Improvements to resampling measures of group support

Several aspects of current resampling methods to assess group support are reviewed. When the characters have different prior weights or some state transformation costs are different, the frequencies under either bootstrapping or jackknifing can be distorted, producing either under‐ or overestimations of the actual group support. This is avoided by symmetric resampling, where the probability p of increasing the weight of a character equals the probability of decreasing it. Problems with interpreting absolute group frequencies as a measure of the support are discussed; group support does not necessarily vary with the frequency itself, since in some cases groups with positive support may have much lower frequencies than groups with no support at all. Three possible solutions for this problem are suggested. The first is measuring the support as the difference in frequency between the group and its most frequent contradictory group. The second is calculating frequencies for values of p below the threshold under which the frequency ranks the groups in the right order of support (this threshold may vary from data set to data set). The third is estimating the support by using the slope of the frequency as a function of different (low) values of p; when p is low, groups with actual support have negative slopes (closer to 0 when the support is higher), and groups with no support have positive slopes (larger when evidence for and against the group is more abundant).     

EFFECTS OF CONE COLOR DIMORPHISM ON REPRODUCTIVE OUTPUT OF WHITE FIR GROWING ALONG ELEVATIONAL GRADIENTS

White fir can produce cones that are either green or purple, and the color is genetically determined. The purpose of this study was to determine the effects of elevation and cone color on the cone and seed characters of this species. We collected cones from trees along two elevational gradients, Red Mountain Pass (1981 and 1983) and Cucharas Pass (1983). Over 600 cones were measured for length, diameter, number of viable seeds, mass of five viable seeds, and percent successful seed set. There was a strong overall effect due to elevation, although the Cucharas and Red Mtn. locations showed somewhat different effects on the reproductive characters. Seed mass decreased with elevation in all three samples. There was significant interaction between cone color and elevation for both 1983 samples, suggesting the presence of genotype-environment interaction. A large difference was seen between the Red Mtn. and Cucharas locations, and the cone colors behaved differently at the two locations. The consistently large differences between the seed characters of green and purple cones suggested that cone color, which is presumably determined by a single gene, may profoundly affect the reproductive potential of individual trees. This appears to be an example of influential coloration in plants which is not associated with pollination or dispersal.     

Is population genetic structure of vascular plants shaped more by ecological or geographic factors? A study case on the Mediterranean endemic Centaurea filiformis (Asteraceae)

• All known populations of the Sardinian endemic Centaurea filiformis Viv. (Asteraceae) were studied in order to understand the impact of both geographic and ecological factors on the genetic structuring of this species.
• Fourteen populations and 234 individuals were sampled. The demographic structure of the populations and the reproductive ecology were estimated in 28 plots. Population genetic analyses were based on SSR markers. Genetic structure was investigated by spatial Bayesian methods.
• Average densities of 0.51 individuals m^?2 were detected, with a prevalence of adults. Ten species of pollinators were identified; C. filiformis ability to self‐pollinate and myrmecochory were demonstrated experimentally. The populations displayed an average heterozygosity value of H _e = 0.576 and high genetic differentiation (overall F _ST = 0.218). Bayesian analysis suggests that five is the most probable number of gene pools of origin. A strong correlation between geographic distances and genetic distances among populations was highlighted.
• The demographic population structure of C. filiformis is dominated by adults, suggesting that it is a stable‐regressive or senile species, investing more in local persistence than colonisation ability. Despite the scattered distribution, the populations studied do not present evidence of genetic erosion. The analysis of genetic differentiation reveals very high differentiation levels among populations, thus indicating that effective barriers exist against gene flow. A general conclusion is that population distribution results in a clear genetic structure for the populations studied, and that geography and not ecology is shaping the present distribution of this species.

     

A comparative study on efficiency of adult fibroblasts and amniotic fluid-derived stem cells as donor cells for production of hand-made cloned buffalo (Bubalus bubalis) embryos

The efficiency of two cell types, namely adult fibroblasts, and amniotic fluid stem (AFS) cells as nuclear donor cells for somatic cell nuclear transfer by hand-made cloning in buffalo (Bubalus bubalis) was compared. The in vitro expanded buffalo adult fibroblast cells showed a typical “S” shape growth curve with a doubling time of 40.8 h and stained positive for vimentin. The in vitro cultured undifferentiated AFS cells showed a doubling time of 33.2 h and stained positive for alkaline phosphatase, these cells were also found positive for undifferentiated embryonic stem cell markers like OCT-4, NANOG and SOX-2, which accentuate their pluripotent property. Further, when AFS cells were exposed to corresponding induction conditions, these cells differentiated into osteogenic, adipogenic and chondrogenic lineages which was confirmed through alizaran, oil red O and alcian blue staining, respectively. Cultured adult fibroblasts and AFS cells of passages 10–15 and 8–12, respectively, were used as nuclear donors. A total of 94 embryos were reconstructed using adult fibroblast as donor cells with cleavage and blastocyst production rate of 62.8 ± 1.8 and 19.1 ± 1.5, respectively. An overall cleavage and blastocyst formation rate of 71.1 ± 1.2 and 29.9 ± 2.2 was obtained when 97 embryos were reconstructed using AFS cells as donor cells. There were no significant differences (P > 0.05) in reconstructed efficiency between the cloned embryos derived from two donor cells, whereas the results showed that there were significant differences (P < 0.05) in cleavage and blastocyst rates between the cloned embryos derived from two donor cell groups. Average total cell numbers for blastocyst generated using AFS cells (172.4 ± 5.8) was significantly (P < 0.05) higher than from adult fibroblasts (148.2 ± 6.1). This study suggests that the in vitro developmental potential of the cloned embryos derived from AFS cells were higher than that of the cloned embryos derived from adult fibroblasts in buffalo hand-made cloning.     

