A phylogenetic study of the palm family (Palmae) based on chloroplast DNA sequences from thetrnL —trnF region

Phylogenies of the palm family based on DNA sequences from thetrnL —trnF region of the chloroplast genome are presented. Although the region is highly conserved in palms and relatively few sites in the aligned data matrix are parsimony informative, a variety of relationships among members of the family are revealed by the analyses, some of which are congruent with the current classification of the palms, and others which are not. However, consensus trees contain high levels of ambiguosity, partly due to the inadequate numbers of informative characters in the dataset. Additional data are required before well resolved palm phylogenies can be generated.     

Phylogeography and conservation genetics of Hygrophila pogonocalyx (Acanthaceae) based on atpB–rbcL noncoding spacer cpDNA

Genetic variation in the atpB–rbcL intergenic spacer region of chloroplast DNA (cpDNA) was investigated in Hygrophila pogonocalyx Hayata (Acanthaceae), an endangered and endemic species in Taiwan. In this aquatic species, seed dispersal from capsules via elasticity is constrained by gravity and is thereby confined within populations, resulting in limited gene flow between populations. In this study, a total of 849 bp of the cpDNA atpB–rbcL spacer were sequenced from eight populations of H. pogonocalyx. Nucleotide diversity in the cpDNA is low (=0.00343±0.00041). The distribution of genetic variation among populations agrees with an isolation-by-distance model. Two geographically correlated groups, the western and eastern regions, were identified in a neighbor-joining tree and a minimum-spanning network. Phylogeographical analyses based on the cpDNA network suggest that the present-day differentiation between western and eastern groups of H. pogonocalyx resulted from past fragmentation. The differentiation between eastern and western populations may be ascribed to isolation since the formation of the Central Mountain Range about 5 million years ago, which is consistent with the rate estimates based on a molecular clock of cpDNA.Huang JC and Wang WK equally contributed to this work.     

Survivin study: What is the next wave?

Survivin, a novel member of inhibitor of apoptosis (IAP) protein family, is aberrantly expressed in cancer but undetectable in normal, differentiated adult tissues. Current studies suggest that survivin is implicated in both control of apoptosis and regulation of cell division. However, due to some inconsistent observations on survivin subcellular localization, there is debate about survivin's function in regulating apoptosis, cell division, or both. This review will discuss concepts, experimental methods, and interesting results that unify the different notions about survivin localization and function or point out gaps of knowledge about controversial issues. The author also intends to review various aspects of survivin studies, which were not emphasized or sufficiently discussed in previous reviews on survivin, and update recent developments that may reveal new applications of disease-oriented therapeutics in the coming years.     

What is the phylogenetic placement of Dipteronia dyerana Henry? An example of plant species placement based on nucleotide sequences

Abstract

DNA sequence data have been widely used to evaluate species delimitations and examine infraspecific relationships. However, species placements inferred from different nucleotide sequences are frequently in conflict. As an example of plant species placement based on nucleotide sequences, the phylogenetic placement of Dipteronia dyerana Henry (Aceraceae) was analyzed in the present study. The study species included eight Acer species (from different sections of Acer), two Dipteronia species, and two outgroup taxa. Phylogenetic trees based on five datasets (ITS, trnL‐F, trnD‐trnT, psbM‐trnD, and rpl16 regions) as well as their combined datasets were generated by using maximum parsimony (MP) and maximum likelihood (ML) analyses. Further analyses were conducted to compare the strict consensus trees based on single regions and the combination of different regions. The results revealed a significant discrepancy among the phylogenetic placements of D. dyerana, inferred from various sequences. Phylogenetic trees using MP analysis based on trnD‐trnT, rpl16, and the four chloroplast combined sequences supported the genus Dipteronia as a monophyletic group, while in the other trees D. dyerana was positioned either in parallel with D. sinensis and Acer species or within the genus Acer. In ML analysis, only rpl16 and the four chloroplast combined sequence datasets supported the genus Dipteronia as a monophyletic group. We concluded that, although significant genetic differentiation occurred between D. dyerana and D. sinensis, D. dyerana was more advanced than D. sinensis. However, whether Dipteronia is monophyletic remains to be further investigated, e.g., by using more closely related taxa and more sequences. Furthermore, in addition to internal transcribed spacer sequences, more chloroplast gene sequences should be used for phylogenetic analyses of species.     

Philibertia (Apocynaceae: Asclepiadoideae) — additional notes and three new species for Bolivia

Summary  Three new species of Philibertia (Apocynaceae: Asclepiadoideae), P. alba Goyder, P. urceolata Goyder and P. zongoensis Goyder are described from Bolivia and illustrated. Preliminary conservation assessments are made for these species. New records are reported for two further species.     

