is common, because rare and highly threatened species are difficult to detect. Biological traits such as body size and range size are expected to be associated with extinction. However, these traits, together with the intensity of search effort, might influence the probability of detection and extinction differently. This makes statistical analysis of extinction and rediscovery challenging. Here, we use a variant of survival analysis known as cure rate modelling to differentiate factors that influence rediscovery from those that influence extinction. We analyse a global data set of 99 mammals that have been categorized as extinct or possibly extinct. We estimate the probability that each of these mammals is still extant and thus estimate the proportion of missing (presumed extinct) mammals that are incorrectly assigned extinction. We find that body mass and population density are predictors of extinction, and body mass and search effort predict rediscovery. In mammals, extinction rate increases with body mass and population density, and these traits act synergistically to greatly elevate extinction rate in large species that also occurred in formerly dense populations. However, when they remain extant, larger‐bodied missing species are rediscovered sooner than smaller species. Greater search effort increases the probability of rediscovery in larger species of missing mammals, but has a minimal effect on small species, which take longer to be rediscovered, if extant. By separating the effects of species characteristics on extinction and detection, and using models with the assumption that a proportion of missing species will never be rediscovered, our new approach provides estimates of extinction probability in species with few observation records and scant ecological information.     

Ion binding or condensation to polyelectrolytes?: A detailed comparison,on the example of sodium heparinate

A modified Poisson-Boltzmann treatment is applied to aqueous solutions of sodium heparinate, in the presence of added salts (NaCl, LiCl, KCl, CaCl2). The results show that 23Na-NMR line widths for the counterions are determined nearly exclusively by Na+ in the immediate vicinity of the linear polyelectrolyte. Hence, two-state treatments, despite their crude character, can reproduce such experimental data rather well.     

Spring Wheat Leaf Appearance and Temperature: Extending the Paradigm?

Extensive research shows temperature to be the primary environmental factor controlling the phyllochron, or rate of leaf appearance, of wheat (Triticum aestivum L.). Experimental results suggest that soil temperature at crown depth, rather than air temperature above the canopy, would better predict wheat leaf appearance rates. To test this hypothesis, leaf appearance in spring wheat ('Nordic') was measured in a 2-year field experiment (Nunn clay loam soil; fine, smectitic, mesic Aridic, Argiustoll) with three planting dates and two soil temperature treatments. One temperature treatment (denoted +3C) consisted of heating the soil at crown depth to 3 degrees C above the ambient soil temperature (denoted +0C). Main stem cumulative leaf number was measured at least weekly until flag leaf emergence. Leaf appearance was essentially linear with both air and soil growing degree-days (GDD), although there was a stronger linear relationship with soil GDD in the +0C plants than in +3C plants. A weak positive relationship between planting date and the phyllochron was observed. Unexpectedly, we found that heating the soil did not increase the rate of leaf appearance, as the paradigm would predict. To explain these results, we propose extending the paradigm in two ways. First, three processes are involved in leaf appearance: (1) cell division at the shoot apex forms the primordium; (2) cell division in the intercalary meristem forms the cells that then (3) expand to produce the leaf. Cell division is predominantly controlled by temperature, but cell expansion is considerably more affected by factors other than temperature, explaining the influence of other factors on the phyllochron. Secondly, the vertical distribution of the two meristems and region of cell expansion occur over a significant distance, where temperature varies considerably, and temperature at a specific point (e.g. crown depth) does not account for the entire temperature regime under which leaves are developing.     

Time and energy constraints and the evolution of sexual size dimorphism — to eat or to mate?

Summary We present an empirical test of the Ghiselin—Reiss small-male hypothesis for the evolution of sexual size dimorphism (SSD). In mating systems dominated by scramble competition, where male reproductive success is a function of encounter rate with females, small males may be favoured when food is limiting because they require lower absolute amounts of food. Given a trade-off between time and energy devoted to foraging and to mate acquisition, small males should be able to devote more time to the latter. If at the same time larger females are favoured, this mechanism will contribute to the evolution of SSD and may be the major determinant of the female-biased SSDs that characterize most animal taxa. We tested this hypothesis using the water strider,Aquarius remigis (Heteroptera: Gerridae), a scramble competitor which mates many times over a prolonged mating season and which shows female-biased SSD. Laboratory experiments demonstrated that foraging success and giving up times (GUTs) are lower for males than for females during the reproductive season and that male water striders flexibly alter their time budgets under conditions of energy limitation. Controlled feeding experiments showed that male and female longevity, female fecundity and male mating success are positively related to food availability. As predicted, male body size is negatively correlated with several indices of male fitness (longevity, number of mating attempts and mating success), while female body size is positively correlated with longevity. These results are consistent with the hypothesis that scramble competition for mates favours small males in this species and provides empirical support for the Ghiselin—Reiss small-male hypothesis.