Vol. 7 Núm. 2 (2021): Agosto, Early View

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The population genomics of adaptive loss of function

Discoveries of adaptive gene knockouts and widespread losses of complete genes have in recent years led to a major rethink of the early view that loss-of-function alleles are almost always deleterious. Today, surveys of population genomic diversity are revealing extensive loss-of-function and gene content variation, yet the adaptive significance of much of this variation remains unknown. Here we examine the evolutionary dynamics of adaptive loss of function through the lens of population genomics and consider the challenges and opportunities of studying adaptive loss-of-function alleles using population genetics models. We discuss how the theoretically expected existence of allelic heterogeneity, defined as multiple functionally analogous mutations at the same locus, has proven consistent with empirical evidence and why this impedes both the detection of selection and causal relationships with phenotypes. We then review technical progress towards new functionally explicit population genomic tools and genotype-phenotype methods to overcome these limitations. More broadly, we discuss how the challenges of studying adaptive loss of function highlight the value of classifying genomic variation in a way consistent with the functional concept of an allele from classical population genetics.

Nawaran Esquerré, Donnellan, Brennan, Lemmon, Lemmon, Zaher, Grazziotin & Keogh, 2020 is an invalid junior synonym of Nyctophilopython Wells & Wellington, 1985 (Squamata, Pythonidae): simple priority without Zoobank pre-registration

In their careful analysis of python phylogeny and evolution, Esquerré et al. (2020) proposed the new genus-series nomen Nawaran for the Oenpelli python, Simalia oenpelliensis (Gow, 1977). However, Nawaran is a junior synonym of Nyctophilopython Wells & Wellington, 1985, a name that was validly, though controversially, published in compliance with the Code. Furthermore, while the nomen Nawaran initially appeared in an “early view” of the article on or about 21 May 2020, it was not registered on Zoobank until 23 September 2020 and did not become available for the purposes of zoological nomenclature until 30 November 2020, the date of the printed publication according to Article 21.3 of the Code. Complications for nomenclature resulting from “pre-publications” and lapses with Zoobank registration are not uncommon, and we urge taxonomists considering the erection of new nomina to give careful attention to the nomenclatural rules of the Code.

The Political Problem

This chapter argues that Hobbes’s late view of human collective power, unlike the early view, is able to grasp informal and emergent collective power. Hobbes’s later works, with their new relational conception of potentia, offer both theoretical resources to conceive informal collective power distinct from the state, and also analytical reasons to expect such power to be politically troubling. The ‘political problem’ emerges: in order to achieve the concrete power sufficient to uphold its absolute authority (potestas), the state needs to harness or tame the informal collective powers within the populace. The chapter argues that the political problem explains the absence of the ‘sleeping sovereign’, so central to the radical democratic interpretation of Hobbes, from Hobbes’s later writings. But informal collective power cannot necessarily be celebrated as a welcome popular insurgency against excessive state power: for its characteristic inner structure is complex oligarchic allegiance rather than equal horizontal affiliation.

Juridical Politics

This chapter sketches Hobbes’s early view of human collective power, arguing that he conceives of this power in exclusively juridical terms. Hobbes’s most obvious account of collective power is his theory of the sovereign state (or commonwealth, civitas), which possesses power as authority, potestas. The holder of potestas could be a popular sleeping sovereign, a more traditional ruling assembly, or a head of state, but in all cases the potestas itself can only arise when the powers of the individual members of the population are brought together in formal juridical union. This chapter argues that in Hobbes’s early view, there is no other kind of collective power; it offers no conceptual rubric to conceive of informal or emergent collective human power. This view is characterized as neo-scholastic; the conceptual limitation of the neo-scholastic view is undergirded by a practical confidence that informal collectivities will not be robust or politically troubling.

Light Activates Brassinosteroid Biosynthesis to Promote Hook Opening and Petiole Development in Arabidopsis thaliana

Although brassinosteroids (BRs) have been proposed to be negative regulators of photomorphogenesis, their physiological role therein has remained elusive. We studied light-induced photomorphogenic development in the presence of the BR biosynthesis inhibitor, brassinazole (Brz). Hook opening was inhibited in the presence of Brz; this inhibition was reversed in the presence of brassinolide (BL). Hook opening was accompanied by cell expansion on the inner (concave) side of the hook. This cell expansion was inhibited in the presence of Brz but was restored upon the addition of BL. We then evaluated light-induced organ-specific expression of three BR biosynthesis genes, DWF4, BR6ox1 and BR6ox2, and a BR-responsive gene, SAUR-AC1, during the photomorphogenesis of Arabidopsis. Expression of these genes was induced, particularly in the hook region, in response to illumination. The induction peaked after 3 h of light exposure and preceded hook opening. Phytochrome-deficient mutants, hy1, hy2 and phyAphyB, and a light-signaling mutant, hy5, were defective in light-induced expression of BR6ox1, BR6ox2 and SAUR-AC1. Light induced both expression of BR6ox genes and petiole development. Petiole development was inhibited in the presence of Brz. Our results largely contradict the early view that BRs are negative regulators of photomorphogenesis. Our data collectively suggest that light activates the expression of BR biosynthesis genes in the hook region via a phytochrome-signaling pathway and HY5 and that BR biosynthesis is essential for hook opening and petiole development during photomorphogenesis.