Allotetraploid origin and divergence in Eleusine (Chloridoideae, Poaceae): evidence from low-copy nuclear gene phylogenies and a plastid gene chronogram

Background and Aims Eleusine

(Poaceae) is a small genus of the subfamily Chloridoideae exhibiting considerable morphological and ecological diversity in East Africa and the Americas. The interspecific phylogenetic relationships of Eleusine are investigated in order to identify its allotetraploid origin, and a chronogram is estimated to infer temporal relationships between palaeoenvironment changes and divergence of Eleusine in East Africa.

Methods

Two low-copy nuclear (LCN) markers, Pepc4 and EF-1α, were analysed using parsimony, likelihood and Bayesian approaches. A chronogram of Eleusine was inferred from a combined data set of six plastid DNA markers (ndhA intron, ndhF, rps16-trnK, rps16 intron, rps3, and rpl32-trnL) using the Bayesian dating method.

Key Results

The monophyly of Eleusine is strongly supported by sequence data from two LCN markers. In the cpDNA phylogeny, three tetraploid species (E. africana, E. coracana and E. kigeziensis) share a common ancestor with the E. indica–E. tristachya clade, which is considered a source of maternal parents for allotetraploids. Two homoeologous loci are isolated from three tetraploid species in the Pepc4 phylogeny, and the maternal parents receive further support. The A-type EF-1α sequences possess three characters, i.e. a large number of variations of intron 2; clade E-A distantly diverged from clade E-B and other diploid species; and seven deletions in intron 2, implying a possible derivation through a gene duplication event. The crown age of Eleusine and the allotetraploid lineage are 3·89 million years ago (mya) and 1·40 mya, respectively.

Conclusions

The molecular data support independent allotetraploid origins for E. kigeziensis and the E. africana–E. coracana clade. Both events may have involved diploids E. indica and E. tristachya as the maternal parents, but the paternal parents remain unidentified. The habitat-specific hypothesis is proposed to explain the divergence of Eleusine and its allotetraploid lineage.     

Dating the fungus-growing termites' mutualism shows a mixture between ancient codiversification and recent symbiont dispersal across divergent hosts

The mutualistic symbiosis between fungus-growing termites and Termitomyces fungi originated in Africa and shows a moderate degree of interaction specificity. Here we estimate the age of the mutualism and test the hypothesis that the major splits have occurred simultaneously in the host and in the symbiont. We present a scenario where fungus-growing termites originated in the African rainforest just before the expansion of the savanna, about 31 Ma (19-49 Ma). Whereas rough age correspondence is observed for the four main clades of host and symbiont, the analysis reveals several recent events of host switching followed by dispersal of the symbiont throughout large areas and throughout different host genera. The most spectacular of these is a group of closely related fungi (the maximum age of which is estimated to be 2.4 Ma), shared between the divergent genera Microtermes, Ancistrotermes, Acanthotermes and Synacanthotermes (which diverged at least 16.7 Ma), and found throughout the African continent and on Madagascar. The lack of geographical differentiation of fungal symbionts shows that continuous exchange has occurred between regions and across host species.     

An optimal degree of physical and chemical heterogeneity for the origin of life?

The accumulation of pure, concentrated chemical building blocks, from which the essential components of protocells could be assembled, has long been viewed as a necessary, but extremely difficult step on the pathway to the origin of life. However, recent experiments have shown that moderately increasing the complexity of a set of chemical inputs can in some cases lead to a dramatic simplification of the resulting reaction products. Similarly, model protocell membranes composed of certain mixtures of amphiphilic molecules have superior physical properties than membranes composed of single amphiphiles. Moreover, membrane self-assembly under simple and natural conditions gives rise to heterogeneous mixtures of large multi-lamellar vesicles, which are predisposed to a robust pathway of growth and division that simpler and more homogeneous small unilamellar vesicles cannot undergo. Might a similar relaxation of the constraints on building block purity and homogeneity actually facilitate the difficult process of nucleic acid replication? Several arguments suggest that mixtures of monomers and short oligonucleotides may enable the chemical copying of polynucleotides of sufficient length and sequence complexity to allow for the emergence of the first nucleic acid catalysts. The question of the origin of life may become less daunting once the constraints of overly well-defined laboratory experiments are appropriately relaxed.     

Role of stable isotopes in life--testing isotopic resonance hypothesis

Stable isotopes of most important biological elements, such as C, H, N and O, affect living organisms. In rapidly growing species, deuterium and to a lesser extent other heavy isotopes reduce the growth rate. At least for deuterium it is known that its depletion also negatively impacts the speed of biological processes. As a rule, living organisms "resist" changes in their isotopic environment, preferring natural isotopic abundances. This preference could be due to evolutionary optimization; an additional effect could be due to the presence of the "isotopic resonance". The isotopic resonance phenomenon has been linked to the choice of earliest amino acids, and thus affected the evolution of genetic code. To test the isotopic resonance hypothesis, literature data were analyzed against quantitative and qualitative predictions of the hypothesis. Four studies provided five independent datasets, each in very good quantitative agreement with the predictions. Thus, the isotopic resonance hypothesis is no longer simply plausible; it can now be deemed likely. Additional testing is needed, however, before full acceptance of this hypothesis.     

