Repetitive DNA Restructuring Across Multiple Nicotiana Allopolyploidisation Events Shows a Lack of Strong Cytoplasmic Bias in Influencing Repeat Turnover

Allopolyploidy is acknowledged as an important force in plant evolution. Frequent allopolyploidy in Nicotiana across different timescales permits the evaluation of genome restructuring and repeat dynamics through time. Here we use a clustering approach on high-throughput sequence reads to identify the main classes of repetitive elements following three allotetraploid events, and how these are inherited from the closest extant relatives of the maternal and paternal subgenome donors. In all three cases, there was a lack of clear maternal, cytoplasmic bias in repeat evolution, i.e., lack of a predicted bias towards maternal subgenome-derived repeats, with roughly equal contributions from both parental subgenomes. Different overall repeat dynamics were found across timescales of <0.5 (N. rustica L.), 4 (N. repanda Willd.) and 6 (N. benthamiana Domin) Ma, with nearly additive, genome upsizing, and genome downsizing, respectively. Lower copy repeats were inherited in similar abundance to the parental subgenomes, whereas higher copy repeats contributed the most to genome size change in N. repanda and N. benthamiana. Genome downsizing post-polyploidisation may be a general long-term trend across angiosperms, but at more recent timescales there is species-specific variance as found in Nicotiana.

Categorization via movement: the syntax and semantics of ambos

ABSTRACT In order to explain the syntactic behavior and describe the meaning of the item ambos in Brazilian Portuguese, we propose, assuming the Distributed Morphology framework, (1) that the acategorial root amb- merges, in the syntactic derivation, to a D that moves from inside a full definite DP, and this D categorizes the root; (2) that amb-+D merges back to the DP which D was the head of; (3) that the lower copy of D is erased (or becomes invisible) when the derivation reaches LF; (4) that the meaning of the combination of D and amb- is defined only if the context provides a unique set of two individuals with the properties defined by the plural NP taken by ambos, and introduces a universal quantification over this set.

Syntactic Phenomena in Peruvian Spanish

This work analyzes the syntactic properties of three constructions in Peruvian Spanish: existential sentences, double possession, and doubled clitic climbing. It considers the interaction between feature bundling and the operation Agree, providing evidence in favor of a microparametric approach to language and dialectal variation. It explains the apparent agreement between the existential verb and its accusative object by postulating a T with a valued [person] feature and a Small v with only [number] but not [person], and also for the doubling of the possessor if Small n has a [genitive] feature transferred from the contact language, which incorporates into the D head, inflecting it as a possessive determiner. In addition, it accounts for the doubled clitic climbing constructions by claiming that the clitic in these cases has a referentiality feature, which gives it an affixal nature. Therefore it blocks the c-command relation with its lower copy, forcing it to be pronounced.

Lower and Higher Copies in Arabic

This paper examines the phenomenon of copying in Standard Arabic (SA) within the copy theory. Following Boskovic and Nunes (2007), the researcher contends that Arabic utilizes two ways for the pronunciation of heads and copies governed by syntactic and phonological constraints. The highest link can be phonetically realized, or copies are pronounced instead of their heads by PLC without causing the derivation to crash. The paper shows how the copy theory accounts for the differences between perfective and imperative forms on one hand and the imperfective form on the other hand. The copy theory helps account for V-to-T0 movement in imperatives and perfectives in comparison with remaining in lower projections in imperfectives. Further, the research reveals that certain fixed word orders in Arabic can be accounted for in terms of the copy theory. The type of the object DP plays a role in which copy is realized, and hence affects word order. The higher copy of the object DP is pronounced when it is an enclitic object pronoun, while the lower copy is pronounced when the object is an R-expression DP. Addressing the topic of copying from a semantics-syntax interface perspective, the paper explains the bearings of copy operations on syntax.

An algorithm to evaluate the efficacy of detecting somatic mutations

Detection of somatic mutations from late stage solid tumors is a critical part of cancer treatment. Although tumor content is used as a convenient parameter to measure efficacy of detection, it fails to include two basic factors: the lower limit of detection (LLOD), and the ratio of the mutant and wild type allele frequencies. Recently, the detection of somatic mutations has expanded to liquid biopsy, early stages of cancer and population screening, which all generally carry lower copy numbers of somatic mutations compared to late stage tumors. With the growing importance of these mutations for targeted chemotherapy and other clinical applications, there is a need re-evaluate the efficacy of detection of somatic mutations. Hence, a new algorithm, Detection Index (DI), is proposed to standardize the efficacy of all molecular methods and is applicable to all types of clinical samples. Detection Index (DI) is based on two basic determinants: lower limit of detection of the mutant allele, and the ratio of the copies of the mutant allele to that of the wild-type. The benefits of DI include (a) standardization of methods detecting somatic mutations so that laboratory reports will have a uniform interpretation related to clinical picture, and (b) the flexibility to use appropriate amounts of DNA and assay conditions to achieve desired DI.

