<Emphasis Type="Italic">Barleria compacta</Emphasis>: a new species in <Emphasis Type="Italic">Barleria</Emphasis> sect. <Emphasis Type="Italic">Prionitis</Emphasis> (Acanthaceae) from Somalia

Following a re-examination of the material treated under Barleria brevispina (Fiori) Hedrén in the recent Flora of Somalia account of the Acanthaceae, it is concluded that two distinct species are involved and Barleria compacta Malombe & I. Darbysh. is described here from north-eastern Somalia. Its affinities and conservation status are discussed.     

People,money, and protected areas: the collection of the caterpillar mushroom <Emphasis Type="Italic">Ophiocordyceps sinensis</Emphasis> in the <Emphasis Type="Italic">Baima Xueshan</Emphasis> Nature Reserve,Southwest China

The caterpillar mushroom Ophiocordyceps sinensis (syn. Cordyceps sinensis) is among the most valuable mushrooms in the world, and plays a major role for the local economies in its distribution area on the Tibetan Plateau and adjacent regions. Large proportions of its habitat fall into protected areas, and best practice of sustainable harvest is under discussion, considering both, O. sinensis as a valuable income source for rural poor and protection of its populations and habitat. This study aims for a detailed analysis of O. sinensis collection in a nature reserve in Southwest China. We found that harvesting is unevenly distributed among households and villages, with households who have access to the resource but lack adequate alternatives for income generation such as rewarding wage labor, fertile agricultural fields or harvest of other high value products being most involved. Although collection is de jure forbidden, authorities of the nature reserve apply adaptive management strategies for sustainable resource use. This includes the allocation of collection areas to communities based on their traditional land use strategies and the control of harvesters from outside, triggering self-policing of the resource by the local people. The strategies applied provide a promising model also for other protected areas where the caterpillar mushroom is collected.     

Frequencies of the <Emphasis Type="Italic">DRB1</Emphasis>, <Emphasis Type="Italic">DQA1</Emphasis>, <Emphasis Type="Italic">DQB1</Emphasis> and <Emphasis Type="Italic">TNFA</Emphasis> alleles in immigrant population of west Siberia

Based on population analysis of the DRB1, DQA1, DQB1 and TNFA allele frequency distribution patterns, regional features of immunogenetic structure of the population of West Siberia were investigated. Statistically significant linkage disequilibrium within the HLA class II region, as well as between the TNFA and DRB1, DQA1, and DQB1 was demonstrated. Population frequency distribution patterns of two- and multilocus haplotypes were examined.     

Multiple alleles at <Emphasis Type="Italic">Early flowering 1</Emphasis> locus making variation in the basic vegetative growth period in rice (<Emphasis Type="Italic">Oryza</Emphasis> <Emphasis Type="Italic">sativa</Emphasis> L.)

A recently established rice breeding program in low latitudes aims to develop varieties with extremely long basic vegetative growth (BVG) periods and weak photoperiod sensitivities. The Taiwanese japonica variety Taichung 65 (T65) harbors a recessive allele ef1 at the Ef1 (Early flowering 1) locus, thereby exhibiting an extremely long BVG period. The previous reported functional allele Ehd1 (Early heading date 1), located on chromosome 10, encodes a B-type response regulator, thereby shortening the BVG period, whereas its nonfunctional allele ehd1 greatly prolongs the BVG period. A conventional analysis using F₂ and F₃ populations and a subsequent CAPS analysis based on the amino acid sequences of Ehd1 and ehd1 showed that Ef1 and Ehd1 were at the same locus. The CAPS analysis also indicated that the Taiwanese japonica varieties with extremely long BVG periods all harbor ef1, but that ef1 does not exist among indica and japonica varieties in the low latitudes. Since ef1 has not been found in any japonica varieties outside Taiwan, this allele might have originated in Taiwan. Sequence analysis revealed that the mutant allele ef1-h, which prolongs the BVG period even more than ef1 does, harbors an mPing insertion in exon 2, which causes the complete loss of gene function. Our results indicate that both ef1 or ef1-h alleles can be used as new gene sources in developing rice varieties with extremely long BVG periods for low latitudes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Submolecular unfolding units of <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> cytochrome <Emphasis Type="Italic">c</Emphasis>-551

Hydrogen exchange rates for backbone amide protons of oxidized Pseudomonas aeruginosa cytochrome c-551 (P. aeruginosa cytochrome c) have been measured in the presence of low concentrations of the denaturant guanidine hydrochloride. Analysis of the data has allowed identification of submolecular unfolding units known as foldons. The highest-energy foldon bears similarity to the proposed folding intermediate for P. aeruginosa cytochrome c. Parallels are seen to the foldons of the structurally homologous horse cytochrome c, although the heme axial methionine-bearing loop has greater local stability in P. aeruginosa cytochrome c, in accord with previous folding studies. Regions of low local stability are observed to correspond with regions that interact with redox partners, providing a link between foldon properties and function. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Duplicate Gene Evolution Toward Multiple Fates at the <Emphasis Type="Italic">Drosophila melanogaster HIP</Emphasis>/<Emphasis Type="Italic">HIP-Replacement</Emphasis> Locus

