Population genomics of wild and laboratory zebrafish (Danio rerio)

Understanding a wider range of genotype–phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large‐scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh, and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1832 polymorphic EST‐based single nucleotide polymorphisms (SNPs) and the cytb mitochondrial gene in 13 wild populations and three lab strains. Natural populations were subdivided into three major mitochondrial DNA clades with an average among‐clade sequence divergence of 5.8%. SNPs revealed five major evolutionarily and genetically distinct groups with an overall F_ST of 0.170 (95% CI 0.105–0.254). These genetic groups corresponded to discrete geographic regions and appear to reflect isolation in refugia during past climate cycles. We detected 71 significantly divergent outlier loci (3.4%) and nine loci (0.5%) with significantly low F_ST values. Valleys of reduced heterozygosity, consistent with selective sweeps, surrounded six of the 71 outliers (8.5%). The lab strains formed two additional groups that were genetically distinct from all wild populations. An additional subset of outlier loci was consistent with domestication selection within lab strains. Substantial genetic variation that exists in zebrafish as a whole is missing from lab strains that we analysed. A combination of laboratory and field studies that incorporates genetic variation from divergent wild populations along with the wealth of molecular information available for this model organism provides an opportunity to advance our understanding of genetic influences on phenotypic variation for a vertebrate species.     

Vegetative anatomy and systematics of subtribe Dendrobiinae (Orchidaceae)

Anatomy of leaf, stem, and root of more than 100 species in subtribe Dendrobiinae (Orchidaceae) was studied with the light microscope to provide a comparative anatomical treatment of these organs, to serve as an independent source of evidence that might be taxonomically important, and to recommend such reinterpretations of existing classifications as are suggested by a phylogenetic assessment of data. We based our classification on that of Rudolf Schlechter as the most complete and widely accepted today. We found that the anatomy of plants in subtribe Dendrobiinae reflects a high degree of morphological diversity, and many of the anatomical characters appear to be homoplasous. When these anatomical data are used to interpret the systematic relationships among the genera, they indicate that Dendrobium is not monophyletic and that Cadetia and Pseuderia are apparently nested within the structure of Dendrobium when section Grastidium is chosen as a functional outgroup. Lack of resolution in the strict consensus tree illustrates the difficulty of determining the phylogenetic relationships of many of Schlechter's sections using anatomical characters. Nevertheless, we recommend that his sectional classification, with appropriate modifications based on available data, be retained for the present, pending a more detailed understanding of the phylogeny of Dendrobiinae based on morphology, micromorphology, anatomy, and DNA studies.     

Isolation and characterization of 20 microsatellite marker loci from the Indri (Indri indri) genome

Twenty novel polymorphic microsatellite loci were isolated and characterized from the Indri, Indri indri, genome. Along with sequence data, this marker suite will be used in future studies to establish population structure throughout its range and to verify the proposed subspecific nomenclature. Gene diversity (0.760 and 0.783) and allelic richness (5.8 and 6.43) were estimated in the Betampona and Andasibe populations, respectively.     

Egg dumping by predatory insects

Synovigenic insects resorb oocytes when food is scarce and mature oocytes when food is plentiful. These two antagonistic processes allow an optimal allocation of resources to reproduction and somatic functions. Unlike hymenopteran parasitoids, ladybirds cannot resorb mature oocytes present in the oviducts. Is the energy contained in these oocytes lost or is there a mechanism for recovering it when needed? Females of two species of ladybird beetles Adalia bipunctata (L.) and Adalia decempunctata (L.) that are starved for >24 h lay single infertile eggs, which they immediately eat, and these eggs comprise the mature oocytes in the oviducts at the onset of starvation. This behaviour has some similarities to egg dumping reported in herbivorous insects and is part, in ladybird beetles, of a process to retrieve energy invested in reproduction. Such behaviour may exist in other predatory synovigenic insects species that do not invest in maternal care.     

Water deficit, root demography, and the causes of internal blackening in field-grown tomatoes:(Lycopersicon esculentum Mill.)

An internal blackening disorder may cause substantial losses in the value of tomatoes grown for processing. The disorder resembles an internal form of blossom-end rot and appears to be more common in dry seasons. In an experiment to test whether the internal blackening is caused by water deficit and whether it is indeed blossom-end rot, plots of cv. Cannery Row were irrigated to keep the soil moisture deficit <50 mm and others were sheltered from rain and not irrigated from early flowering onwards. Shoot growth (total and fruit dry mass) was measured destructively at intervals, and root growth and death nondestructively using minirhizotrons. There was a greater incidence of internal blackening and blossom-end rot, and lower Ca concentrations, in the fruit of non-irrigated plants. Root growth and root death were accelerated in these plants around the time that internally-blackened fruit were set. Although the internal blackening syndrome shared some features with blossom-end rot some differences were apparent in this experiment. It is suggested that internal blackening could have resulted from increased root competition for photosynthate, leading to abnormal seed development. Root turnover was appreciable (30–40% of the roots survived 28 days). This suggests there may be substantial errors in contemporary models of dry matter partitioning in tomato crops.     

Systematic and comparative anatomy of Maxillarieae (Orchidaceae), sans Oncidiinae

On the basis of floral and vegetative morphology, 63 tropical American genera have been recognized within Maxillarieae. We were able to examine anatomical material of all subtribes, excluding Oncidiinae. Stegmata with conical silica bodies occur in leaves and stems of all subtribes excluding Ornithocephalinae, and pericyclic stegmata found in roots are characteristic of Lycastinae. Lycastinae and Maxillariinae are characterized by foliar glands, foliar fibre bundles and tilosomes. Endodermal cells are U-thickened in most Zygopetalinae; O-thickened in most Lycastinae, Ornithocephalinae and Telipogoninae; variously thickened in Maxillariinae; and thin-walled in Cryptarrhena lunata . Water-storage cells varied from thin-walled to variously banded throughout Maxillarieae. Cladistic analyses using anatomical characters yielded no resolution among subtribes, illustrating that anatomical characters are of limited value in assessing relationships within this tribe.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 144 , 251–274.