Journal of Phylogenetics & Evolutionary Biology

SLC9B genes and proteins are members of the sodium/lithium hydrogen antiporter family which function as solute exchangers within cellular membranes of mammalian tissues. SLC9B2 and SLC9B1 amino acid sequences and structures and SLC9B-like gene locations were examined using bioinformatic data from several vertebrate genome projects. Vertebrate SLC9B2 sequences shared 56-98% identity as compared with ~50% identities with mammalian SLC9B1 sequences. Sequence alignments, key amino acid residues and conserved predicted transmembrane structures were also studied. Mammalian SLC9B2 and SLC9B1 genes usually contained 11 or 12 coding exons with differential tissue expression patterns: SLC9B2, broad tissue distribution; and SLC9B1, being testis specific. Transcription factor binding sites and CpG islands within the human SLC9B2 and SLC9B1 gene promoters were identified. Phylogenetic analyses suggested that SLC9B1 originated in an ancestral marsupial genome from a SLC9B2 gene duplication event.

The recent taxonomy and phylogeny of Otomyinae has been in a state of flux as new systematic revisions combining molecular, karyotypic and morphometric information have identified changes at various taxonomic levels. Currently two genera of Otomyinae and eight species of Otomys are recognized in South Africa. However, the position of Otomys sloggetti on the phylogeny of Otomyinae has not been resolved, and since this species was not well represented in recent revisions it may also reveal multiple cryptic evolutionary species. In this study four mitochondrial and one nuclear gene regions and external morphological characters were analysed to elucidate relationships within O. sloggetti, as well as between O. sloggetti and other Otomys species occurring in South Africa. The data from this study suggested O. sloggetti belongs to neither the Otomys, nor the Parotomys genera. Instead, we propose returning to the classification of Otomyinae and recognize Myotomys as the valid genus for O. sloggetti. Within O. sloggetti, our data does not support the traditional view of the distribution and intraspecific variation of the species, and invites a new hypothesis. Specimens identified in the field as O. sloggetti were found to represent two different clades. One of the clades was genetically and morphologically consistent with the description for O. sloggetti, while the other was distinct from O. sloggetti and other Otomys species known to occur in South Africa. Our data suggests that this is a novel species within the Otomys genus.

Trypanosoma evansi, the agent of trypanosomiasis commonly known as Surra or Guffar, is regarded as one of the most economically important animal parasitic pathogen affecting livestock in Egypt. The current study aims to discuss genetic characterization and phylogenetic analysis of Trypanosoma isolates from local and imported naturally infected camels in Egypt. The study was initially started with parasitological and molecular surveillance on 411 native and 117 imported camels by using PCR- RoTat 1.2 VSG gene targeting 205 bp. Further, the molecular characterization and sequencing were achieved on four positive samples using PCR-TR3/TR4 primers that derived from a trypanosome-specific repetitive nucleotide sequence fragment. Product sequences were aligned against the corresponding GenBank sequences of known isolates of T. evansi and subjected to phylogenetic analysis. Results revealed that T. evansi was present in 66.67% and 74.36% of the local and imported camels respectively, regardless of age and sex factors. Basic Local Alignment Search Tool (BLAST) data of the obtained PCR TR3/TR4 gene sequences revealed that they corresponded to those of T. evansi, with the homology of 93% to 99%. Phylogenetic and molecular analyses of this gene showed that three genotypes of T. evansi in Egypt are present showed two common SNPs (G136A and G189T) in all samples, two SNPs in ISM and ISD (C3T and A207G) and six SNPs in HSA (T12C, C14T, T15C, G19C, C21G, and G22C). We conclude that T. evansi is described as presenting genotype variability among its isolates according to geographical distribution in Egypt.

Histone 4 replacement (H4r) can replace replication-dependent H4 in Drosophila. To study the evolution of epigenetic mechanisms, the H4 and H4r genes from 14 Drosophila species were compared with regard to gene arrangement, codon bias and flanking sequences. Although the amino acid sequences of H4 and H4r are identical or nearly identical, the gene structures are quite different. The H4r gene is a single copy gene located 3R88C9 in D. melanogaster between punt and CEP78K, as it is in 11 closely related Drosophila species, but not in the three distantly related species. The H4r gene, unlike the H4 gene, has two introns and generates polyadenylated transcripts. The codon usage bias at particular sites differed between H4r and H4. The H4r gene had more GC pairs at 3^rd codon position. Strongly conserved signal sequence was not found in the 5’-region or 3’-region of the H4r gene. These results suggested that the post transcriptional process such as modifying histone at or after translation will be important for replacing histones and remodeling the chromatin. The evolutionary changes that affect gene structure and codon usage might be a key step to develop epigenetic systems by replacement histones.

Superior rice varieties tend to be highly adopted by farmers across the country. Over time, samples of a variety coming from different places may exhibit some differences. Morphological descriptors are traditionally used to determine these differences however; these descriptors are limited in number and suffer from drawbacks such as influence of environment on trait expression and could not differentiate morphologically identical varieties. The highly reproducible molecular marker assay offers a powerful alternative to establish true identity and discriminate morphologically identical varieties. A study was conducted to determine the identity of several rice varieties based on DNA fingerprinting using genome-wide SSR markers. Samples of NSIC Rc240 from four sources, Aromatic Rice from three sources, and IR64 from two sources, were included in the study. Genetic similarity was calculated as proportion of shared alleles and cluster analysis was conducted using UPGMA. Results showed that the genetic similarity of three NSIC Rc240 samples was 1.0 confirming that these three samples were 100% genetically similar with each other while a fourth NSIC Rc240 sample from another source was only 89% similar to the other three. On the other hand, the three Aromatic Rice samples formed separate clusters at a range of 71-80% similarity. Lastly, a farmer’s “improved” IR64 was only 59.5% similar to the original IR64. The observed divergence of samples with the same names in the study could be a result of further selection, gene flow, drift, admixture, or a combination of these mechanisms. This study underscores the importance of DNA fingerprinting analysis in variety identification, variation arising from selection and possible protection biopiracy.

Mutations, transposable elements, and recombination are the main mechanisms for genome size evolution. The quantitative impact of mutations, excluding polyploidy, on genome size is well studied in some genomes while the impact of other factors has not been investigated. Mutation rate was used to estimate the evolution time of origin genome to form a higher size genome and test if the estimated age of earth fits for these evolution events. Results indicated that the evolution time of the smallest detected genome through mutation rate to the largest detected genome is much higher than the estimated age of earth. The cumulative evolution time of the studied origin genomes was estimated at 5300 folds of earth's age and the average evolution time is 2.7 × 10¹² years per genome. The relationship among genome size, mutation rate, and evolution time indicated that evolution time is positively correlated with genome size suggesting that larger genomes take longer time to evolve in size. Estimation of evolution time would lead to establishment of genome evolution timeline to replace or support the fossil evolution timeline.