A histological and immunohistochemical study of the effects of N-acetyl cysteine on retinopathy of prematurity by modifying insulin-like growth factor-1

Retinopathy of prematurity (ROP) is a vasoproliferative disorder that occurs in premature infants and may lead to permanent visual impairment. We investigated both the possible protective role of N-acetyl cysteine (NAC) for preventing ROP and the role of IGF-1 in the disorder. Forty-five newborn rats were divided into three groups. Group 1 was raised in room air as controls. Group 2 was exposed to 60% oxygen for 14 days after birth, then transferred to room air. Group 3 was exposed to the same conditions as group 2, but received intraperitoneal injections of NAC on postnatal days 7–17. After 35 days, both eyes of all rats were processed for histology. Some sections were stained with hematoxylin and eosin to assess structural changes and other sections were immunostained to determine the location of IGF-1. Frozen sections also were prepared and stained for adenosine triphosphatase to detect retinal blood vessels. Compared to the controls, more blood vessels, many of which were abnormal, and increased IGF-1 expression were observed in group 2. In group 3, abnormal blood vessels and IGF-1 expression were less evident. NAC appeared to be an effective vascular-protective agent for ROP by decreasing IGF-1 expression.     

Natural selection on the plant-water relations of Cleome serrulata growing along natural moisture gradients

Summary I investigated the extent and adaptive importance of genetically-based variation in plant water relations in two populations of the annual plant Cleome serrulata found growing along relatively short (<30 m) and mild soil moisture gradients. Field measurements of predawn plant water potentials showed that plants at the dry end of the moisture gradients had consistently lower _Plant in May and June of 1984; differences up to 0.9 MPa were seen along the gradients. Seeds were collected from maternal plants growing along the moisture gradients and then grown under well-watered conditions in the greenhouse. Pressure-volume curves were constructed for a total of 92 seedlings from 25 maternal plants when the seedlings were four weeks old.Considerable genetic variation in the four highly correlated water potential components was seen in both populations, suggesting relatively high heritabilities (h²0.5). A partial correlation analysis revealed that cell wall elasticity was higher in seedlings from maternal plants which grew in the dry portions of each site. This suggested that natural selection had acted on this character during one or more previous generations. It appears that slight variations in the physiological genotype can significantly affect overall fitness in C. serulata.     

Studies on hemophilia A in Sardinia bearing on the problems of multiple allelism, carrier detection, and differential mutation rate in the two sexes.

A large survey of hemophilia A carried out with almost complete ascertainment on the island of Sardinia suggests that the variation of plasma levels of Factor VIII coagulant activity in normal individuals is largely controlled by a series of normal isoalleles or by closely linked modifiers. This variation is expected to affect the laboratory detection of the hemophilia A (HA) heterozygotes in addition to the X-inactivation-dependent mosaicism and the type of deficient mutant present in a given pedigree. The Sardinian pedigrees yielded 13 new cases of nonrecombinants between the loci for HA and glucose-6-phosphate dehydrogenase (G6PD), as well as four nonrecombinants between HA and Deutan color blindness. These findings bring to a total of 58 the number of scorable sibs and nonrecombinants thus far known for the linkage HA-G6PD. From such a figure it has been possible to infer that the 90% upper limit of meiotic recombination between the two loci is below 4%, thus justifying the application of the "linkage diagnostic test" for the detection of HA heterozygotes and the prenatal diagnosis of the hemophilic fetuses in families that segregate at both loci. In three out of the five HA pedigrees of our series that segregate also for G6PD or Deutan color blindness, the observed segregation of the combined phenotypes can be best explained by assuming the occurrence of a fresh mutation in the maternal grandfathers. Such a finding points out the opportunity to reevaluate Haldane's hypothesis of a possible higher incidence of X-linked mutations in the human male. It is anticipated that each of the issues addressed by the present study will be amenable to experimental verification as soon as suitable molecular probes become available to screen for common multiallelic DNA polymorphisms in the subtelomeric region of the X-chromosome long arm.