Journal of Phylogenetics & Evolutionary Biology

Since its inception seventy-five years ago, the field of phylogenetics has steadily been expanding to contribute in a number of scientific fields including biogeography, medicinal chemistry, forensics, transcriptomics, cancer biology and even linguistics, in addition to systematic biology -for which it was originally erupted by Willi Hennig. In this invited editorial contributed to the Journal of Phylogenetics and Evolutionary Biology a big picture of this ever evolving field is expounded. Application of phylogenetic inference in biosystematics, phylogeography, phylogenetic selection of target taxa in medicinal chemistry, cancer phylogenetics, and linguistic phylogeny are reviewed with a personal perspective summarizing contribution to this interdisciplinary field from my group. Parametric methods such as Maximum Likelihood and Bayesian Inference have dramatically improved for last one decade, yet empirical solutions to some of the most fundamental issues, including homoplasmy and lineage sorting, remains to be materialized.

We used a relaxed-clock program (Multidivtime) to estimate the phylogenetic relatedness and substitution rates by comparative analyses of 16S rRNA gene and ITS region sequences. Four rhizobial strains isolated from three Tunisian wild Sulla legumes were used together with reference strains to obtain the 16S rRNA gene and ITS region alignments. Bayesian inferred trees were congruent, and showed a clear split between Agrobacterium and Rhizobium species. Among the four Tunisian isolates, Hsc01 belonged to Rhizobium species and formed a monophyletic clade with Rhizobium sullae. The strain Hc04 was placed into the Agrobacterium group, but it belonged to Rhizobium species. Two remaining strains (Hc01 and Hcar01) belonged to typically Agrobacterium species. Divergence times between these four strains were earlier the existence of legumes. Using sequence alignments of the 16S rRNA genes and ITS regions, we inferred different rates of nucleotide substitutions across these two molecular markers. The ITS region evolutionary rate was 15-fold higher than the 16S rRNA gene rate, suggesting that the ITS region represented an appropriate molecular marker for inferring phylogenies and divergence times in bacteria.

Calcium ions are utilised as a second messenger in all forms of cellular life. In contrast to bacteria and archaea, eukaryotes possess endomembrane systems, exemplified by the endoplasmic reticulum. Such organelles act as intracellular stores in Ca2+ signalling processes, with two distantly related calcium channels, the inositol 1,4,5- trisphosphate receptors and ryanodine receptors, acting as Ca2+ release mechanisms. Despite their fundamental role, the evolutionary origins of such Ca2+ release channels have proven difficult to elucidate. The current study presents updates on the phylogeny of this channel superfamily and analyses of the domain architectures of these proteins. We demonstrate that inositol 1,4,5-trisphosphate receptor homologues are present in every major taxonomic group of eukaryotic life, suggesting that they were utilised early on in the evolution of these organisms. Certain taxonomic groups contain multiple Ca2+ release channel homologues, suggesting expansion and diversification. Early diverging fungi and green plants contain a single canonical inositol 1,4,5-trisphosphate receptor, which is absent in later branching members, suggesting loss from at least two distinct lineages. A key difference in the protein architecture of the two channel families is the presence or absence of ryanodine receptor domains. Such ryanodine receptor domains occur in multiple families of proteins present in eukaryotes, bacteriophage viruses, bacteria and archaea. In eukaryotes, canonical ryanodine receptors are first detected in the choanoflagellate/metazoan lineage, but a distinct family of ryanodine receptor domain-containing proteins with the potential to form cation channels, that we name the ‘PKD-RR’ family, are conserved among oomycetes. Modelling of the tertiary structures of ryanodine receptor domains from viruses, bacteria, fungi and oomycetes indicates that they are likely to closely resemble those from mammalian ryanodine receptor channels. We also present evidence that horizontal gene transfer has occurred during the evolution of ryanodine receptor domain-containing proteins, thereby contributing to calcium release channel structural and functional diversity.

