Genetic Variation Among Certain Fish Species in Terms of Evolution and Lineages

Three tests of phylogenetic including likelihood-joining tree, neighbour-joining tree, and minimum evolution tree have been used based on sox3 gene. Phylogenetic analysis was used to detect the genetic affinity and common ancestors for selected species that belong to the same or different families. This study showed the most appropriate methods for testing the genetic affinity among species and the methodology of each test according to the requirement of molecular applications. Secondary RNA predicted structure and minimum free energy were also included in this study because of their contribution to the detection of the orthologous gene and variance in RNA folding among species related to the different families. The genetic distance in the studied populations was calculated to know the most appropriate way to find out the genetic similarity among the studied species. The low distance-variance value of each group indicated significant genetic affinity among the species of the same family, this result is more consistent with the test of maximum-likelihood tree indicating the validity of this test to measure the genetic affinity among species that have common ancestors.

Norovirus GII.2[P16] strain in Shenzhen, China: a retrospective study

Background Norovirus (NoV) is the main cause of non-bacterial acute gastroenteritis (AGE) outbreaks worldwide. From September 2015 through August 2018, 203 NoV outbreaks involving 2500 cases were reported to the Shenzhen Center for Disease Control and Prevention. Methods Faecal specimens for 203 outbreaks were collected and epidemiological data were obtained through the AGE outbreak surveillance system in Shenzhen. Genotypes were determined by sequencing analysis. To gain a better understanding of the evolutionary characteristics of NoV in Shenzhen, molecular evolution and mutations were evaluated based on time-scale evolutionary phylogeny and amino acid mutations. Results A total of nine districts reported NoV outbreaks and the reported NoV outbreaks peaked from November to March. Among the 203 NoV outbreaks, 150 were sequenced successfully. Most of these outbreaks were associated with the NoV GII.2[P16] strain (45.3%, 92/203) and occurred in school settings (91.6%, 186/203). The evolutionary rates of the RdRp region and the VP1 sequence were 2.1 × 10–3 (95% HPD interval, 1.7 × 10–3–2.5 × 10–3) substitutions/site/year and 2.7 × 10–3 (95% HPD interval, 2.4 × 10–3–3.1 × 10–3) substitutions/site/year, respectively. The common ancestors of the GII.2[P16] strain from Shenzhen and GII.4 Sydney 2012[P16] diverged from 2011 to 2012. The common ancestors of the GII.2[P16] strain from Shenzhen and previous GII.2[P16] (2010–2012) diverged from 2003 to 2004. The results of amino acid mutations showed 6 amino acid substitutions (*77E, R750K, P845Q, H1310Y, K1546Q, T1549A) were found only in GII.4 Sydney 2012[P16] and the GII.2[P16] recombinant strain. Conclusions This study illustrates the molecular epidemiological patterns in Shenzhen, China, from September 2015 to August 2018 and provides evidence that the epidemic trend of GII.2[P16] recombinant strain had weakened and the non-structural proteins of the recombinant strain might have played a more significant role than VP1.

Composition and Genealogical Relation Network of the Medical Family in the Late Joseon Dynasty

Uiyeokju Palsebo (醫譯籌八世譜) is a genealogy record that contains the eighth generation of patrilineal ancestors, maternal grandfathers, and fathers-in-law of technical officials who worked in three fields: medicine, linguistics, and mathematics. This book covers members of influential families who monopolized the positions of technical officers. In that respect, it seems to have had an effect like a kind of 'white list'. This paper identifies the range of families based on common ancestors above eight generations according to the editing method of this book, attempting various statistical analysis. The results of the analysis shows that it is possible to determine the size of the medical families, which varied according to the number of medical bureaucrats and the distance of kinship between them. Most of the families had workers in the three fields of medicine, linguistics, and mathematics, but there were also ‘families more specialized in medicine’ that produced a large number of medical figures. The ancestors of medical figures were mainly engaged in the three fields of medicine, linguistics, and mathematics, but there were also a small number of officials in charge of “unhak(雲學: including astronomy, geography, and fortune-telling),” law, art, and transcription. For distant ancestors from common ancestors to the fifth generation, the proportion of technical officers was small, but for relatively close ancestors, the proportion of technical officers, especially medical officers, increased. It can be seen that the status as a medical officer tends to be hereditary further down the generations. The fields of activity of the maternal grandfathers and fathers-in-law of medical figures were more concentrated in the medical field. This can be the result of confirming the influence of the marital relationship network that was formed in the close period with the medical persons being investigated. In this paper, only medical figures were considered as primary research subjects, but their macroscopic networks were relatively evenly spread out in the three fields of medicine, linguistics, and mathematics. In this network, Uiyeokju Palsebo contained homogeneous hierarchies that could continuously dominate a specific field of government office.

Precise genotyping of circular mobile elements uncovers human associated plasmids with surprisingly recent common ancestors

Mobile genetic elements with circular genomes play a key role in the evolution of microbial communities. These circular genomes correspond to cyclic paths in metagenome graphs, and yet, assemblies derived from natural microbial communities produce graphs riddled with spurious cycles, complicating the accurate reconstruction of circular genomes. We present an algorithm that reconstructs true circular genomes based on the identification of so-called ′dominant′ cycles. Our algorithm leverages paired reads to bridge gaps between assembly contigs and scrutinizes cycles through a nucleotide-level analysis, making the approach robust to mis-assembly artifacts. We validated the approach using simulated and reference data. Application of this approach to 32 publicly available DNA shotgun sequence data sets from diverse natural environments led to the reconstruction of hundreds of circular mobile genomes. Clustering revealed 20 clusters of cryptic, prevalent, and abundant plasmids that have clonal population structures with surprisingly recent common ancestors. This work enables the robust study of evolution and spread of mobile elements in natural settings.

