DNA sequence evidence for speciation,paraphyly and a Mesozoic dispersal of cancellothyridid articulate brachiopods

Because the classification of extant and fossil articulate brachiopods is based largely upon shell characters observable in fossils, it identifies morphotaxa whose biological status can, in practice, best be inferred from estimates of genetic divergence. Allozyme polymorphism and restriction fragment length polymorphism of mitochondrial DNA (mtDNA RFLP) have been used to show that nuclear and mitochondrial genetic divergence between samples of the cancellothyridid brachiopods Terebratulina septentrionalis from Canada and T. retusa from Europe is compatible with biological speciation, but the genetic distances obtained were biased by methodological limitations. Here, we report estimates of divergence in 12S rDNA mitochondrial sequences within and between samples of these brachiopods. The sequence-based genetic distance between these samples (5.98ǂ.07% SE) is at least 10 times greater than within them and, since they also differ in a complex life-history trait, their species status is considered to be securely established. Divergence levels between 12S rDNA genes of three other cancellothyridids, T. unguicula from Alaska, T. crossei from near Japan, and Cancellothyris hedleyi from near Australia are higher than between the two North Atlantic species, and the mean nucleotide distance between all these cancellothyrids is similar to the mean distance between species of Littorina (Mollusca: Gastropoda). Sequences of both 12S and 16S genes from cancellothyridids and other short-looped brachiopod species show neither saturation nor lineage-specific rate differences and, when analysed with different outgroups, either separately or together, yield one unexpected, but well-supported, tree with Alaskan T. unguicula basal and C. hedleyi nested within Terebratulina, i.e. these genera are paraphyletic. A geologically dated divergence between Antarctic and New Zealand species of the short-looped brachiopod Liothyrella is used to calibrate the rate of 12S divergence at ca. 0.1% per million years (MY), and this rate is used to infer that T. septentrionalis and T. retusa have been diverging for ca. 60 MY and that they and T. unguicula have been diverging from their last common ancestor for ca. 100 MY. This indicates a Mesozoic origin for the present-day distribution of cancellothyridids and the basal position of T. unguicula suggests a possible North Pacific centre of origin, with separate Atlantic and Pacific radiations. The inclusion of Cancellothyris within Terebratulina also shows that adult shell characters such as umbo, foramen and symphytium shape, whilst probably indispensible for the practical classification of fossils, are not reliable guides to genealogy.     

GHG Mitigation Potential and Cost in Tropical Forestry - Relative Role for Agroforestry

This paper summarizes studies of carbon mitigation potential (MP) and costs of forestry options in seven developing countries with a focus on the role of agroforestry. A common methodological approach known as comprehensive mitigation assessment process (COMAP) was used in each study to estimate the potential and costs between 2000 and 2030. The approach requires the projection of baseline and mitigation land-use scenarios derived from the demand for forest products and forestland for other uses such as agriculture and pasture. By using data on estimated carbon sequestration, emission avoidance, costs and benefits, the model enables one to estimate cost effectiveness indicators based on monetary benefit per t C, as well as estimates of total mitigation costs and potential when the activities are implemented at equilibrium level. The results show that about half the MP of 6.9 Gt C (an average of 223 Mt C per year) between 2000 and 2030 in the seven countries could be achieved at a negative cost, and the other half at costs not exceeding $100 per t C. Negative cost indicates that non-carbon revenue is sufficient to offset direct costs of about half of the options. The agroforestry options analyzed bear a significant proportion of the potential at medium to low cost per t C when compared to other options. The role of agroforestry in these countries varied between 6% and 21% of the MP, though the options are much more cost effective than most due to the low wage or opportunity cost of rural labor. Agroforestry options are attractive due to the large number of people and potential area currently engaged in agriculture, but they pose unique challenges for carbon and cost accounting due to the dispersed nature of agricultural activities in the tropics, as well as specific difficulties arising from requirements for monitoring, verification, leakage assessment and the establishment of credible baselines.     

Exoautometabolic regulation of transgenes in microorganisms

Data on the existence of a specific system regulating the growth, size, and structure of enterobacterial populations are first summarized in terms of the chemical ecology concept formulated by S.S. Shvarts. The role of this system in transgene functioning is described using the example of the lux operon integrated into Escherichia coli. A relatively simple test for estimating such interactions is proposed.Translated from Ekologiya, No. 2, 2005, pp. 91–96.Original Russian Text Copyright © 2005 by Pshenichnov, Maslennikova, Nikitina.     

Ecological and genetic characteristics of the distribution of <Emphasis Type="Italic">Bradybaena fruticum</Emphasis> Mull. (mollusca,gastropoda, pulmonata) in a forest-steppe landscape

The distribution pattern of the gastropod Bradybaena fruticum has been studied in a forest-steppe landscape. Analysis of the frequencies of polymorphic biochemical and conchological characters has yielded preliminary results on the characteristics of the species population structure whose formation was determined by a set of natural and anthropogenic factors.Translated from Ekologiya, No. 1, 2005, pp. 39–47.Original Russian Text Copyright © 2005 by Snegin.     

