The fossil record and estimating divergence times between lineages: Maximum divergene times and the importance of reliable phylogenies

Summary Bounded estimates on divergence times between lineaes are crucial to the calculation of absolute rates of molecular evolution. Upper (minimum) bounds on divergence times are easily estimated based on earliest fossil finds. Lower (maximum) bounds are more difficult to estimate; the age of putative ancestors may be used, though in practice it is virtually impossible to distinguish ancestors from primitive sister groups, which do not, of logical necessit, consitute lower bounds on divergence times. Two relatively new approaches to estimating lower bounds directly assess the incompleteness of the fossil record. The first uses taphonomic control groups to distinguish real absences from nonpreservation, while the second, and probably more powerful, uses the quality of the fossil recored to estimate confidence intervals on the bases of stratigraphic ranges. For some groups, especially vertebrates, the inclusion or exclusion of problematic fossils can dramaticaly affect estimated lower bounds on divergence times, often swamping the uncertainties due to the incompleteness of the fossil record and/or corelation and dating errors. When datable paleogeographic events reflect ancient divisions of faunas, a lower bound on the divergence time of speices within a fauna can be established based on the geologic, rather than fossil, record. The fossil records of hominids, eutherianmammals, echinoids, and geese are used as examples.This article was presented at the C.S.E.O.L. Conferrence on DNA-DNA Hybridization and Evolution, Lake Arrowhead, California, May 11–14, 1989     

Prediction Intervals in Nonlinear Regression

By treating the nonlinear model as if it were linear in the parameterization θ in the neighbourhood of the least squares estimate θ, we construct two-sided nominally-q-prediction intervals by applying the usual linear model theory. The derivation of the truncated series expansion of the expected coverage of the prediction intervals at a feasible value of the parameter vector is described. The quadratic approximation of the expected coverage is then obtained for a two-parameter nonlinear model. Finally we show how we may construct the prediction intervals when a certain type of nonlinear transformation of the parameter vector has been applied.     

Involvement of INF-γ functional single nucleotide polymorphism +874 T/A (rs2430561) in breast cancer risk

According Global Cancer Statistics 2020 GLOBOCAN estimates female breast cancer was found as the most commonly diagnosed cancer, with an estimated 2.3 million new cases (11.7%), and the fourth leading cause (6.9%) of cancer death among women worldwide. Identification of new diagnostic marker sharply characterize the tumor feature is intensive need. The present work was performed to investigate the involvement of the INF-γ + 874 T/A gene polymorphism in different breast cancer prognostic factors. Polymorphism detection analysis was performed on 163 subjects from breast cancer patients, 79 with inflamed cells of breast patients and 144 controls. The gene polymorphism was detected using the amplification refractory mutation system- polymerase chain reaction method (ARMS-PCR). The distribution of INF-γ T + 874A gene polymorphism shows strong significant association between INF-γ + 874 T/A genotypes TT in BC patients (ORTT: 6.41 [95% CI = 2.72–15.1] P < 0.0001) as well as strong significant association regarding T allele (ORT: 1.99 [95% CI = 1.43–2.76] P < 0.0001) when compared to the healthy control. In ICB group the strong association was noted with INF-γ + 874 T/A genotypes AT genotype (ORAT: 2.28 [95% CI = 1.22–4.29] P = 0.007). From the different histological BC hormonal markers the human epidermal growth factor receptor 2 (HER2) was showing significant association in INF-γ + 874 T/A genotypes TT (P = 0.03) and recessive model (TT versus AA + AT P = 0.03). Concerning different BC prognostic models, the poor prognostic one of luminal B, (ER^+ve PR^+ve Her2^+ve) show significant association in the host INF-γ + 874 T/A genotype (TT, P = 0.03) and recessive model (TT versus AA + AT P = 0.02) when compared to the good prognostic hormonal status luminal A model, (ER^+ve PR^+ve Her2-ve). It seems that this is the first study that interested in correlate the INF-γ + 874 T/A gene polymorphisms in Egyptian BC patients. T allele, TT genotype and recessive model of the INF-γ + 874 T/A gene variants were documented as risk factors for BC pathogenesis. It may be used as practical biomarker to guide the BC carcinogenesis and risk process.     

High throughput measure of diversity in cytoplasmic and nuclear traits for unravelling geographic distribution of rosemary

In the present work, variability of both cytoplasmic and nuclear microsatellite traits was investigated with the aim of characterizing a set of rosemary germplasm resources (Salvia rosmarinus). Most of the materials were collected in Italy and France. High‐resolution melting curves were compared each other computing their Euclidean distances and estimating the differences within their principal component as a measure of genetic diversity. Mantel correlation results combined to linear discriminant analysis allowed examined populations to be divided in four principal groups corresponding to four geographic areas, with few interesting and discussed exceptions. As rosemary propagates by seeds coming from insect mediated pollination, steady wild populations can be expected to be in panmictic equilibrium. Gained results confirmed and extended precedent characterization of rosemary genotypes and are compatible with the distribution of other Mediterranean species, as well as with the presence of a glacial refugium in the north‐east area of Sardinia previously described. As the officinal use of this aromatic shrub is spreading, characterization and conservation of wild Mediterranean germplasm is gaining strategic importance. A core collection of 100 genotypes was pointed out as suitable for a cheaper biodiversity ex situ preservation as well as for subsequent metabolic and linkage disequilibrium analyses.     

The structure of feeding behavior in a phytophagous insect (Hylobius abietis)

Analysis of the feeding behavior of animals using such a high temporal resolution that meals can be defined may improve our understanding of the mechanisms regulating feeding. Meals can be distinguished in an ethologically meaningful manner by using the ‘meal criterion’, the shortest non‐feeding interval between feeding bouts recognized as meals. However, such a criterion has only been determined for a few insect species. Applying a recent method developed for assessing meal criteria for vertebrates, we determined the meal criterion for Hylobius abietis (L.) (Coleoptera: Curculionidae) based on data from video recordings of single individuals feeding on seedlings of Norway spruce, Picea abies (L.) Karst. (Pinaceae). The pine weevil is an economically important pest insect, because it feeds on the stem bark of planted conifer seedlings. Weevils had 4–5 meals per day. Each meal lasted about 24 min during which about 13 mm² of bark per meal were removed. Females had longer total meal durations and longer non‐feeding intervals within meals than males. Girdling seedlings did not affect the weevils' feeding properties. The size of meals was significantly correlated with the duration of non‐feeding intervals before and after them. This study is one of few describing the feeding behavior of an insect at a temporal resolution that allows individual meals to be distinguished. With more meal‐related data from insects available, differences in meal properties may be interpreted based on phylogeny, ecology, and physiology. Our results may also assist in the setup and interpretation of studies of plant‐insect interactions, and facilitate the evaluation and development of methods to protect plants against herbivores.