Visualization of DNA replication in the vertebrate model system DT40 using the DNA fiber technique

Maintenance of replication fork stability is of utmost importance for dividing cells to preserve viability and prevent disease. The processes involved not only ensure faithful genome duplication in the face of endogenous and exogenous DNA damage but also prevent genomic instability, a recognized causative factor in tumor development. Here, we describe a simple and cost-effective fluorescence microscopy-based method to visualize DNA replication in the avian B-cell line DT40. This cell line provides a powerful tool to investigate protein function in vivo by reverse genetics in vertebrate cells(1). DNA fiber fluorography in DT40 cells lacking a specific gene allows one to elucidate the function of this gene product in DNA replication and genome stability. Traditional methods to analyze replication fork dynamics in vertebrate cells rely on measuring the overall rate of DNA synthesis in a population of pulse-labeled cells. This is a quantitative approach and does not allow for qualitative analysis of parameters that influence DNA synthesis. In contrast, the rate of movement of active forks can be followed directly when using the DNA fiber technique(2-4). In this approach, nascent DNA is labeled in vivo by incorporation of halogenated nucleotides (Fig 1A). Subsequently, individual fibers are stretched onto a microscope slide, and the labeled DNA replication tracts are stained with specific antibodies and visualized by fluorescence microscopy (Fig 1B). Initiation of replication as well as fork directionality is determined by the consecutive use of two differently modified analogues. Furthermore, the dual-labeling approach allows for quantitative analysis of parameters that influence DNA synthesis during the S-phase, i.e. replication structures such as ongoing and stalled forks, replication origin density as well as fork terminations. Finally, the experimental procedure can be accomplished within a day, and requires only general laboratory equipment and a fluorescence microscope.     

Polycyclic Aromatic Hydrocarbons (PAHs) in Soil and Sediment from Industrial,Residential, and Agricultural Areas in Central South Africa: An Initial Assessment

Polycyclic aromatic hydrocarbons (PAHs) are of global concern due to their ubiquitous presence, toxicity, and carcinogenicity. No data on PAHs in soils from South Africa have been published, even though it has the largest economy and industrial base in Africa. During this initial assessment, the levels of PAHs were determined in soils and sediments collected from central South Africa, specifically targeting industrial, residential, and agricultural areas. Analysis was performed by gas chromatography/mass spectrometry (GC/MS). The total concentration of PAHs (Σt-PAH) ranged between 44 and 39,000 ng/g, dw and the concentration of carcinogenic PAHs (Σc-PAH) ranged between 19 and 19,000 ng/g, dw. Pyrogenic processes were the most likely sources, with minimal petrogenic contributions. PAH levels were in the same range as levels reported from other countries, and the majority of the sites did not exceed Canadian environmental quality guidelines. Based on assumptions for dermal contact and ingestion of PAH-contaminated soil, we provisionally calculated only a small increase in cancer risk, but additional PAH inhalation could add considerably to this risk. Our data indicates a need for more analysis in industrial and residential areas, and should include air.     

Feeding ecology of early marine phase Atlantic salmon Salmo salar post-smolts

Dietary analyses of Atlantic salmon Salmo salar post-smolt stomachs collected from 2001 to 2005 in Penobscot Bay, Maine, U.S.A., have yielded insights into the feeding ecology of early marine phase post-smolts from different rearing origins. Most stomachs contained only one or two prey types, suggesting active prey selection. Post-smolts that lived in the river longer (i.e. from naturally reared and parr-stocked origins) were smaller and consumed more fishes than invertebrates compared to larger post-smolts that emigrated immediately post-stocking (i.e. from smolt-stocked origins). Naturally reared S. salar consumed c. 84% fishes and 16% crustaceans and parr-stocked S. salar consumed 64% fishes and 34% crustaceans. Stocked smolts consumed 48% fishes and 40% crustaceans. Differences in the type and quantity of consumed prey may be indicative of behavioural differences among rearing origins that influence post-smolt survival.     

Brief communication: Y-chromosome haplogroup analysis indicates that Chinese Tuvans share distinctive affinity with Siberian Tuvans

Tuvans are mainly distributed in Siberia (the Republic of Tuva), Mongolia, and China. The genetic origin of Chinese Tuvans remains controversial. The Tuvans in China were classified as Mongolians in the early 1950s by the National Ethnic Affairs Commission of China, but they defined themselves as a separate group. To resolve this dispute and determine their genetic relationships with the peoples in Central Asia, we randomly selected 150 male subjects from the Tuvans in the Altai region of Xinjiang Uygur Autonomous Region in China. Fourteen Y chromosomal markers were genotyped using the RFLP method or direct sequencing. These haplogroup data were combined with public data for 15 populations in South Siberia and Central Asia. Tuvans in both China and the Republic of Tuva had the highest frequencies of haplogroups K-M9 and Q-M242. Principal component analysis demonstrated that the Tuvans in China were of a distinct cluster, separated from their neighbors, the Mongolians and Kazakhs, which finding was consistent with the Analysis of Molecular Variances. Further population tree analysis revealed that Tuvans were on a far-separated cluster from their neighbors. Based on these results, we propose that the Tuvans (in both China and the Republic of Tuva) constitute a group distinct from Mongolians and from other Central Asia populations. However, the genetic results might be the consequence of some evolutionary forces like genetic drift and founder effect, and do not necessarily reflect their ultimate origin.