Weaning is one of the most stressful periods in a foal’s life. The traditional and most common weaning method is total and abrupt in China. The purpose of the research was to examine the stress-related behavioral response of foals and find the optimal weaning age by using abrupt and group weaning method. A total of 15 thoroughbred mare-foal pairs were divided into three groups A (6-month foals, n=5), B (7-month foals, n=5) and C (8-month foals, n=5) according to the weaning age. These foals were observed for 3 days before weaning and 9 days after separation, and 15 behavioral patterns were compiled. All statistical analysis was performed by R2.14.2 (R Development Core Team). Comparing to pre-weaning, frequency of drinking, urination, fast-moving, aggression behaviors increased and the frequency of standing, lying and individual rolling behaviors decreased after separation for three groups. On the weaning day (Day 0), drinking, urination, social game, friend were most pronounced and standing, slow-moving, individual rolling was least pronounced in foals of group A (p<0.05). Except for the same pronounce with group A, the frequency of fast-moving and individual nibbling were the highest in foals of group B (0.53 ± 0.49, 0.77 ± 0.15 times /h, respectively) and the frequency of defecation, social kidding, individual nibbling behaviors were the highest in foals of group C (0.38 ± 0.11, 1.75 ± 0.87, 0.71 ± 0.08 times /h, respectively) on the weaning day, whilst the frequency of slow-moving were strongly decreased in foals of group B (10.88 ± 0.69 times /h) and the frequency of social suck were strongly decreased in foals of group C (0.33 ± 0.07 times /h ) on the weaning day. 8, 12 and 13 behavior categories had changes in group A, group B and group C during the observation phase. Weaning is associated with stress but 6-month years old was least pronounced in foals by abrupt - group weaning method in China.

The teleological though is a well-known misunderstanding of evolutionary biology and it is frequently understood as the vision that organs, species (and genes) have evolved to achieve specific ends. The theory of evolution as predisposed by Charles Darwin is based on differential reproduction of randomly produced variants with no direction. This commentary intend to look into molecular genetics and genomics trying to point out major evolutionary conceptual problems on naming genes according to their most likely, first-described function. Naming genes in accord to their function may lead to misunderstandings and finalistic thoughts assumptions that genes might have “evolved for” accomplishing that function. Besides, the idea that a gene would be responsible for a single and unique function in the cellular environment became over simplistic. We now accept that genes have multiple splicing variants, messenger RNAs can attach multiple molecules in the cytoplasm, proteins have multiple sites of recognition by the immune system (epitopes), interact with many other proteins and most genes present regulatory roles in the cell metabolism. Gene name databases and biological ontologies consist in a powerful repositoire of gene characteristics and will certainly help further studies of gene systematics and taxonomy. Genes should be considered free-living entities evolving by the processes of natural selection and self-organization that cannot foresee functions to evolve for. Here I discuss the intellectual teleological background behind naming genes based on their functions and suggest new approaches for gene naming and classification in the future.

Achieving early detection at the onset of cancer is a major goal of cancer research. The early presence of aberrant DNA methylation makes the use of DNA methylation biomarkers an attractive candidate for early detection. Altered DNA methylation is ubiquitous in human cancers and specific methylation changes are often correlated with clinical features. DNA methylation biomarkers provide a range of opportunities for early detection, diagnosis, prognosis, therapeutic stratification and post-therapeutic monitoring. Furthermore, aging is one of the primary risk factors associated with cancer development. We conducted computational biology analyses of published High-grade serous ovarian cancer (HGSOC) epigenetic profiles using gene lists bearing human embryonic stem cell (hESC) characteristics. Through aging correlated features, epigenetic age-dependent marker panel on HGSOC was conducted. It is to be noted, the genes in the refined marker panel were found all included in the age-dependent features. The further experiment results showed not only the refined marker panel is able to represent the age-dependent features but performed better performance than the reported marker panel without associated with age parameter. Furthermore, the refined prognostic marker panel, including HOXA9, HSPA1A, and CALCA-associated with ovarian cancer and tumor growth, is strongly connected with literature support the potential for considering into clinical assay for patients’ stratification and future personalized medicine interventions.