Ribosomal RNA sequence conservation and gene number in the larval brine shrimp

The haploid genome size of Artemia is determined to be about 0.9·10¹², as evidenced both by Feulgen microspectrophotometry of individual diploid class nuclei, which are but one of five polyploid classes present within the larvae, and by analysis of the reassociation kinetics of the isolated single copy DNA component. Polysomes isolated from 24-h incubation stage larvae contain an average of 10 ribosomes per messenger RNA molecule. Their rRNAs are found to have sedimentation coefficients of 18 S and 26 S, corresponding to molecular weights of 0.70·10⁶ and 1.40·10⁶, respectively, as determined by polyacrylamide electrophoresis and also by sucrose density centrifugation. Denaturation in glyoxal followed by agarose gel electrophoresis shows that unlike deuterostome rRNAs, Artemia 26 S rRNA contains a cryptic nick about midway in the molecule, which is not found in the 18 S molecule. Isolated rRNAs were labelled in vitro with ¹²⁵I and hybridized with filter-immobilized DNA to saturation, which occurred at 0.051% for Xenopus, and at 0.074% for Artemia. From these results, it is calculated that in the haploid Artemia genome there are about 320 copies of the (18 S + 26 S) ribosomal RNA genes. Reciprocal heterologous hybridizations between these two species show that they share about 30% homology between their rDNA coding sequences.     

Genetic structure and differentiation of the Japanese extremely long-tailed chicken breed (Onagadori), associated with plumage colour variation: suggestions for its management and conservation

The Onagadori is a distinguished chicken breed that is characterized by an extremely long tail in the male. In this breed, three different plumage colour varieties have been developed (black-breasted white, black-breasted red and white) in which the black-breasted white is believed to be the original colour of the Onagadori, based on historical records. To establish a conservation strategy, 176 birds were genotyped for autosomal microsatellites. Significant genetic distinctness was found between the original (black-breasted white) and two derivative varieties ( F _ST = 0.091 and 0.093). At the same time, a Bayesian model-based clustering revealed that the majority of individuals belonging to the black-breasted red and white varieties had an extremely low proportion of the genome shared with the original type (black-breasted white). This suggests that derivative varieties were created by crossing with other breeds, with low introgression of the original-type genome. We propose that the three plumage colour varieties should be treated as separate genetic units in a conservation programme.     

Editorial: Twin peaks mission

The Y human chromosome has many ancient genes whose fidelity seems to have been preserved by tandem sequences and palindromic ‘hairpins’, compared/repaired by ‘gene conversion’. That a primary function of recombination machinery is DNA repair has been suggested, and rejected, several times; this new evidence is very persuasive. The process, better called gene conservation than gene conversion, could operate in all diploid organisms, accounting for the retention of long gene sequences without ‘informational meltdown’ ('concerted evolution'). It resembles rocket‐science computer‐redundancy error‐checking, comparison of three or four sequences, not just two. If recognition of errors in ‘converted’ sequences can be followed by either repair or rejection, the rejection option can account for the vast wastage of meiotic products. The repair option might be used in Drosophila oocytes and even zygotic nuclei, possibly other oocytes, ancient asexual lineages such as mycorrhizal fungi, perhaps the Y itself. Both evolutionary stasis (conservatism) and development and deployment of complex developmental modules can be understood in these terms so both the evolution of biodiversity and the practice of systematics may have these mechanisms as their bases. The main individual‐fitness and evolutionary advantages of diploidy were not primarily cloaking of recessive al‐leles, or allelic recombination and Mendelism, but conserving long DNA sequences.     

The persistence and conservation of Borneo’s mammals in lowland rain forests managed for timber: observations, overviews and opportunities

Lowland rainforests on Borneo are being degraded and lost at an alarming rate. Studies on mammals report species responding in various ways to habitat changes that occur in commercial forestry concessions. Here we draw together information on the relationship between the ecological, evolutionary, and biogeographic characteristics of selected Bornean non-volant mammals, and their response to timber harvesting and related impacts. Only a minority of species show markedly reduced densities after timber harvesting. Nonetheless there are many grounds for concern as various processes can, and often do, reduce the viability of wildlife populations. Our review of what we know, and of current understanding, helps predict mammalian dynamics and subsequent mammal-induced ecosystem changes in logged forests. We identify groups of mammal species that, although largely unstudied, are unlikely to tolerate the impacts associated with timber harvesting. On a positive note we find and suggest many relatively simple and low-cost ways in which concession management practices might be modified so as to improve the value of managed forests for wildlife conservation. Improving forest management can play a vital role in maintaining the rich biodiversity of Borneo’s tropical rain forests.     

Cis-regulatory characterization of sequence conservation surrounding the Hox4 genes

Hox genes are key regulators of anterior-posterior axis patterning and have a major role in hindbrain development. The zebrafish Hox4 paralogs have strong overlapping activities in hindbrain rhombomeres 7 and 8, in the spinal cord and in the pharyngeal arches. With the aim to predict enhancers that act on the hoxa4a, hoxb4a, hoxc4a and hoxd4a genes, we used sequence conservation around the Hox4 genes to analyze all fish:human conserved non-coding sequences by reporter assays in stable zebrafish transgenesis. Thirty-four elements were functionally tested in GFP reporter gene constructs and more than 100 F1 lines were analyzed to establish a correlation between sequence conservation and cis-regulatory function, constituting a catalog of Hox4 CNEs. Sixteen tissue-specific enhancers could be identified. Multiple alignments of the CNEs revealed paralogous cis-regulatory sequences, however, the CNE sequence similarities were found not to correlate with tissue specificity. To identify ancestral enhancers that direct Hox4 gene activity, genome sequence alignments of mammals, teleosts, horn shark and the cephalochordate amphioxus, which is the most basal extant chordate possessing a single prototypical Hox cluster, were performed. Three elements were identified and two of them exhibited regulatory activity in transgenic zebrafish, however revealing no specificity. Our data show that the approach to identify cis-regulatory sequences by genome sequence alignments and subsequent testing in zebrafish transgenesis can be used to define enhancers within the Hox clusters and that these have significantly diverged in their function during evolution.     

Multiple species of wild tree peonies gave rise to the ‘king of flowers’, Paeonia suffruticosa Andrews

The origin of cultivated tree peonies, known as the ‘king of flowers'' in China for more than 1000 years, has attracted considerable interest, but remained unsolved. Here, we conducted phylogenetic analyses of explicitly sampled traditional cultivars of tree peonies and all wild species from the shrubby section Moutan of the genus Paeonia based on sequences of 14 fast-evolved chloroplast regions and 25 presumably single-copy nuclear markers identified from RNA-seq data. The phylogeny of the wild species inferred from the nuclear markers was fully resolved and largely congruent with morphology and classification. The incongruence between the nuclear and chloroplast trees suggested that there had been gene flow between the wild species. The comparison of nuclear and chloroplast phylogenies including cultivars showed that the cultivated tree peonies originated from homoploid hybridization among five wild species. Since the origin, thousands of cultivated varieties have spread worldwide, whereas four parental species are currently endangered or on the verge of extinction. The documentation of extensive homoploid hybridization involved in tree peony domestication provides new insights into the mechanisms underlying the origins of garden ornamentals and the way of preserving natural genetic resources through domestication.