Some Miscellaneous Properties of Valuated Binary Tree

The paper proves several new properties of the valuated binary tree, including calculation of direct ancestors of a node, transition of a node in or out of a subtree, evaluation of a node by its brothers and distribution of common ancestors of given consecutive nodes. The contents can be a reference for future deep study of the valuated binary tree.

Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria

The bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia (Ecdysozoa and the Lophotrochozoa) and Deuterostomia (Chordata and the Xenambulacraria). Recent molecular phylogenetic studies have not consistently supported deuterostome monophyly. Here, we compare support for Protostomia and Deuterostomia using multiple, independent phylogenomic datasets. As expected, Protostomia is always strongly supported, especially by longer and higher-quality genes. Support for Deuterostomia, however, is always equivocal and barely higher than support for paraphyletic alternatives. Conditions that cause tree reconstruction errors—inadequate models, short internal branches, faster evolving genes, and unequal branch lengths—coincide with support for monophyletic deuterostomes. Simulation experiments show that support for Deuterostomia could be explained by systematic error. The branch between bilaterian and deuterostome common ancestors is, at best, very short, supporting the idea that the bilaterian ancestor may have been deuterostome-like. Our findings have important implications for the understanding of early animal evolution.

Genetic composition and evolution of the prevalent Mycobacterium tuberculosis lineages 2 and 4 in the Chinese and Zhejiang Province populations

The causative agent of tuberculosis (TB) comprises seven human-adapted lineages. Human movements and host genetics are crucial to TB dissemination. We analyzed whole-genome sequencing data for a countrywide collection of 1154 isolates and a provincial collection of 1296 isolates, constructed the best-scoring maximum likelihood phylogenetic tree, conducted Bayesian evolutionary analysis to compute the most recent common ancestors of lineages 2 and 4, and assessed the antigenic diversity in human T cell epitopes by calculating pairwise dN/dS ratios. Of the 1296 Zhejiang isolates, 964 (74.38%) belonged to lineage 2 and 332 (25.62%) belonged to lineage 4. L2.2 is the most ancient sub-lineage in Zhejiang, first appearing approximately 6897 years ago (95% HDI: 6513-7298). L4.4 is the most modern sub-lineage, first appearing approximately 2217 years ago (95% HDI: 1864-2581). The dN/dS ratios revealed that the epitope and non-epitope regions of lineage 2 strains were significantly (P<0.001) more conserved than those of lineage 4. An increase in the frequency of lineage 4 may reflect its successful transmission over the last 20 years. The recent common ancestors and transmission routes of the sub-lineages are related to the entry of humans into China and Zhejiang Province.

Haplosporosomes, sporoplasmosomes and their putative taxonomic relationships in rhizarians and myxozoans

This paper reviews current knowledge of the structure, genesis, cytochemistry and putative functions of the haplosporosomes of haplosporidians (Urosporidium, Haplosporidium, Bonamia, Minchinia) and paramyxids (Paramyxa, Paramyxoides, Marteilia, Marteilioides, Paramarteilia), and the sporoplasmosomes of myxozoans (Myxozoa – Malacosporea, Myxosporea). In all 3 groups, these bodies occur in plasmodial trophic stages, disappear at the onset of sporogony, and reappear in the spore. Some haplosporidian haplosporosomes lack the internal membrane regarded as characteristic of these bodies and that phylum. Haplosporidian haplosporogenesis is through the Golgi (spherulosome in the spore), either to form haplosporosomes at the trans-Golgi network, or for the Golgi to produce formative bodies from which membranous vesicles bud, thus acquiring the external membrane. The former method also forms sporoplasmosomes in malacosporeans, while the latter is the common method of haplosporogenesis in paramyxids. Sporoplasmogenesis in myxosporeans is largely unknown. The haplosporosomes of Haplosporidium nelsoni and sporoplasmosomes of malacosporeans are similar in arraying themselves beneath the plasmodial plasma membrane with their internal membranes pointing to the exterior, possibly to secrete their contents to lyse host cells or repel haemocytes. It is concluded that these bodies are probably multifunctional within and between groups, their internal membranes separating different functional compartments, and their origin may be from common ancestors in the Neoproterozoic.

Lineage and Virtue in Josephus: The Respective Roles of Priestly Worldview and Roman Culture

This article assesses the importance of lineage and virtue in Josephus’ notions of Jewish nobility and the Jewish people. Furthermore, it investigates the respective roles of Josephus’ priestly education and his exposition to Roman culture in his use of such concepts. I argue that while Josephus adopted some aspects of Roman or Greco-Roman discourses on nobility, such as the notion that true nobility goes along with virtue, he resisted the Roman sociopolitical view of nobility, because he tended to identify Jewish aristocracy with the priesthood and thus stuck to a genealogical model. By contrast, Josephus’ definition of the kinship (oikeiotēs) that unites the members of the Jewish people as based either on birth/common ancestors or on choice (the choice to live under Jewish laws, implicitly characterized as virtuous) in Against Apion reflects the impact on the Judean historian of Roman citizenship grants and the pro-Roman discourses that praised this policy.