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.     

Mangroves as nursery sites: comparisons of the abundance and species composition of fish and crustaceans in mangroves and other nearshore habitats in tropical Australia

Daytime sampling of mangrove and seagrass (Halophila/Halodule community) habitats every 7 wk at Alligator Creek, Queensland, Australia, over a period of 13 mo (February 1985–February 1986) using two types of seine net, revealed distinct mangrove and seagrass fish and crustacean faunas. Total abundance of fish and relative abundance of small and large fish also varied between habitats and seasonally. Post-larval, juvenile and small adult fish captured with a small seine-net (3 mm mesh) were significantly more abundant (4 to 10 times) in the mangrove habitat throughout the 13 mo of sampling. Mangrove fish abundance showed significant seasonality, greatest catches being recorded in the warm, wet-season months of the year. Relative abundances of larger fish (captured in a seine net with 18 mm mesh) in the two habitats varied throughout the year, but did not show a seasonal pattern. At the same site, small crustaceans were significantly more abundant in the mangroves in all but one dryseason sample. Similar comparisons for three riverine sites, sampled less frequently, in the dry and wet seasons of 1985 and 1986, respectively, showed that in general mangrove habitats had significantly more fish per sample, although the relative abundance of fish in mangroves and other habitats changed with season. Crustacean catches showed a similar pattern, except that densities among sites changed with season. Fish and crustacean abundance in mangroves varied among sites, indicating that estuaries differ in their nursery-ground value. The juveniles of two commercially important penaeid prawn species (Penaeus merguiensis and Metapenaeus ensis) were amongst the top three species of crustaceans captured in the study, and both were significantly more abundant in the mangrove habitat. By contrast, mangroves could not be considered an important nursery for juveniles of commercially important fish species in northern Australia. However, based on comparisons of fish catches in other regions, the results of the present study indicate the importance of mangroves as nursery sites for commercially exploited fish stocks elsewhere in South-East Asia. Contribution No. 378 from the Australian Institute of Marine Science     

EFFECTS OF ADJACENT AGRICULTURAL ACTIVITIES AND WATERSHED CHARACTERISTICS ON STREAM MACROINVERTEBRATE COMMUNITIES1

Benthic macroinvertebrate communities in streams adjacent to cornfields, streams where cows had unrestricted access, and reference locations without agriculture were compared to examine the effects of local land use and land use/land cover in the watershed. At each local site, macroinvertebrates and a variety of habitat parameters were measured upstream, adjacent, downstream, and farther downstream of the local land use. A geographic information system (GIS) was used to calculate drainage basin area, land use/land cover percentages in each basin, and the distance from sample sites to the stream source. Three‐way analysis of covariance (ANCOVA) tests with date, site type, and sampling location as main effects were used to explore differences in macroinvertebrate metrics using median substrate size, percent hay/pasture area, and stream depth as covariates. The covariates significantly improved model fit and showed that multiple contributing factors influence community composition. Local impacts were greatest at sites where cows had access, probably because of sedimentation and embeddedness in the substrate. Differences between the upstream and the adjacent and downstream locations were not as great as expected, perhaps because upstream recolonization was reduced by agricultural impacts or because of differences in the intensity or proximity of agriculture to riparian areas in the watershed. The results underscore the importance of both local and watershed factors in controlling stream community composition.     

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.     

Restrictive dermopathy and fetal behaviour

We report three siblings from consecutive pregnancies affected with restrictive dermopathy (RD). During the second pregnancy, fetal behavioural development and growth were studied extensively using ultrasound at 1–4 week intervals. Dramatic and sudden changes occurred in fetal body movements and growth but not until the end of the second trimester of pregnancy. Prominent at that time were prolonged periods of fetal quiescence and very low heart rate variability, together with abnormally executed body movements of short duration. Retarded femoral development and jerky abrupt fetal body movements (abnormal movement quality) were already present in the early second trimester of pregnancy. Facial anomalies emerged despite the presence of fetal mouth movements. The clinical features of RD were only partly explained by present knowledge of skin development and the fetal akinesia deformation sequence hypothesis. Quantitative assessment of fetal movements proved to be a poor early marker for antenatal diagnosis of this disorder. Copyright © 2001 John Wiley & Sons, Ltd.     

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.     

Nest-building by crested tit Parus cristatus males: an analysis of costs and benefits

In a population of crested tits in Belgium, one out of three breeding males participated in nest-building. Since variation in the amount of nest-building among 11 building males was low, analysis of male nest-building allowed a logistic regression design. The probability of building increased with male condition and for late nests. The effect of male condition decreased with date, and date was the only factor predicting nest-building for repeat broods. The effect of male condition on nest-building suggests that building entails important costs for males. Based on correlative data, we argue that building by males shortens the interval between the start of nest-building and the onset of egg-laying by about 5 days. Since clutch size, incubation and nestling time did not differ between early and late broods, male nest-building apparently affects fledging date. Since early fledgers (early dispersers) are more likely to settle in future winter flocks, building behaviour by crested tit males should be favoured by natural selection. So far, male nest-building in hole-breeding birds might have been overlooked due to the widespread use of artificial nest-boxes in behavioural studies.