Hsc/Hsp70-interacting protein (HIP) is a rapidly evolving Hsp70 cofactor. Analyses of multiple Drosophila species indicate that the HIP gene is duplicated only in D. melanogaster. The HIP region, in fact, contains seven distinctly evolving duplicated genes. The regional duplication occurred in two steps, fixed rapidly, and illustrates multiple modes of duplicate gene evolution. HIP and its duplicate HIP-R are adaptively evolving in a manner unique to the region: they exhibit elevated divergence from other drosophilids and low polymorphism within D. melanogaster. HIP and HIP-R are virtually identical, share polymorphisms, and are subject to gene conversion. In contrast, two other duplicate genes in the region, CG33221 and GP-CG32779, are pseudogenes, and the chimeric gene Crg1 is subject to balancing selection. HIP and HIP-R are evolving rapidly and adaptively; however, positive selection is not sufficient to explain the molecular evolution of the region as a whole. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Habitat,density, and spatial distribution of <Emphasis Type="Italic">Rivulus giarettai</Emphasis> (<Emphasis Type="Italic">Actinopterygii</Emphasis>, <Emphasis Type="Italic">Cyprinodontiformes</Emphasis>) in southeastern Brazil

We present data on the habitat, density, and spatial distribution of Rivulus giarettai, and discuss some biotic and abiotic variables related to its abundance in Free Flowing Waters (FFW) and Dam Reservoirs (DR) in palm grove (Mauritia flexuosa) marshes (Veredas) in Uberlandia, Minas Gerais, southeastern Brazil. The mean density (individuals/plot) of R. giarettai was about 13 times higher in FFW than in DR. In FFW, the density of R. giarettai was highest at intermediate amounts of substrate (plant mass) and it was positively rank-correlated with the depth, and the number of arthropods. Individuals occurred in an aggregated distribution. The aggregated pattern could be related to a concentration of individuals in microhabitats neither too much exposed nor completely saturated by plants. R. giarettai was relatively abundant and tolerant to slight man-made habitat modifications. Damming appeared to be especially problematic by negatively affecting its density.     

A deep nursery for juveniles of the zebra angelfish <Emphasis Type="Italic">Genicanthus caudovittatus</Emphasis>

Juveniles of many coral reef fish species are thought to either follow the same bathymetric distribution patterns as the adults, or to occupy shallower waters. However, our knowledge base suffers a dearth of data from the deep reefs (>40 m). In a recent survey of the deep reefs of the northern Gulf of Aqaba (<65 m), we examined the bathymetric distribution of 26 diurnal zooplanktivorous species. In sharp contrast to the general trend known from the literature and from this research, the abundance of juvenile zebra angelfish, Genicanthus caudovittatus, peaked at deeper waters (60–65 m) compared with the adults (30 m). This suggests that the deeper reefs may serve as nursery grounds for the zebra angelfish. Peak juvenile abundance coincided with relatively low predator abundances. This raises the question, which factors constrain the bathymetric distribution of the remaining species. Our findings stress the potential importance of deep coral reef research for understanding the ecological patterns and processes that govern reef community structure.     

<Emphasis Type="Italic">Gagea robusta</Emphasis> (Liliaceae), a new species from <Emphasis Type="Italic">Flora Iranica</Emphasis> area

A new species, endemic to the Flora Iranica area, Gagea robusta (Liliaceae) is described and illustrated. It differs from G. reticulata (Pall.) Schult. & Schult. f. in having a puberulent indumentum on the basal leaf and from G. setifolia Baker ex Aitch. in having a long neck (up to 12 cm long). Its ecology, distribution and conservation status are discussed.     

<Emphasis Type="Italic">Xenopus laevis</Emphasis> (Daudin, 1802), a new exotic amphibian in Portugal

The African clawed frog Xenopus laevis has been introduced at several locations, including Mediterranean climate-type regions. In 2006, several individuals of this species were found inhabiting a stream at Oeiras, about 20 km W of Lisbon, Portugal. Although the place and time of introduction are not clearly identified, there are reasons to believe that this population may be the result of an almost 30-year-old introduction proceeding from research laboratories located nearby. Field surveys were conducted in 2007 and 2008 on the distribution and abundance of this species in the region. The species was found in two streams, about 5 km from each other. While being locally abundant, the adults of X. laevis are smaller than those from South Africa and California. In spite of an abundant production of eggs and tadpoles at one of the streams, no tadpoles were found in advanced developmental stages. Until now, most individuals were found in heavily urbanized areas that should constrain their ability to cross overland to other water bodies. An eradication program may be feasible, but the presence of adults on two streams indicates that the species may be expanding, in spite of the urban landscape.     

