mtDNA diversity in rhesus monkeys reveals overestimates of divergence time and paraphyly with neighboring species

Reconstructions of the human-African great ape phylogeny by using mitochondrial DNA (mtDNA) have been subject to considerable debate. One confounding factor may be the lack of data on intraspecific variation. To test this hypothesis, we examined the effect of intraspecific mtDNA diversity on the phylogenetic reconstruction of another Plio- Pleistocene radiation of higher primates, the fascicularis group of macaque (Macaca) monkey species. Fifteen endonucleases were used to identify 10 haplotypes of 40-47 restriction sites in M. mulatta, which were compared with similar data for the other members of this species group. Interpopulational, intraspecific mtDNA diversity was large (0.5%- 4.5%), and estimates of divergence time and branching order incorporating this variation were substantially different from those based on single representatives of each species. We conclude that intraspecific mtDNA diversity is substantial in at least some primate species. Consequently, without prior information on the extent of genetic diversity within a particular species, intraspecific variation must be assessed and accounted for when reconstructing primate phylogenies. Further, we question the reliability of hominoid mtDNA phylogenies, based as they are on one or a few representatives of each species, in an already depauperate superfamily of primates.      

A revision of the family Petrosaviaceae in Vietnam

The family Petrosaviaceae is represented by two species in Vietnam, viz. Petrosavia sakuraii restricted to the northern part of the country and P. stellaris distributed in its southern part. The latter species is shown to possess a wide range of distribution in Vietnam, though it was previously believed to be an exclusively Malesian species. The inclusion of P. sinii in P. sakuraii is confirmed. Details on distribution, illustrations and an identification key for these species are provided.     

Nonflowers near the base of extant angiosperms? Spatiotemporal arrangement of organs in reproductive units of Hydatellaceae and its bearing on the origin of the flower

Reproductive units (RUs) of Trithuria, the sole genus of the early-divergent angiosperm family Hydatellaceae, are compared with flowers of their close relatives in Cabombaceae (Nymphaeales). Trithuria RUs combine features of flowers and inflorescences. They differ from typical flowers in possessing an "inside-out" morphology, with carpels surrounding stamens; furthermore, carpels develop centrifugally, in contrast to centripetal or simultaneous development in typical flowers. Trithuria RUs could be interpreted as pseudanthia of two or more cymose partial inflorescences enclosed within an involucre, but the bractlike involucral phyllomes do not subtend partial inflorescences and hence collectively resemble a typical perianth. Teratological forms of T. submersa indicate a tendency to fasciation and demonstrate that the inside-out structure-the primary feature that separates RUs of Hydatellaceae from more orthodox angiosperm flowers-can be at least partially modified, thus producing a morphology that is closer to an orthodox flower. The Trithuria RU could be described as a "nonflower", i.e., a structure that contains typical angiosperm carpels and stamens but does not allow recognition of a typical angiosperm flower. The term nonflower could combine cases of secondary loss of flower identity and cases of a prefloral condition, similar to those that gave rise to the angiosperm flower. Nonhomology among some angiosperm flowers could be due to iterative shifts between nonfloral construction and flower/inflorescence organization of reproductive organs. Potential testing of these hypotheses using evolutionary-developmental genetics is explored using preliminary data from immunolocalization of the floral meristem identity gene LEAFY in T. submersa, which indicated protein expression at different hierarchical levels.     

Vegetative morphology and anatomy of Maundia (Maundiaceae: Alismatales) and patterns of peripheral bundle orientation in angiosperm leaves with three‐dimensional venation

Collateral bundles with external position of the phloem characterize the stem vasculature of most seed plants. An earlier study highlighted the occurrence of inverted peripheral bundles in the leafless inflorescence peduncle of the rare Australian aquatic Maundia triglochinoides. This unusual feature and other morphological and molecular data supported the recognition of the monogeneric Maundiaceae, but the anatomy of the leaves, rhizomes and roots of Maundia remained unknown and is studied here. Maundia has an iterative sympodial growth with all shoots bearing five tubular cataphylls splitting longitudinally and simulating open sheaths at maturity and two (or three) linear foliage leaves without a conspicuous basal sheath. This morphology distinguishes Maundiaceae from all other Alismatales. The rhizome has an atactostele with collateral bundles of normal orientation; peripheral bundles are absent. Cataphylls have a series of normally oriented bundles. Foliage leaves are thick, bifacial, semi‐elliptical in cross‐section, with a thin subepidermal layer of chlorenchyma on both sides, accompanied by peripheral bundles with xylem facing outwards (thus abaxial peripheral bundles are inverted) and central large bundles of normal orientation. Strong anatomical similarity between leaves and peduncles is related to their shared function as assimilatory organs. As in angiosperm succulents, the three‐dimensional leaf venation in thick aquatic and helophyte leaves of Alismatales serves to reduce transport distances between veins and photosynthetic cells. In both cases, the patterns of orientation of peripheral bundles (with inverted adaxial or abaxial bundles) are unstable in large clades. These slender bundles cannot be used for the identification of unifacial leaves. Some anatomical characters express homoplastic similarities between Maundiaceae and Aponogetonaceae.     

An invisible ubiquitin conformation is required for efficient phosphorylation by PINK1

The Ser/Thr protein kinase PINK1 phosphorylates the well‐folded, globular protein ubiquitin (Ub) at a relatively protected site, Ser65. We previously showed that Ser65 phosphorylation results in a conformational change in which Ub adopts a dynamic equilibrium between the known, common Ub conformation and a distinct, second conformation wherein the last β‐strand is retracted to extend the Ser65 loop and shorten the C‐terminal tail. We show using chemical exchange saturation transfer (CEST) nuclear magnetic resonance experiments that a similar, C‐terminally retracted (Ub‐CR) conformation also exists at low population in wild‐type Ub. Point mutations in the moving β5 and neighbouring β‐strands shift the Ub/Ub‐CR equilibrium. This enabled functional studies of the two states, and we show that while the Ub‐CR conformation is defective for conjugation, it demonstrates improved binding to PINK1 through its extended Ser65 loop, and is a superior PINK1 substrate. Together our data suggest that PINK1 utilises a lowly populated yet more suitable Ub‐CR conformation of Ub for efficient phosphorylation. Our findings could be relevant for many kinases that phosphorylate residues in folded protein domains.     

Flower development and vasculature in Xyris grandis (Xyridaceae,Poales); a case study for examining petal diversity in monocot flowers with a double perianth

Floral morphology, anatomy and development are examined in Xyris grandis (Xyridaceae: Poales), with an emphasis on petal and sepal organogenesis and vasculature. Xyris is one of relatively few monocots in which the perianth is differentiated into two distinct whorls (here termed a double perianth). Xyris also possesses highly unusual perianth vasculature, with each petal being supplied by three veins and each sepal by a single vein, compared with the opposite condition in most other angiosperms with a double perianth. However, perianth development in X. grandis shows a pattern that is typical for monocots, with petals not markedly delayed in development. Xyris grandis is also remarkable for its petal aestivation, with each petal surrounding a stamen and two branches of adjacent staminodes, a type that is not reported for other Xyridaceae and may contribute to secondary pollen presentation. The results are discussed in the context of the diversity of a double perianth in monocots, compared with eudicots. Based on current data, our preferred hypothesis is that meristic differences are at least partly responsible for the apparently widespread occurrence of three‐traced petals in monocots. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 93–111.