Journal of Phylogenetics & Evolutionary Biology

Different approaches are in progress to study phylogenetic relatedness and divergence among organisms. Genomic study is the most effective method for resolving phylogenetic relationships. Multiple genes are preferred over single gene sequence analysis and whole genome sequences are nowadays is the best nucleotide sequence-based approach to identify and classify the taxonomically complex group of organisms to deal with several phylogenetic issues. Various bioinformatics tools are providing valuable information to study significant evolutionary relationships such as next generation sequencing, proteomics etc. DNA barcoding technology is also recently used skill to study phylogeny and identify the morphologically ambiguous species by amplifying a small fragment of Cytochrome c Oxidase Subunit I (COI). We recently reported multiple gene phylogenies of Indian termites resulting in incongruent results. However, whole genome analysis will provide a significant outcome to resolve the diverse observations studied in these species.

Left-Right system is a well-known political spectrum apropos across the global politics. A number of social, cultural, linguistic, religious and economic attributes are identifiable in either of these two spectral extremities throughout the world. It is also widely known that intra- and inter-population heterogeneity of gene pools contributes in speciationthe split of genealogical lineage into two or more. However, a connection between Left-Right political spectra, or any political spectra for that matter, and the human gene pool remain consummately unknown. The present ab initio analysis reveal that the identifiable traits of left-right political spectra has strong and inherent potentials to directly affect the human gene pool to an extent to contribute in inter- and intra-population genetic heterogeneity, and, therefore, can affect processes of speciation and hybridization. The stereotypic leftist attributes can potentially result in high intra-population genetic heterogeneity, low inter-population genetic heterogeneity, and hybridization between divulging gene pools. On the other hand, rightist attributes can result in low intra-population heterogeneity, high inter-population heterogeneity, and ultimately the speciation. A plausible reason is the differential contribution of these traits towards assortative mating in human population via assortment of shared ancestry; i.e., population stratification and positive assortative mating due to homogamy. In the light of this central premise, repercussions of Left-Right political spectra on human evolution are deliberated. Argued here is that Left-Right political spectra have shared abstraction with Nurture-Nature axis of human perception. Therefore, it is plausible that Leftist and Rightist preferences are interposed by cerebral cortex and amygdala, respectively, and can very well have genetic rationale.

Sweet potato Ipomoea batatas L. (Lam.) is a symbol in the fight for a global nutrition plan that can save millions of children and help build a healthier and more productive future. However, characterisation of sweet potato varieties with optimal morphological features suitable for both food and feed has not been done. A population of 10,000 first filial generations (F1) sweet potato lines derived from seeds was generated through polycross crossing design in Uganda using 11 parents. Preliminary evaluation for the suitability of dual use of the F1’s led to selection of 11 varieties which were the basis of this study. This study therefore sought to morphologically characterise selected Ugandan sweet potato varieties to identify those with superior characteristics suitable for food and feed purposes. Sweet potato plants were raised from seeds after scarification. A selection of seedlings possessing single leaf lobes was done, after which they entered observation yield trials (OT). This was done in order to discard those that clearly did not meet the lowest acceptable gross morphological descriptors. The data were subjected to analysis of variance in order to find out if significant differences exist between the varieties based on morphological characterization. Cluster analysis was done using Minitab version 17 software. This study enables the selection of sweet potato varieties with optimal characteristics for both food and feed use. The data generated from this study could help recommend to farmers on how dual-purpose sweet potato could be produced, in order to provide enough healthier food to millions of children in Uganda and in the world, and better feed for live-stock farmers.