Ellipsis in Wh-in-Situ Languages: Deriving Apparent Sluicing in Hindi-Urdu and Uzbek

Wh-in-situ languages have a special role to play in investigating the relation between the wh-syntax of a language and the availability of sluicing-like constructions (SLCs). Van Craenenbroeck and Lipták (2013) propose that whether a language exhibits genuine sluicing should be predictable from the syntax of the language’s wh-questions in nonelliptical contexts. We refine this formulation by considering SLCs in two contrasting wh-in-situ languages, Hindi-Urdu and Uzbek. Hindi-Urdu wh-movement occurs in the narrow syntax, but is obscured by PF processes; in Uzbek, no narrow syntax dependency is involved. Correspondingly, only Hindi-Urdu SLCs involve genuine sluicing; Uzbek SLCs are derived from reduced copular clauses. Thus, narrow syntax wh-movement may be obscured by lower-copy pronunciation in nonelliptical environments; the head of the wh-chain is then pronounced in combination with ellipsis, but not otherwise. Here, we demonstrate that the availability of genuine sluicing in Hindi-Urdu and Uzbek corresponds directly to the specific properties of their wh-systems, but not necessarily to the surface position of wh-material in a typical constituent question.

A Restriction on Vehicle Change and Its Interaction with Movement

This squib presents a restriction on the phenomenon descriptively known as ‘‘vehicle change’’ that has not, to our knowledge, previously been noted. With vehicle change construed as a kind of ‘‘tolerable mismatch’’ between an ellipsis site and its antecedent, the data we present suggest that exactly the same mismatches cannot be tolerated between the members of a movement chain. While in principle one might consider the possibility that ellipsis and movement could be reduced to the same operation ( Chomsky 1995:252–253 )—that the deletion usually described as ellipsis might be the same operation as the deletion or ‘‘chopping’’ (in the sense of Ross 1967) that applies to the unpronounced (usually lower) copy in a movement chain—the differences in the kinds of mismatches that can be tolerated will pose a difficulty for this unification. We present the crucial data that suggest that such a unification is not tenable in section 1 and then outline an explanation of these facts in section 2 . We state this explanation in terms of the way movement, ellipsis, and vehicle change interact, while remaining largely agnostic about the exact mechanisms that implement these somewhat pretheoretic notions. In section 3 , we consider the consequences for these more fine-grained questions about the nature of ellipsis and movement, and in section 4 , we consider some further implications that depend on how vehicle change is understood. Section 5 addresses a challenge for our proposed explanation that turns out to be only illusory, and section 6 briefly concludes.

‘Verb floating’ and VP-ellipsis

In this paper I propose that ellipsis is licensed by overt movement. Examining variation in VP-ellipsis across English dialects, I show that movement is crucially implicated in whether or not a given element can license ellipsis. I discuss well-known restrictions on VP-ellipsis and present new data that shows that a movement-based account of these restrictions is superior to previous ones. I show that the proposed account can be extended to other cases involving A′ movement with empirical benefits, and I conclude by sketching the technical implementation of the theory, arguing that ellipsis is a ‘repair’ operation that prevents a linearization failure following non-deletion of a lower copy. I suggest that types of movement that are unable to spell out lower copies (i.e. A-movement) do not license ellipsis, thus explaining ellipsis licensing in terms of general conditions on copy deletion. Keywords: ellipsis licensing; VP-ellipsis; sluicing; Copy Theory of Movement; A/A′-distinction

Evolutionary Competitiveness of Two Natural Variants of the IncQ-Like Plasmids, pRAS3.1 and pRAS3.2

ABSTRACT Plasmids pRAS3.1 and pRAS3.2 are natural variants of the IncQ-2 plasmid family, that except for two differences, have identical plasmid backbones. Plasmid pRAS3.1 has four 22-bp iterons in its oriV region, while pRAS3.2 has only three 6-bp repeats and pRAS3.1 has five 6-bp repeats in the promoter region of the mobB-mobA/repB genes and pRAS3.2 has only four. In previous work, we showed that the overall effect of these differences was that when the plasmid was in an Escherichia coli host, the copy numbers of pRAS3.1 and pRAS3.2 were approximately 41 and 30, respectively. As pRAS3.1 and pRAS3.2 are likely to have arisen from the same ancestor, we addressed the question of whether one of the variants had an evolutionary advantage over the other. By constructing a set of identical plasmids with the number of 22-bp iterons varying from three to seven, it was found that plasmids with four or five iterons displaced plasmids with three iterons even though they had lower copy numbers. Furthermore, the metabolic load that the plasmids placed on E. coli host cells compared with plasmid-free cells increased with copy number from 10.9% at a copy number of 59 to 2.6% at a copy number of 15. Plasmid pRAS3.1 with four 22-bp iterons was able to displace pRAS3.2 with three iterons when both were coresident in the same host. However, the lower-copy-number pRAS3.2 placed 2.8% less of a metabolic burden on an E. coli host population, and therefore, pRAS3.2 has a competitive advantage over pRAS3.1 at the population level, as pRAS3.2-containing cells would be expected to outgrow pRAS3.1-containing cells.