The Effect of Different Levels of N Limitation on Sugars, Amino Acids, Growth and Biomass Partitioning in Broadbean (Vicia faba L.)

Broadbean plants (Vicia faba L.) were submitted to three differentlevels of steady state N limitation. Relative addition ratesof N were 0.06, 0.1 and 0.14d^-1. Plants were harvested at fiveevenly distributed times over a 2d period. Shoot growth correspondedwell with the imposed treatment. Root growth, relative to shootgrowth, was highest at the 0.06d^-1treatment. Diurnal patternsof soluble sugars, amino acids and starch were analysed. Onaverage, soluble sugar levels were highest in the plants ofthe 0.06d^-1treatment whereas average free amino acid levelswere highest in the 0.14d^-1treatment. Shoot growth increasedas the concentration of shoot amino acids increased. No suchcorrelation however could be found between root growth and freesugar levels in the root. Broadbean; Vicia faba L.; exponential addition; N limitation; free sugar; amino acids; diurnal cycle; functional equilibrium; starch     

Nuclear DNA from a 180‐year‐old study skin reveals the phylogenetic position of the Kinglet Calyptura Calyptura cristata (Passeriformes: Tyrannides)

The Kinglet Calyptura Calyptura cristata is one of the most enigmatic bird species in South America, known only from specimens collected in the 19th century and a few recent observations. Knowledge of its biology is scanty and its systematic position is obscure. Traditionally, Calyptura was placed in the Cotingidae, but associated with genera that are now known to fall outside the Cotingidae. In an attempt to clarify its phylogenetic position, sequence data from four nuclear markers were obtained from a 180‐year‐old museum study skin of Calyptura, and incorporated into a comprehensive dataset of tyrant flycatchers, cotingas, manakins and allies. Our analyses demonstrate that Calyptura is most closely related to Platyrinchus and Neopipo and that these three genera constitute a deep branch in the clade containing the Rhynchocyclidae (tody‐tyrants and flatbills) and Tyrannidae (typical tyrant flycatchers). The Calyptura specimen is one of the oldest avian museum specimens from which a substantial amount of nuclear DNA sequence data have been obtained, and highlights the immense value of museum collections for DNA‐based phylogenetic studies.     

Temperature,size, reproductive allocation,and life‐history evolution in a gregarious caterpillar

The present study aimed to investigate the relationship between growth rate, final mass, and larval development, as well as how this relationship influences reproductive trade‐offs, in the context of a gregarious life‐style and the need to keep an optimal group size. We use as a model two sympatric populations of the pine processionary moth Thaumetopoea pityocampa, which occur in different seasons and thus experience different climatic conditions. Thaumetopoea pityocampa is a strictly gregarious caterpillar throughout the larval period, which occurs during winter in countries all over the Mediterranean Basin. However, in 1997, a population in which larval development occurs during the summer was discovered in Portugal, namely the summer population (SP), as opposed to the normal winter population (WP), which coexists in the same forest feeding on the same host during the winter. Both populations were monitored over 3 years, with an assessment of the length of the larval period and its relationship with different climatic variables, final mass and adult size, egg size and number, colony size, and mortality at different life stages. The SP larval period was reduced as a result of development in the warmer part of the year, although it reached the same final mass and adult size as the WP. Despite an equal size at maturity, a trade‐off between egg size and number was found between the two populations: SP produced less but bigger eggs than WP. This contrasts with the findings obtained in other Lepidoptera species, where development in colder environments leads to larger eggs at the expense of fecundity, but corroborates the trend found at a macro‐geographical scale for T. pityocampa, with females from northern latitudes and a colder environment producing more (and smaller) eggs. The results demonstrate the importance of the number of eggs in cold environments as a result of an advantage of large colonies when gregarious caterpillars develop in such environments, and these findings are discussed in accordance with the major theories regarding size in animals. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 340–349.     