A comparison of different lysis buffers to assess allele dropout from single cells for preimplantation genetic diagnosis

Single cell polymerase chain reaction (PCR) for preimplantation genetic diagnosis (PGD) requires high efficiency and accuracy. Allele dropout (ADO), the random amplification failure of one of the two parental alleles, remains the most significant problem in PCR-based PGD testing since it can result in serious misdiagnosis for compound heterozygous or autosomal dominant conditions. A number of different strategies (including the use of lysis buffers to break down the cell and make the DNA accessible) have been employed to combat ADO with varying degrees of success, yet there is still no consensus among PGD centres over which lysis buffer should be used (ESHRE PGD Consortium, 1999 ). To address this issue, PCR amplification of three genes (CFTR, LAMA3 and PKP1) at different chromosomal loci was investigated. Single lymphocytes from individuals heterozygous for mutations within each of the three genes were collected and lysed in either alkaline lysis buffer (ALB) or proteinase K/SDS lysis buffer (PK). PCR amplification efficiencies were comparable between alkaline lysis and proteinase K lysis for PCR products spanning each of the three mutated loci (ΔF508 in CFTR 90% vs 88%; R650X in LAMA3 82% vs 78%; and Y71X in PKP1 91% vs 87%). While there was no appreciable difference between ADO rates between the two lysis buffers for the LAMA3 PCR product (25% vs 26%), there were significant differences in ADO rates between ALB and PK for the CFTR PCR product (0% vs 23%) and the PKP1 PCR product (8% vs 56%). Based on these results, we are currently using ALB in preference to PK/SDS buffer for the lysis of cells in clinical PGD. Copyright © 2001 John Wiley & Sons, Ltd.     

Ammonia production and kinetic properties of glutamate dehydrogenase in the sipinculid Phascolosoma arcuatum exposed to anoxia

The amounts of total NH ₄ ⁺ detected in the external media in which Phascolosoma arcuatum had been exposed to various periods of anoxia were significantly greater than those in which the worms were exposed to normoxia for a similar period. The increased NH ₄ ⁺ production by P. arcuatum during anoxic exposure was unlikely to be due to an increased catabolism of adenine nucleotides or urea. In contrast, there were significant decreases in the concentrations of several free amino acids in the coelomic plasma and body tissues of individuals during the 48 h of anoxic exposure. The amount of NH ₄ ⁺ produced by the anoxic P. arcuatum could be accounted for by the decreases in the concentrations of aspartate or glycine. Increases in the catabolism of free amino acids (FAA), leading to the increased production of NH ₄ ⁺ , in P. arcuatum during anoxia were supported by the detection of significant changes in the kinetic properties of glutamate dehydrogenase (GDH), in the deaminating direction, from worms exposed to anoxia for 48 h. The apparent increase in the affinity of GDH from the anoxic worm to glutamate would bring about a greater deaminating activity at physiological concentrations of ths substrate. P. arcuatum used in these experiments were collected from the mangrove swamp at Mandai, Singapore between 1990 and 1993.     

Photodegradation of TCDD in soil containing organic solvents

Studies were conducted to understand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) behaviour in the near surface zone in relation to the operating conditions: UV-intensity, temperature and exposure modes. Comparisons have been made between Oriel lamp exposure tests and sunlight exposure tests. Under Oriel lamp exposure, the convective transport of TCDD, which depends on operating temperature, was the limiting factor in the cleanup process. The product differences between Oriel exposure tests and sunlight exposure tests probably result from the difference of UV-intensities.     

Small queens in the ant Ectatomma tuberculatum: a new case of social parasitism

Social parasites exploit the worker force of colonies of other social insects to rear their own young. Social parasitism occurs in several Hymenoptera and is particularly common in several tribes of the ant subfamilies Myrmicinae and Formicinae. Here, we document the occurrence of miniaturized queens (microgynes) in colonies of Ectatomma tuberculatum, an ant belonging to the subfamily Ectatomminae. Behavioral observations and genetic analyses show that microgynes concentrate their reproductive efforts almost exclusively on the production of sexual offspring (microgynes and males), whereas the regular, large queens (macrogynes) produce workers in addition to sexuals. According to mitochondrial and nuclear markers, gene flow between microgynes and macrogynes is extremely limited. Whereas the co-occurrence of microgynes and macrogynes in the related species Ectatomma ruidum constitutes an intraspecific polymorphism associated with alternative dispersal tactics, microgynes found in colonies of E. tuberculatum appear to be a distinct species and to represent the first case of social parasitism in the poneromorph subfamilies of ants.     

The State of the Mammal Community of Boreal Forest Ecosystems in the Vicinity of a Nickel-Smelting Plant

The effect of industrial air pollution on natural small mammal populations has been studied in the northern taiga subzone of the boreal forest zone. The results of long-term monitoring have been used to demonstrate the possibility of predicting changes in the main population and community characteristics of the animal species studied as dependent on the degree of anthropogenic impact.