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Topic Review
Directed Cycles Evolve with Junk DNA
Cell responses are usually viewed as transitive events with fixed inputs and outputs that are regulated by feedback loops. In contrast, directed cycles (DCs) have all nodes connected, and the flow is in a single direction. Consequently, DCs can regenerate themselves and implement intransitive logic. DCs are able to couple unrelated chemical reactions to each edge. The output depends upon which node is used as input.
  • 153
  • 22 Nov 2023
Topic Review
Distinguishing Evolutionary Conservation from Derivedness
While the concept of “evolutionary conservation” has enabled biologists to explain many ancestral features and traits, it has also frequently been misused to evaluate the degree of changes from a common ancestor, or “derivedness”. From a methodological aspect, “conservation” mainly considers genes or traits which species have in common, while “derivedness” additionally covers those that are not commonly shared, such as novel or lost traits and genes to evaluate changes from the time of divergence from a common ancestor. Due to these differences, while conservation-oriented methods are effective in identifying ancestral features, they may be prone to underestimating the overall changes accumulated during the evolution of certain lineages.
  • 546
  • 06 Apr 2022
Topic Review
Ecology and Evolution of Saccharomyces cerevisiae
The yeast distributes ubiquitously in nature with clearly structured populations. The baker’s yeast Saccharomyces cerevisiae has become a powerful model in ecology and evolutionary biology. The global genetic diversity of S. cerevisiae is mainly contributed by strains from Far East Asia, and the ancient basal lineages of the species have been found only in China, supporting an ‘out-of-China’ origin hypothesis. The wild and domesticated populations are clearly separated in phylogeny and exhibit hallmark differences in sexuality, heterozygosity, gene copy number variation (CNV), horizontal gene transfer (HGT) and introgression events, and maltose utilization ability. The domesticated strains from different niches generally form distinct lineages and harbor lineage-specific CNVs, HGTs and introgressions, which contribute to their adaptations to specific fermentation environments. 
  • 1.1K
  • 01 Mar 2022
Topic Review
Egyptian Carob Pods (Ceratonia siliqua L.) Aqueous Extract
Ceratonia siliqua (Carob) is an evergreen Mediterranean tree, and carob pods are potentially nutritive and have medicinal value. 
  • 486
  • 15 Dec 2021
Topic Review
Encyclopedia in Phylogenomic and Biogeography of Toddalia asiatica
Toddalia is a monotypic genus consisting of sole species Toddalia asiatica (L.) Lam., widely distributed in Africa and Asia. It belongs to tribe Amyridoideae, family Rutaceae and order Sapindales. This genus together with genera Phellodendron Rupr., Tetradium Lour., and Zanthoxylum L. were found to produce alkaloids. The relationship of these chemical constituents has been hypothesized for the past years. The ancestor for Rutaceae has been linked to the several alkaloids recognized in these four genera, thus naming the group to date proto-Rutaceae. The four genera have attracted the attention of many scientists and they have been studied widely in previous studies. However, there is insufficient genomic resources in this genus. Additionally the origin and dispersal points of Toddalia species remains unclear. Here, researchers sequenced the two samples of Toddalia asiatica species, both collected from Kenya, and made comparison of their genome structures with T. asiatica species from China, available in the NCBI database. Phylogenomic analysis and impacts of climate change on Toddalia species were also conducted. The availability of the sequenced cp genomes will provide valuable genetic resources for further population genetics and biogeographic studies of these species by sampling them from a wider geographical range. 
  • 365
  • 28 Jan 2022
Topic Review
Endogenous Retroviruses and Placental Diversity
In mammals, although size differences exist, most of organs consists of the same cells and exhibits the same structures. However, placentas are quite diverse in cell components, structures and the association between fetal membranes and maternal uteri. These differences have not been well characterized. Recently, endogenous retroviruses (ERVs) have been thought to have caused such diversity, which require both PEG type genes and syncytins. 
  • 371
  • 05 Sep 2022
Topic Review
Eumelanin in the Living World
A lot of still unexplained aspects characterize eumelanin, a macromolecule able to play in living organisms several, sometimes conflicting, roles. This contribution aims  to emphasize the unique characteristics and the consequent unusual behaviors of a molecule that in an evolutionary context survived natural selection and still holds the main chemical/physical features detected in fossils dating to the late Carboniferous. 
  • 278
  • 29 May 2023
Topic Review
Evolution of 14-3-3 Proteins in Angiosperm Plants
14-3-3 proteins are key regulatory factors in plants and are involved in a broad range of physiological processes. We focused on the evolutionary history of 14-3-3s from 46 angiosperm species, including basal angiosperm Amborella and major lineage of monocotyledons and eudicotyledons. 
  • 429
  • 20 Dec 2021
Topic Review
Exploring Behavioural Plasticity of Cats
Understanding behavioural plasticity and other recently evolved traits of domestic cats may lead to management strategies that maximise health and welfare of cats, wildlife, and humans—otherwise domestic cat behaviour may be ‘misunderstood’. Importantly, interdisciplinary research using expertise from biological and social sciences, and engaging human communities, should evaluate these management strategies to ensure they maintain optimal welfare of free-ranging domestic cats while preserving biodiversity and protecting wildcats.
  • 825
  • 26 Jul 2022
Topic Review
False Alarm Flight of Birds
Bird flocks often take flight suddenly, as though escaping from a predator, even though no predator is present. This is called “false alarm flighting”. 
  • 398
  • 14 Feb 2022
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