To understand the contribution of gut microflora to the feeding and health of Mugil cephalus in a Mediterranean estuary, we have explored and evaluated the diversity of rRNA genes in gut contents of both of adults and fingerlings. Bulk DNAs were extracted from the fish guts, followed by PCR, cloning and sequencing of eukaryote 18S rRNA gene; bacterial and archaeal 16S rRNA genes. Rarefaction analyses recorded 11, 18 and 13 phylotype groups of rRNA genes for eukaryotes, bacteria and archaea, respectively, in the adult guts. The fingerling guts contained 6 and 11 phylotype groups of rRNA genes for eukartyotes and bacteria, respectively, while lacked archaea. Adult and fingerling guts were dominated by zooplankton-like 18S rRNA gene phylotypes, belonging to those of rotifers, genus Brachionus and copepods, genus Apocyclops. Both of diatoms, genus Cyclotella- and fish-like rRNA gene phylotypes were recorded only in adult guts. Phylotypes, which belonged to uncultured proteobacteria and cyanobacteria, covered most of the bacterial 16S rRNA gene composition of adult guts. Bacteroidetes-like phylotypes characterized the fingerling guts. The study showed the first record of uncultured thaumarchaeote-like 16S rRNA genes in the fish guts, opening a window for exploring thaumarchaeote biological significances in fish metabolism. The fish guts represented a reservoir for geographic distant species and reflected the plankton ecosystem variability at the studied estuary. The pollution in the estuary could shape a fraction of the fish gut microbiota. To our knowledge, this work presented the first complete profile of rRNA gene diversities for all known microbiome domains in fish guts.

Bacterial genomes evolve through two different mechanisms: 1) changes in or occasional loss of ancestral genes, which preserve the founder clonal genealogy or frame, and 2) sporadic gains of new genes via horizontal gene transfer, which introduces DNA with a different genealogy or clonal frame. Evolution has led to the emergence of a pathogenic strain pandemic of Vibrio parahaemolyticus, which has propagated globally, causing large outbreaks of seafood-associated diarrhea. The low sequence diversity of the pathogenic strain of Vibrio parahaemolyticus genome provides a model that can reveal evolutionary mechanisms that are hidden in bacteria with a greater diversity. Here, we assess the clonal genealogy of the genome components of Vibrio parahaemolyticus and identify recombinant segments in 31 isolates obtained worldwide. By comparing whole genomes using a procedure that accounts for at least 98% of the reads obtained from any isolate after high throughput sequencing, we determined that the fraction of the whole genome retaining the founder clonal frame varied from 96.7%-100% of the accountable reads. The fraction in chromosomes with other genealogies varied from 0%-3.3% and in extra-chromosomal elements from 0%-4.2%, with the relative impact of mutation and recombination varying greatly between isolates. The likely causes for this variation are proposed.

The capybara (Hydrochoerus hydrochoeris) is the largest rodent on the world and it is strongly linked to the river systems of a large fraction of South America and part of Central America (Panama). Thus, it is an interesting species to test hypotheses about the origin of the high biodiversity within the Amazon Basin and in a sizeable fraction of the Neotropics. To test these hypotheses, we sequenced two mitochondrial genes (control region and Cytochrome b) of 78 wild capybaras sampled in Colombia, Peru, Ecuador and Brazil. At least, five different “populations” or ESUs were detected in well delimited geographical areas. However, our results do not support the more recent view that two different species of capybara are present (H. hydrochoeris and H. isthmus), unless chromosomal speciation (stasipatric or parapatric) can be demonstrated between these two groups. A Bayesian tree with the aforementioned two mitochondrial genes, and another Bayesian tree with a subset of 25 capybaras for 10 mitochondrial genes, showed that the initial diversification of the mitochondrial haplotype in capybaras was initiated in the Late Miocene. The trees also showed that the other haplotype diversification processes extended into the Pliocene and Pleistocene. We also detected population expansion events during different moments of the Pleistocene. Although some authors strongly suggest that the Miocene diversification explains the extreme biodiversity in the Amazon Basin and in surroundings areas (for instance, the Paleogeography hypothesis), others consider it the result of available forest refugia (Refuge hypothesis) during the Pleistocene. However, our results suggest that both hypotheses (and others, such as the Riverrefuge, the Recent Lagoon and the Hydrogeological Recent Change hypotheses) could have affected the evolution of the capybara to generate the current mitochondrial diversity. Thus, it is difficult to generalize a unique Amazon biota diversification hypothesis because each species or taxon could be affected by different processes and because the temporal antiquity of each taxon in South America is also different. Many mammalian taxa, and others, migrated into South America during the Great American Biotic Interchange (GABI) and their diversification processes in South America were mainly driven by Pleistocene events as those proposed by the Refuge hypothesis. Older taxa within this continent could have begun their current genetics diversification processes earlier, such as in the case of the capybara.