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Methods: Using next-generation sequence data, we assembled the plastid genome of saguaro cactus and probed the nuclear genome for transferred plastid genes and functionally related nuclear genes. We combined these results with available data across Cactaceae and seed plants more broadly to infer the history of gene loss and to assess the strength of phylogenetic association between gene loss and loss of the inverted repeat (IR).
Key results: The saguaro plastid genome is the smallest known for an obligately photosynthetic angiosperm (∼113 kb), having lost the IR and plastid ndh genes. This loss supports a statistically strong association across seed plants between the loss of ndh genes and the loss of the IR. Many nonplastid copies of plastid ndh genes were found in the nuclear genome, but none had intact reading frames; nor did three related nuclear-encoded subunits. However, nuclear pgr5, which functions in a partially redundant pathway, was intact.
Conclusions: The existence of an alternative pathway redundant with the function of the plastid NADH dehydrogenase-like complex (NDH) complex may permit loss of the plastid ndh gene suite in photoautotrophs like saguaro. Loss of these genes may be a recurring mechanism for overall plastid genome size reduction, especially in combination with loss of the IR.
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This article looks closely at two types of errors children have been shown to make with universal quantification—Exhaustive Pairing (EP) errors and Underexhaustive errors—and asks whether they reflect the same underlying phenomenon. In a large-scale, longitudinal study, 140 children were tested 4 times from ages 4 to 7 on sentences involving the universal quantifier every. We find an interesting inverse relationship between EP errors and Underexhaustive errors over development: the point at which children stop making Underexhaustive errors is also when they begin making EP errors. Underexhaustive errors, common at early stages in our study, may be indicative of a non-adult, non-exhaustive semantics for every. EP errors, which emerge later, and remain frequent even at age 7, are progressive in nature and were also found with adults in a control study. Following recent developmental work (Drozd and van Loosbroek 2006; Smits 2010), we suggest that these errors do not signal lack of knowledge, but may stem from independent difficulties appropriately restricting the quantifier domain in the presence of a salient, but irrelevant, extra object.