Taxonomy of the African giant pouched rats (Nesomyidae: Cricetomys): molecular and craniometric evidence support an unexpected high species diversity

Our study combined a mitochondrial cytochrome b phylogeny with cranial measurements from giant pouched rats collected across sub‐Saharan Africa. The mitochondrial phylogeny resolves two West African clades and a clade with east and central Africa representatives. This last clade can be further divided into four subclades. Altogether they represent six species (Cricetomys gambianus, Cricetomys ansorgei, Cricetomys emini, and three undescribed taxa) that can be distinguished on the basis of their mitochondrial DNA sequences and craniometry. In the absence of adequate craniometric data the existence of Cricetomys kivuensis cannot be confirmed by our data. Our combined molecular and craniometric data allowed us to broadly delineate the distribution ranges of the detected species. Cricetomys gambianus occurs in the savannah and forest clearings of West Africa. Cricetomys ansorgei is distributed in the savannah of East and southern Africa. Cricetomys emini, as currently recognized across the Guineo‐Congolian forest of Africa, is shown to be diphyletic. Cricetomys sp. 1, a separate operational taxonomic unit closely resembling C. emini, occurs in the forest zone of West Africa. An undescribed sister‐species of C. ansorgei, Cricetomys sp. 2, occurs in the forest of Central Africa along the left bank of the Congo River. Cricetomys sp. 3 occurs on the right bank of the Congo River from Cameroon to the Republic of Congo, whereas the true C. emini also occurs on the right bank of the Congo River but appears to be restricted to the Democratic Republic of Congo. Cranial phenotype within the genus tends to conform to ecological zonation (either forest or savannah) rather than to phylogenetic affiliation of the species concerned, suggesting that diversifying selection across environmental gradients could be responsible for biological diversification within the genus.     

A refined graptolite biostratigraphy for the late Ordovician–early Silurian of central Wales

Morphometric analysis of graptolites from the persculptus and acuminatus biozones of central Wales identifies four successive morphospecies of normalograptids. These graptolites can be used for biostratigraphical subdivision of these strata as follows: (i) an early persculptus Biozone interval containing broad forms with geniculate thecae that have the morphology of Persculptograptus persculptus with an early insertion point for the full median septum (theca 1¹); (ii) a supra‐adjacent level of early persculptus Biozone age, with narrower, parallel‐sided forms, that have been referred to as Normalograptus? aff. parvulus and have a slightly later insertion point for the full median septum (theca 1²); (iii) a third interval, encompassing the later part of the persculptus Biozone to the early acuminatus Biozone, with Normalograptus? cf. parvulus, which has the full median septum delayed to the level of theca 3–7; and (iv) a younger interval, in the mid‐acuminatus Biozone with Persculptograptus cf. persculptus specimens that do not display the median septum on its reverse side. These taxa can be used for refined biostratigraphy and correlation in the late Ordovician and early Silurian of central Wales. The progressive delay in the insertion of the median septum in these taxa may have wider application for the correlation of the interval immediately after the Hirnantian glacial maximum.     

Adult life spans of butterflies (Lepidoptera: Papilionoidea + Hesperioidea): broadscale contingencies with adult and larval traits in multi-species comparisons

Adult life spans of insects are part of supposedly adaptive life-history syndromes, which involve a variety of reproductive strategies with regard to mating, egg maturation and egg laying. Contingencies of life span with many other morphological, behavioural, and ecological traits are to be expected. We used a data-mining approach, incorporating controls for phylogeny, to uncover broad patterns of trait contingencies in a literature-derived data set of adult life spans for 350 butterfly species. We found that adult feeding habit has strong links with life spans, with pollen-feeders living longer than fruit feeders, which in turn live longer than nectar feeders. Furthermore, traits reducing susceptibility to predators (i.e. aposematism, eye-spots) are associated with longer life. Mud-puddling behaviour as a means of gaining access to minerals, and possibly nitrogen, was generally associated with a short life. We also found strong impacts of the region of occurrence of species (i.e. whether they were tropical or temperate taxa), but received conflicting results depending on whether we analysed field data (longer life in the tropics) or data from caged individuals (shorter life in the tropics). Adult longevity was associated with the growth form of larval host plants (higher on lianas as opposed to herbs, shrubs, or trees), whereas other larval host plant traits did not have strong links with species' life spans. We discuss the hypothetical evolutionary mechanisms explaining those patterns and suggest predictions that could be tested in further research.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 166–184.     