Two isoforms of peroxiredoxin 6 of <Emphasis Type="Italic">Xenopus laevis</Emphasis>

The genome of Xenopus laevis codes for two genes of peroxiredoxin 6, i.e., xen1 (Acc. no. EMBL Data Bank-BCO54278) and xen2 (Acc. no. EMBL Data Bank-BCO54309). Both the genes were cloned and expressed in Escherichia coli. The amino acid sequences of Xen1 and Xen2 enzymes are identical by 95%, and they possess the same peroxidase activity as well as similar optimums of temperature, pH, and thermostability. The genes of peroxiredoxin 6 of Xenopus laevis considerably differ in the period of expression during ontogenesis; i.e., xen2 is expressed during every stage of development, somewhat more intensively after stages 0–5; the expression of xen1 is initiated later, i.e., during the developmental stages of 47–48 h. Expression of xen2 increases after the incubation of embryos in a medium with hydrogen peroxide. Comparison of the amino acid sequences of Xen1 and Xen2 proteins shows that only Xen2 can possess phospholipase activity because its amino acid sequence contain residues of the phospholipase A2 active center: Ser31, His25, and Asp139.     

General <Emphasis Type="Italic">G</Emphasis><Subscript>ST</Subscript> and <Emphasis Type="Italic">θ</Emphasis> inflation due to biased intra-population sampling,and its consequences for the conservation of the Canarian Flora

While knowledge of the degree of inter-population genetic differentiation underlies the understanding of microevolutionary processes in any organism, its calculation through G _ST, F _ST, or θ (which, unlike the previous two, was designed to correct for unequal and small sample sizes) is often based in severely restricted intra-population samples, which are nonetheless tacitly assumed adequate to their accurate estimation. Empirical assessment of the influence of the number and intra-population distribution of samples on the values of G _ST and θ for several Canarian endemic plants compellingly suggests that (1) contrary to expectations based on simulated datasets, θ does not account for empirical sampling bias better than G _ST; (2) sample sizes being equal, collections scattered across each population’s occupancy area entail significantly lower over-estimates of G _ST and θ than if they only consider one of the population extremes, especially in narrow allogamous taxa with small populations; (3) in small samples, a scattered sampling strategy is significantly less sensitive to G _ST inflation than sampling in one of the population extremes; and (4) a software-related component of bias should be considered when pooling values of G _ST from different studies to calculate averages. Thus, unlike the sampling methods used for many plant endemics from the Canaries and other regions, collections for a reliable estimation of inter-population differentiation using molecular markers should encompass the whole occupancy area of each population, and include a higher proportion of individuals respect to the total size in narrow endemics than in widespread congeners. Critically, the high average allozyme inter-population differentiation reported for the Canarian endemic Flora is possibly an over-estimate, and could be explained predominantly by the generally biased intra-population sampling associated with G _ST estimates, rather than by specific factors of insularity that restrict gene flow radically, as it has been hitherto assumed.     

Ecological conditions and the distribution of alpine juniper (<Emphasis Type="Italic">Juniperus communis</Emphasis> subsp. <Emphasis Type="Italic">alpina</Emphasis>) in the Hrubý Jeseník Mts

In the Hruby Jeseník Mts of the Czech Republic, research was carried out from 2001–2005 aimed at completing an up-to-date census of alpine juniper [Juniperus communis subsp. alpine (Smith) Čelakovsky] and an evaluation of the overall health status of the populations, and at investigating the impacts of the main environmental factors on the viability of this species. 13 sites were identified with 283 individuals in total, but the sites differed dramatically in the number of recorded individuals. Comparisons with historical literature sources show that the species has been in decline. The main reasons for this decline include: a lack of suitable sites for colonization connected with a lack of adequate disturbance factors, competition from shading trees, and the presumed high age of the juniper populations combined with zero generative reproduction. More than two thirds of the individuals showed slight damage to their assimilation system. A health status of bad or very bad was determined for 5 % of the alpine juniper individuals. These trees in the Hruby Jeseník Mts are also exposed to pressure from some herbivore insects and mammals. The populations are not yet in a literally critical state, but considering the range of impacts affecting them, it will be necessary to pay significant attention to their conservation strategies. Some recommendations for future management are suggested.     