Centres of Endemism in the Espinhaço Range: identifying cradles and museums of Asclepiadoideae (Apocynaceae)

Although the high diversity of neotropical plants is often associated with rain forests, another important location is open vegetation at mountain tops. In the present study, we investigated the phytogeographic patterns of the Espinhaço Range, in eastern Brazil, a region characterized by campos rupestres and marked by high levels of plant richness and endemism. Based on the occurrence of Asclepiadoideae (Apocynaceae) in a grid of 0.5º × 0.5º cells, we conducted cluster analyses and parsimony analysis of endemicity (PAE). We also calculated indexes of diversity and endemism and examined the distribution of palaeo- and neo-endemics. According to our data, the topographic gap between the Espinhaço Range of Minas Gerais and Bahia seems to be an important constraint for the dispersion of endemics, and the floristic similarity between northern Minas Gerais and Bahia is a result of species with broad distribution. Based on the seven areas of endemism that emerged from PAE, we defined five principal centres of endemism in the Espinhaço Range, including the region comprising Serra do Cipó and the Diamantina Plateau, in Minas Gerais, as the major Asclepiadoideae cradle, and Chapada Diamantina, in Bahia, as an Asclepiadoideae museum.     

Molecular evidence for the hybridity ofIlex × wandoensis and the phylogenetic study of KoreanIlex based on ITS sequence data

In this study, internal transcribed spacer (ITS) regions within the nuclear ribosomal DNA of KoreanIlex were analyzed in order to investigate any molecular evidence thatI. × wandoensis could serve as a putative hybrid betweenI. cornuta andI. integra. We also sought to clearly identify taxonomic relationships and problems caused by consecutive external morphological characters among taxa in the genus. We sequenced 20 clones fromI. × wandoensis and found these individuals displayed intra-genomic polymorphisms within ITS regions. The analysis of the clones clearly demonstrated the presence of discrete sequences from bothI. cornuta andI. integra, thereby confirmingI. × wandoensis is a species that was formed by crossingI. cornuta andI. integra. Lastly, the subgenusIlex, which contains the evergreen species, failed to form a monophyletic group in a strict consensus tree that was prepared based upon ITS regions.I. crenata var.microphylla in the subgenus KoreaIlex, which has presented taxonomic problems previously, formed an independent clade within the consensus tree, thereby showing distinction fromI. crenata.) Genetic discontinuity ofI. macropoda andI. Macropoda for.pseudo-macropoda individuals couldn't be confirmed.     

Development of microsatellite markers for the endangered grassland perennial herb Vincetoxicum atratum (Apocynaceae–Asclepiadoideae)

Eight microsatellite markers were developed for the endangered grassland perennial herb Vincetoxicum atratum. The number of alleles ranged from 4 to 14, and the expected heterozygosities were from 0.575 to 0.933 in a population of V. atratum. Five of the eight loci did not significantly deviated from the Hardy–Weinberg equilibrium. All eight loci were tested for cross-species amplification in five other species of Vincetoxicum in Japan. These microsatellite loci will be useful for conservation genetics of V. atratum and other species of Vincetoxicum.     

A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?

The proposal to implement a phylogenetic nomenclatural system governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.     

How many marmoset (Primates: Cebidae: Callitrichinae) genera are there? A phylogenetic analysis based on multiple morphological systems

The marmosets, tribe Callitrichini, are the most speciose clade in the subfamily Callitrichinae, containing 21 species. However, there is no consensus among molecular and morphological systematists as to how many genera should be recognized for the group. To test the morphological support for the alternative generic classifications, this study presents a comprehensive phylogenetic analysis. It is the first such analysis to include all 21 species and employ continuous and discrete osteological, pelage and tegument, karyological and vocal characters. This dataset was combined with nucleotide sequences from two mitochondrial and four nuclear regions. Separate analyses showed that, among morphological datasets, osteological characters were best at solving relationships at more inclusive levels, whilst pelage characters were most informative at the interspecific level. This suggests the presence of different transformation rates for the two character sets. When a single most parsimonious tree was obtained using the 83‐character matrix, three main clades were identified, supporting the division of the marmosets into three genera: Callithrix, Cebuella and Mico. The total evidence analysis that included an additional 3481 molecular characters corroborated most of the morphology‐based clades and also supported a three‐genus classification of the marmosets. This is the first morphological study to support an Amazonian marmoset clade (Cebuella + Mico), which is also strongly supported in exclusively molecular phylogenies, and to synonimize Callibella under Mico.     

Alien futures: What is on the horizon for biological invasions?

Aim

To collect and identify the issues that may affect the future global and local management of biological invasions in the next 20–50 years and provide guidance for the prioritization of actions and policies responding to the management challenges of the future.

Location

Global

Methods

We used an open online survey to poll specialists and stakeholders from around the world as to their opinion on the three most important future issues both globally and at their respective local working level.

Results

The 240 respondents identified 629 global issues that we categorized into topics. We summarized the highest rated topics into five broad thematic areas: (1) environmental change, particularly climate change, (2) the spread of species through trade, (3) public awareness, (4) the development of new technologies to enhance management and (5) the need to strengthen policies. The respondents also identified 596 issues at their respective local working levels. Management, early detection, prevention and funding‐related issues all ranked higher than at the global level. Our global audience of practitioners, policymakers and researchers also elicited topics not identified in horizon scanning exercises led by scientists including potential human health impacts, the need for better risk assessments and legislation, the role of human migration and water management.