Developmental patterns of the crocodilian and avian columella auris: reappraisal of interpretations of the derivation of the dorsal hyoid arch in archosaurian tetrapods

The morphogenesis of the crocodilian and avian columella auris is analysed, using Alligator and Struthio as models that are studied in detail, and Crocodylus, Gallus, and Coturnix as models for comparative purposes. This investigation was undertaken to address controversies emanating from previous studies concerning the identity of archosaurian hyal elements, and to clarify confounding nomenclature that has been used for both topographic and phylogenetic purposes. We found that confusion in the identification of the reptilian and avian hyoid arch derivatives is attributable to: (1) redundant and/or inconsistently applied topographical terminology; (2) mixing of topographical and phylogenetic terminology; (3) interpretation in a recapitulatory framework; and (4) failure to consider that developmental pathways of recent archosaurians (reptilians and birds) might be divergently modified. Our analysis identifies errors in previous interpretations, misinterpretations of prior work, and histological observations that have been idealized. The most controversial issues are addressed – the derivation of the supracolumellar process; the concept of the laterohyal component; and segmentation of the distal part of the reptilian and avian columella auris. Based on new data, we suggest that the osteichthyan infrapharyngohyal, suprapharyngohyal, epihyal, and ceratohyal are not applicable terms for reptilian and avian columellar components from a phylogenetic perspective, and should not be used as topographical terms either. We further propose that the original morphogenetic program of the hyoid arch has been overwritten in newly derived evolutionary pathways of crocodilians and birds, in which a new functional and morphological patterning of the hyoid arch, as a specific sound‐transmitting apparatus, have evolved. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 156 , 384–410.     

Higher and lower‐level relationships of the deep‐sea fish order Alepocephaliformes (Teleostei: Otocephala) inferred from whole mitogenome sequences

Fishes of the order Alepocephaliformes, slickheads and tubeshoulders, constitute a group of deep‐sea fishes poorly known in respect to most areas of their biology and systematics. Morphological studies have found alepocephaliform fishes to display a mosaic of synapomorphic and symplesiomorphic characters, resulting in great difficulties when attempting to resolve intra‐ and interrelationships. Molecular data recently added to the confusion by removing Alepocephaliformes from the Euteleostei and placed them as incertae sedis within the Otocephala. In the present study we attempt to further clarify relationships of Alepocephaliformes by adding newly determined whole mitogenome sequences from 19 alepocephaliforms in order to address 1) phylogenetic position of Alepocephaliformes within the Otocephala; and 2) intrarelationships of Alepocephaliformes. The present study includes 96 taxa of which 30 are alepocephaliforms and unambiguously aligned sequences were subjected to partitioned maximum likelihood and Bayesian analyses. Results from the present study support Alepocephaliformes as a genetically distinct otocephalan order as sister clade to Ostariophysi (mostly freshwater fishes comprising Gonorynchiformes, Cypriniformes, Characiformes, Siluriformes and Gymnotiformes). The disputed family Bathylaconidae was found to be an artificial assemblage of the two genera Bathylaco and Herwigia, with the former as the sister group of the family Alepocephalidae and the latter nested within Alepocephalidae. Platytroctidae was found to be monophyletic as sister clade to the rest of Alepocephaliformes. Previously unrecognized clades within the family Alepocephalidae are presented and a clade comprising Alepocephalus, Conocara and Leptoderma was recovered as the most derived. As long as the current classification is being followed, the genera Alepocephalus, Bathytroctes, Conocara and Narcetes were all found non‐monophyletic. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 923–936.     

Xeml Lab: a tool that supports the design of experiments at a graphical interface and generates computer-readable metadata files, which capture information about genotypes, growth conditions, environmental perturbations and sampling strategy

Data mining depends on the ability to access machine-readable metadata that describe genotypes, environmental conditions, and sampling times and strategy. This article presents Xeml Lab. The Xeml Interactive Designer provides an interactive graphical interface at which complex experiments can be designed, and concomitantly generates machine-readable metadata files. It uses a new eXtensible Mark-up Language (XML)-derived dialect termed XEML. Xeml Lab includes a new ontology for environmental conditions, called Xeml Environment Ontology. However, to provide versatility, it is designed to be generic and also accepts other commonly used ontology formats, including OBO and OWL. A review summarizing important environmental conditions that need to be controlled, monitored and captured as metadata is posted in a Wiki ( http://www.codeplex.com/XeO ) to promote community discussion. The usefulness of Xeml Lab is illustrated by two meta-analyses of a large set of experiments that were performed with Arabidopsis thaliana during 5 years. The first reveals sources of noise that affect measurements of metabolite levels and enzyme activities. The second shows that Arabidopsis maintains remarkably stable levels of sugars and amino acids across a wide range of photoperiod treatments, and that adjustment of starch turnover and the leaf protein content contribute to this metabolic homeostasis.