Isolation of a <Emphasis Type="Italic">Ve</Emphasis> homolog, <Emphasis Type="Italic">mVe1</Emphasis>, and its relationship to verticillium wilt resistance in <Emphasis Type="Italic">Mentha longifolia</Emphasis> (L.) Huds

As a step toward greater understanding of the genetics of verticillium wilt resistance in plants, we report the sequencing of a candidate wilt resistance gene, mVe1, from the mint diploid model species, Mentha longifolia (Lamiaceae). mVe1 is a putative homolog of tomato (Solanum lycopersicum L.) verticillium wilt (Ve) resistance genes. The mVe1 gene has a coding region of 3,051 bp. The predicted mVe1 protein contains a leucine-rich repeat domain, a common feature of plant disease resistance proteins. We compared 13 mVe1 alleles from three mint species. These alleles shared 96.2–99.6% nucleotide identity. We analyzed four M. longifolia populations segregating with respect to mVe1 alleles and wilt resistance versus susceptibility and found one association between mVe1 genotype and wilt phenotype. We conclude that mVe1 may play a role in mint verticillium wilt resistance, but variation for resistance in our segregating progenies is likely polygenic. Therefore, further investigations of mVe1 and identification of additional candidate genes are both warranted.     

<Emphasis Type="Italic">Cardamine plumieri</Emphasis> (<Emphasis Type="Italic">Brassicaceae</Emphasis>) confirmed to the Flora of Serbia

The south-European Cardamine plumieri Vill. (sect. Pteroneurum subsect. Cryptopterum) is confirmed for the Flora of Serbia. Several populations were discovered in the central and western part of country, exclusively on the serpentine bedrocks. Morphological, chorological and ecological characteristics of C. plumieri was studied.     

Low genetic structuring among <Emphasis Type="Italic">Pericharax heteroraphis</Emphasis> (Porifera: Calcarea) populations from the Great Barrier Reef (Australia), revealed by analysis of nrDNA and nuclear intron sequences

A new nuclear marker system for sponges, the second intron of the nuclear ATP synthetase beta subunit gene (ATPSbeta-iII), was analysed together with nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences aiming to uncover phylogeographic patterns of the coral reef sponge Pericharax heteroraphis in the south-west Pacific, focussing on the Great Barrier Reef (GBR). Variation among ITS sequences was low (<1.1% p-distance), in contrast to ATPSbeta-iII (<8.3% p-distance). Single-Stranded Conformation Polymorphism (SSCP) analysis proved to be an effective tool for phasing ATPSbeta-iII alleles of 292 bp length. Although sample sizes were limited for most populations and these results await corroboration by an extended sampling regime, a past population subdivision with subsequent range expansion was indicated by a ‘dumb-bell’ shaped statistical parsimony network of GBR ATPSbeta-iII alleles. Although no clear phylogeographic break was discovered on the GBR, the northern GBR was genetically differentiated from the central/southern GBR and Queensland Plateau, based on significant pairwise F _st values (0.137–0.275 and p ≤ 0.05) of pooled regional populations. The ATPSbeta-iII used in this study outperformed the frequently employed nrDNA ITS and might also turn out to be useful for phylogeographic studies of other coral reef taxa. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A non-invasive genetic method to identify the sympatric mustelids pine marten (<Emphasis Type="Italic">Martes martes</Emphasis>) and stone marten (<Emphasis Type="Italic">Martes foina</Emphasis>): preliminary distribution survey on the northern Iberian Peninsula

The closely related mustelids European pine marten (Martes martes) and stone marten (Martes foina) sympatrically inhabit a large area of Europe. However, given our limited knowledge of their bioecological relationships, their extremely elusive behaviour and the fact that their faeces cannot be distinguished on the basis of morphology alone, it is very difficult to monitor their populations. In this study, we describe a reliable non-invasive polymerase chain reaction (PCR)–restriction fragment length polymorphism (PCR-RFLP) method for distinguishing between M. martes and M. foina based on the analysis of deoxyribonucleic acid extracted from faeces samples. The method was specifically designed to avoid possible interference from potential prey mammals and other sympatric carnivores. The procedure consists of PCR amplifying a mitochondrial D-loop region followed by digesting the resulting 276-bp-long amplicons with the restriction enzymes HaeIII and RsaI. To assess the efficiency of this technique, we conducted a preliminary field study across the potential sympatric distribution areas of both marten species in the northern Iberian Peninsula. Out of 359 faeces samples collected, we identified 80 as specimens from the stone marten and 235 from the pine marten. Unequivocal species identification was thus possible in 88% of the faeces samples collected. These findings reveal the combined use of non-invasive genetic sampling and GIS technology to be a reliable and cost-effective procedure for improving our knowledge of the spatial distributions of sympatric marten species. This protocol could also be used to identify and improve information gaps, to develop effective research and management programmes and in population and landscape genetics studies of marten species. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.