Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals

Background  

Gene losses played a role which may have been as important as gene and genome duplications and rearrangements, in modelling today species' genomes from a common ancestral set of genes. The set and diversity of protein-coding genes in a species has direct output at the functional level. While gene losses have been reported in all the major lineages of the metazoan tree of life, none have proposed a focus on specific losses in the vertebrates and mammals lineages. In contrast, genes lost in protostomes (i.e. arthropods and nematodes) but still present in vertebrates have been reported and extensively detailed. This probable over-anthropocentric way of comparing genomes does not consider as an important phenomena, gene losses in species that are usually described as "higher". However reporting universally conserved genes throughout evolution that have recently been lost in vertebrates and mammals could reveal interesting features about the evolution of our genome, particularly if these losses can be related to losses of capability.     

Quantifying the relationship between disease severity and the amount of Aphanomyces euteiches detected in roots of alfalfa and pea with a real-time PCR assay

A real-time PCR assay was used to quantify the relationship in alfalfa and pea between disease severity and the amount of Aphanomyces euteiches detected in roots. The study included isolates of race 1 and race 2 of the alfalfa pathovar of A. euteiches and an isolate obtained from diseased pea. Spearman rank correlations between pathogen DNA content and disease severity index (DSI) ratings were positive ( ? 0.57) and significant (P  0.0007) for individual alfalfa plants, bulked alfalfa plant samples, and individual pea plants. In all experiments, significantly more pathogen was detected in susceptible populations than in resistant populations. The results clearly demonstrate that resistance to A. euteiches in both alfalfa and pea is characterized by a reduction in pathogen colonization relative to levels observed for susceptible reactions. The assay was very specific for A. euteiches, producing very linear assays with DNA extracted from pathogen isolates obtained from alfalfa, pea, and bean. Possible applications of the assay in conjunction with other real-time PCR assays specific to other legume pathogens are discussed in relation to simultaneous disease screening for multiple plant pathogens and the study of microbial population dynamics in mixed plant infections.     

Confirmation of quantitative trait loci affecting fatness in chickens

In this report we describe the analysis of an advanced intercross line (AIL) to confirm the quantitative trait locus (QTL) regions found for fatness traits in a previous study. QTL analysis was performed on chromosomes 1, 3, 4, 15, 18, and 27. The AIL was created by random intercrossing in each generation from generation 2 (G₂) onwards until generation 9 (G₉) was reached. QTL for abdominal fat weight (AFW) and/or percentage abdominal fat (AF%) on chromosomes 1, 3 and 27 were confirmed in the G₉ population. In addition, evidence for QTL for body weight at the age of 5 (BW5) and 7 (BW7) weeks and for the percentage of intramuscular fat (IF%) were found on chromosomes 1, 3, 15, and 27. Significant evidence for QTL was detected on chromosome 1 for BW5 and BW7. Suggestive evidence was found on chromosome 1 for AFW, AF% and IF%, on chromosome 15 for BW5, and on chromosome 27 for AF% and IF%. Furthermore, evidence on the chromosome-wise level was found on chromosome 3 for AFW, AF%, and BW7 and on chromosome 27 for BW5. For chromosomes 4 and 18, test statistics did not exceed the significance threshold.     

Evaporative water loss simulation improves models’ prediction of habitat suitability for a high-elevation forest skink

Accurate evaluation of habitat availability for wildlife is relevant for ecological applications. Researchers have frequently used models to simulate habitats thermally suitable for reptiles, but these results have limited application for species highly selective for habitat humidity. Here, we use the biophysical Niche Mapper™ model to investigate impacts of vegetation cover on the habitat quality of a high-elevation forest skink, Sphenomorphus taiwanensis, and to predict changes in habitat suitability in a future warmer climate (3 °C increase in air temperature). We assess habitat suitability with different densities of canopy cover in our study areas using two ecologically relevant estimates for lizards: maximum activity time and evaporative water loss (EWL) during the activity season. We measured preferred body temperature and EWL of this species for model parameterization, and behavioral response to EWL to supplement habitat quality assessment. The results indicated that this species is sensitive to EWL and reduces its activity when dehydrated. The model predicted that denser canopy levels increase microclimate cooling and humidity, and that most canopy levels are thermally suitable for this species, as the lizard can thermoregulate to manage adverse temperatures. Nevertheless, increasing canopy density could significantly decrease EWL during activity. In the warmer climate scenario, simulated maximum activity time and EWL changed little because of thermoregulation behavior. Our results suggest that habitat preference of this species is a consequence of water and energy requirements, and we note that combining EWL and maximum activity time data can enhance model accuracy of lizards’ habitat quality in a warmer climate.