Main conclusions

The topic areas identified in this horizon scan provide guidance where future policy priorities for invasive alien species should be set. First, to reduce the magnitude and speed of environmental change and its impacts on biological invasions; second, to restrict the movement of potentially invasive alien species via trade; third, to raise awareness with the general public and empower them to act; and finally, to invest in innovative technologies that can detect and mitigate adverse impacts of introduced species.

     

Restoration of Seminatural Grasslands: What is the Impact on Ants?

The number of species‐rich seminatural grasslands in Northern Europe has decreased significantly due to the abandonment of traditional land use practices. To preserve these habitats, an increasing number of abandoned and overgrown grasslands have been restored by cutting down trees and shrubs and reintroducing grazing. These practices are considered a useful tool to recover the species richness of vascular plants, but their impact on other taxa is hardly known. Here we studied ants as one important group of grassland insects. We investigated (1) the effects of restoration of nongrazed and afforested seminatural grasslands, compared to continuously managed reference sites; and (2) the modulating impacts of habitat characteristics and time elapsed since restoration. We found a total of 27 ant species, 11 of these were characteristic of open habitats and seven characteristic of forests. Neither species richness per site nor the number of open‐habitat species, nor the number of forest species differed between restored and reference sites. Yet, within the restored sites, the total species richness and the number of open‐habitat species was positively related to the time since restoration and the percentage of bare rock. High frequencies of most open‐habitat species were associated with low vegetation, older restored sites, and reference sites. Most forest species showed their highest frequencies in tree‐ and shrub‐dominated habitat. We conclude that restoration efforts have been successful in terms of retrieving species richness. A regular and moderate grazing regime subsequent to the restoration is suggested in order to support a high abundance of open‐habitat species.     

What is the function of MSP-I on the malaria merozoite?

In the absence o f any clear enzymatic activity, attempts to define the role of merozoite surface protein-I have focused mainly on analysis of its structure, on its interaction with the immune system and on binding assays. But how does our knowledge of the structure o f this protein contribute to functional studies? Are there data to suggest a role in the evasion of effective host immune responses? Binding studies have used the intact protein or various fragments and peptides, but do such approaches provide a reliable indicator of function? In this article, Tony Holder and Mike Blackman review these areas.     

Does polyembryony confer a competitive advantage to the invasive perennial vine Vincetoxicum rossicum (Apocynaceae)?

Determining which traits may allow some introduced plant species to become invasive in their new environment continues to be a key question in invasion biology. Vincetoxicum rossicum is an invasive, perennial vine colonizing natural and seminatural habitats primarily in the northeastern United States and southeastern Canada. More than half its seeds exhibit polyembryony, a relatively uncommon condition in which a single seed produces multiple seedlings. For evaluating the potential consequences of polyembryony on invasiveness, V. rossicum plants derived from seeds of three embryonic classes-singlets, doublets, and triplets (one, two, and three seedlings per seed, respectively)-were paired in all combinations intraspecifically and with the co-occurring native herbs Solidago canadensis and Asclepias syriaca in a greenhouse study. Vincetoxicum rossicum biomass was 25-55% greater and follicle production 55-100% greater under intraspecific competition compared with interspecific competition. However, within a competitive environment, follicle production varied little. Regardless of competitive environment, V. rossicum originating from seeds with a greater number of embryos typically performed no better than plants arising from seed with fewer embryos (singlets = doublets = triplets)-except intraspecifically where doublets outperformed singlets, and with S. canadensis where triplets outperformed singlets. Our findings suggest that overall performance and fitness of V. rossicum is higher in monocultures than in mixed stands and that its ability to invade new habitats may not be attributable to the production of polyembryonic seeds.     

Monitoring intra-annual cambial activity based on the periodic collection of twigs – A feasibility study

This study aims at monitoring the cambial activity and xylogenesis along the growing season under Mediterranean climate using a newly designed sampling method based on the periodic collection of twigs from the crown, in order to test its efficacy. Ten species were selected; seven hardwood (Acer pseudoplatanus L., Ceratonia siliqua L., Schinus terebinthifolius Raddi, Olea europaea L., Fraxinus angustifolia Vahl, Populus alba L., Quercus suber L.) and three softwood species (Abies alba Mill., Cupressus sempervirens L., Pinus pinea L.). The twigs were collected monthly during one year. After microtome sectioning and staining, the sections were photographed and analyzed to monitor ring development and the period of cambial activity.The twigs revealed large differences in radial growth, within and among species, which might be associated to their particular position in the tree, to the effect of the different crown microclimates, and/or to the crown conformation and type of leaves. The method showed effectiveness in the study of cambial activity, but limitations in the study of ring development due to impossibility of comparing samples. Improvements to the method are proposed, aiming essentially at minimizing the variability among samples.