Evolutionary Analysis of the YABBY Gene Family in Brassicaceae

The YABBY gene family is one of the plant transcription factors present in all seed plants. The family members were extensively studied in various plants and shown to play important roles in plant growth and development, such as the polarity establishment in lateral organs, the formation and development of leaves and flowers, and the response to internal plant hormone and external environmental stress signals. In this study, a total of 364 YABBY genes were identified from 37 Brassicaceae genomes, of which 15 were incomplete due to sequence gaps, and nine were imperfect (missing C2C2 zinc-finger or YABBY domain) due to sequence mutations. Phylogenetic analyses resolved these YABBY genes into six compact clades except for a YAB3-like gene identified in Aethionema arabicum. Seventeen Brassicaceae species each contained a complete set of six basic YABBY genes (i.e., 1 FIL, 1 YAB2, 1 YAB3, 1 YAB5, 1 INO and 1 CRC), while 20 others each contained a variable number of YABBY genes (5–25) caused mainly by whole-genome duplication/triplication followed by gene losses, and occasionally by tandem duplications. The fate of duplicate YABBY genes changed considerably according to plant species, as well as to YABBY gene type. These YABBY genes were shown to be syntenically conserved across most of the Brassicaceae species, but their functions might be considerably diverged between species, as well as between paralogous copies, as demonstrated by the promoter and expression analysis of YABBY genes in two Brassica species (B. rapa and B. oleracea). Our study provides valuable insights for understanding the evolutionary story of YABBY genes in Brassicaceae and for further functional characterization of each YABBY gene across the Brassicaceae species.

Imagining a new ‘abnormal’ amidst COVID-19: Seeking guidance from evolutionary anthropology and theology

The coronavirus disease 2019 (COVID-19) pandemic is responsible for the large-scale devastation experienced all over the world. This ‘invisible stranger’ interrupting our daily lives is highlighting in a new and acute way the vulnerability of the human race. Life as we knew it is being changed forever. COVID-19 also exposed the injustices embedded in social structures all over the world. What will life with and after COVID-19 look like in South Africa? The pandemic reveals that South Africa is not the fair and just society we hoped for since the transition to a democratic country in 1994. In light of this, we should be preparing ourselves for the new ‘abnormal’ as what seemed normal was problematic and therefore, truly abnormal. Seeking guidance from evolutionary anthropology, this article will explore whether the evolutionary story of Homo sapiens might offer us insights on how to successfully navigate the multiple challenges COVID-19 unmasks and also brings forth. A discussion on the evolutionary history of homo sapiens within the context of niche construction theory reveals that our unique capacity for imagination and creative collaboration made us successful as a species. It is these capacities for imagination and cooperation that might facilitate us in successfully imagining and thereafter living the new ‘abnormal’. In this article, the question of imaging the new ‘abnormal’ will be explored.Contribution: By creatively integrating the perspectives evident in this research, this article explores whether the Prophets of Israel might offer a feasible paradigm to determine coordinates for the imagined new ‘abnormal’ to be a more fair and just society.

Morphological evidence for paraphyly of Holopothrips Hood (Thysanoptera: Phlaeothripidae), a Neotropical genus of gall-inducing thrips

Holopothrips is a diverse group of thrips associated to galls in the Neotropics, with a variety of host plants and wide morphological diversity. Relationships to other Neotropical groups have been proposed, but are still untested, and the monophyly of the genus remains doubtful. Here, we perform a phylogenetic analysis of Holopothrips, based on morphological characters. A total of 87 species were included in the matrix and eight analyses were carried out, but all of them failed to recover Holopothrips as a monophyletic grouping. Bremer and Bootstrap support values were low, and the topologies varied among all analyses, with uncertain internal relations for the ingroup. These results indicate that the relationships for Holopothrips species, and the proposed related genera, are more complex than previously reported; and morphological characters may not be enough to recover the evolutionary story within this group. We also discuss the influences of different character coding, continuous characters and weighting schemes in our results.

How is Rice Organ Painted: the Genetic Basis of Anthocyanin Biosynthesis in Rice

Anthocyanins are major subclasses of flavonoids, which have diverse biological functions and benefit human health. In Oryza sativa, organs exhibit various color due to the accumulation of anthocyanins. On the other hand, anthocyanins biosynthesis is a domestication related trait. Revealing the genetic basis of anthocyanins biosynthesis in rice is not only important for the engineering of anthocyanins, but also helpful for understanding the evolutionary story of Oryza sativa. Here we summarize the recent progresses in rice anthocyanins biosynthesis, including the anthocyanins biosynthetic pathway, the genes that participate in anthocyanins biosynthesis, the cloning of anthocyanins related genes and the domestication process of rice anthocyanins. Possible applications of rice anthocyanin biosynthesis genes in rice breeding and the remaining unknown mechanism of anthocyanins accumulation in stigma, apiculus and awn are also discussed.

You Can Lead a Horse to Water, But You Can’t Make It Drink

As I understand it, the central aim of the field of CSR is to reconcile (in the sense of “consilience”) methods and theories from the natural sciences with research on religion, which though defined in various ways, is usually understood as a universal human phenomenon. This does not necessarily mean religion is innate, but like all universal human phenomena, there will be an evolutionary story to tell about how it, or its constituent elements, came about. The stories are usually about the phenomena of religion writ-large, variously defined, rarely reaching the granularity to make claims about specific historical and cultural circumstances where religion is most relevant to agents. I challenge all scholars of religion to make their metaphysics explicit.

The evolution of water-breathing respiratory faculties in invertebrates

This chapter aims at piecing together the evolution of water breathing in invertebrates. Dedicated respiratory faculties, consisting of an external exchanger, an internal transport system (circulatory system or an equivalent), and some control element are first clearly recognizable among invertebrates in annelids, which excel in the number of different respiratory proteins they display. Molluscs and arthropods use primarily haemocyanin, each group showing evolutionary trends in respiratory proteins that have some bearing on the phylogenetic position. Each major group of molluscs has its own evolutionary story, but in general we see a reduction in the number of gills and often a release from bilateral symmetry. Among arthropods, crustaceans can develop gills on various parts of the legs and the body wall, each group showing a taxon-specific type. Arachnids and hexapods are primarily terrestrial, but several groups have independently and secondarily developed mechanisms for even long-term survival under water.

“The Ingenious Unravelling of Evidence”: Empathy, Extinction, and Wells’s The Croquet Player

While we are increasingly challenged to imagine a world without humans, we have also become increasingly attentive to the subject of empathy, in popular culture, the humanities, and the sciences. In The Time Machine (1895), and a number of essays on evolution or extinction, H. G. Wells articulated a speculative evolutionary theory, a vision of nature unencumbered by everyday anthropocentricism. His little-known 1936 novella, The Croquet Player, continues his evolutionary story of humanity by turning to the future’s entanglement with the past and culture’s entanglement with nature. Prescient, Wells’s novella speaks to the parallel phenomena entangled in the strange relation between extinction and empathy.