Population viability analysis of Walia ibex (Capra walie) at Simien Mountains National Park (SMNP), Ethiopia

Population viability analysis (PVA) has been applied to the management of many threatened populations. The objective of this study was, therefore, to estimate the PVA of Walia ibex at the Simen Mountains National Park, in the north‐central highlands of Ethiopia, with respect to population growth parameters, the probability of the population reaching a lower extinction threshold and the mean time to extinction. Direct census of the population was carried out in 2009. Secondary census data were also collected from park authorities and the literature reviews. The result revealed that the estimates of the infinitesimal mean, μ (0.04117) was greater than the infinitesimal variance, σ² (0.0219). The probability that the population reaches the extinction threshold was very low (0.15%). The mean time required for the counts to decline from the existing population size to one individual animal was 160 years. But threatened species are adversely affected by changes in landscape. These changes can be brought by short‐ and long‐term human and climate change impacts, respectively. Therefore, with the absence of environmental and demographic stochasticity and, with the application of appropriate reproductions and habitat management, the population of Walia ibex will be viable and reaches its mean time of extinctions after 160 years.     

A diverse chasmataspidid (Arthropoda: Chelicerata) fauna from the Early Devonian (Lochkovian) of Siberia

Examination of material held at the Palaeontological Institute, Moscow, enables the identification of two novel chasmataspidid species: Nahlyostaspis bergstroemi gen. et sp. nov. and Skrytyaspis andersoni gen. et sp. nov. ‘Eurypterus’ stoermeri and ‘Tylopterella’ menneri are both redescribed as chasmataspidids, having previously been assigned to Eurypterida. ‘T’. menneri is transferred to the new genus Dvulikiaspis gen. nov. An identical prosomal structure is identified in ‘Eurypterus’ stoermeri and Heteroaspis novojilovi from the Devonian of Germany and the two species are synonymized, with ‘E’ stoermeri having priority. The previous synonymy of H. novojilovi with Diploaspis casteri is rejected. The presence of ophthalmic ridges is confirmed within Diploaspididae, and new structural characteristics of their bucklers are identified.     

Nematodes associated with Ips cembrae (Coleoptera: Curculionidae): comparison of generations,sexes and sampling methods

A study of nematodes associated with the large larch bark beetle Ips cembrae (Heer 1836) was carried out at three locations in the Czech Republic. The proportion of beetles infested by endoparasitic nematodes (representatives of genera Contortylenchus, Parasitylenchus, Cryptaphelenchus and Parasitorhabditis) ranged from 29.9 to 50.9%. Significant differences were determined in nematode infestation levels among locations, generations and sampling methods. No differences were found in infestation rates between males and females. The percentage of bark beetles with phoretic nematodes ranged from 18 to 42.9%. Phoretic nematodes directly found under elytra, on wings and between body segments of the bark beetles belong to the genus Micoletzkya. However, adults and juveniles of other two phoretic species Laimaphelenchus penardi and Bursaphelenchus sp. were found in the gallery frass of I. cembrae. Infestation by phoretic nematodes positively correlated with the presence of mites under elytra.     

The 12th International Workshops on Opportunistic Protists (IWOP‐12)

The 12th International Workshops on Opportunistic Protists (IWOP‐12) was held in August 2012 in Tarrytown, New York. The objectives of the IWOP meetings are to: (1) serve as a forum for exchange of new information among active researchers concerning the basic biology, molecular genetics, immunology, biochemistry, pathogenesis, drug development, therapy, and epidemiology of these immunodeficiency‐associated pathogenic eukaryotic microorganisms that are seen in patients with AIDS and (2) foster the entry of new and young investigators into these underserved research areas. The IWOP meeting focuses on opportunistic protists, e.g. the free‐living amoebae, Pneumocystis, Cryptosporidium, Toxoplasma, the Microsporidia, and kinetoplastid flagellates. This conference represents the major conference that brings together research groups working on these opportunistic pathogens. Slow but steady progress is being achieved on understanding the biology of these pathogenic organisms, their involvement in disease causation in both immune‐deficient and immune‐competent hosts, and is providing critical insights into these emerging and reemerging pathogens. This IWOP meeting demonstrated the importance of newly developed genomic level information for many of these pathogens and how analysis of such large data sets is providing key insights into the basic biology of these organisms. A great concern is the loss of scientific expertise and diversity in the research community due to the ongoing decline in research funding. This loss of researchers is due to the small size of many of these research communities and a lack of appreciation by the larger scientific community concerning the state of art and challenges faced by researchers working on these organisms.     

Evaluating the capacity of plant DNA barcodes to discriminate species of cotton (Gossypium: Malvaceae)

Although two plastid regions have been adopted as the standard markers for plant DNA barcoding, their limited resolution has provoked the consideration of other gene regions, especially in taxonomically diverse genera. The genus Gossypium (cotton) includes eight diploid genome groups (A–G, and K) and five allotetraploid species which are difficult to discriminate morphologically. In this study, we tested the effectiveness of three widely used markers (matK, rbcL, and ITS2) in the discrimination of 20 diploid and five tetraploid species of cotton. Sequences were analysed locus‐wise and in combinations to determine the most effective strategy for species identification. Sequence recovery was high, ranging from 92% to 100% with mean pairwise interspecific distance highest for ITS2 (3.68%) and lowest for rbcL (0.43%). At a 0.5% threshold, the combination of matK+ITS2 produced the greatest number of species clusters. Based on ‘best match’ analysis, the combination of matK+ITS2 was best, while based on ‘all species barcodes’ analysis, ITS2 gave the highest percentage of correct species identifications (98.93%). The combination of sequences for all three markers produced the best resolved tree. The disparity index test based on matK+rbcL+ITS2 was significant (P < 0.05) for a higher number of species pairs than the individual gene sequences. Although all three barcodes separated the species with respect to their genome type, no single combination of barcodes could differentiate all the Gossypium species, and tetraploid species were particularly difficult.     

New records of Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) predation by Brazilian Hemipteran predatory bugs

The tomato borer Tuta absoluta, native to western South America, is an extremely devastating pest in tomato crops in most of South America, Europe and Africa North of the Sahel, causes yield losses up to 100% and decreases fruit quality in open field and greenhouse crops if control methods are not applied. In Brazil two other important lepidopteran pests – Neoleucinodes elegantalis and Helicoverpa zea – occur in tomato, as well as thrips, whiteflies and aphids. For control of these pests, frequent applications of pesticides of up to 5 times per week are needed, and these resulted in the appearance of resistant populations to a number of active ingredients and decimation of natural enemies. Biological control may offer a better, safer and more sustainable opportunity for pest management. Mirid predatory bugs are currently used with success in southern Europe to control T. absoluta and other pests. In Brazil, four Hemipteran predatory bugs, not yet known to attack T. absoluta, were found to successfully prey on eggs and larvae of this pest. The first results on their predation capacity, development, survival and reproduction on T. absoluta on tomato plants are presented.     

Molecular mechanism underlying pseudopeloria in Habenaria radiata (Orchidaceae)

Habenaria radiata (Orchidaceae) has two whorls of perianth, comprising three greenish sepals, two white petals and one lip (labellum). By contrast, the pseudopeloric (with a decreased degree of zygomorphy) mutant cultivar of H. radiata , ‘Hishou’, has changes in the identities of the dorsal sepal to a petaloid organ and the two ventral sepals to lip‐like organs. Here, we isolated four DEFICIENS ‐ like and two AGL 6 ‐like genes from H. radiata , and characterized their expression. Most of these genes revealed similar expression patterns in the wild type and in the ‘Hishou’ cultivar, except Hr DEF ‐C3. The Hr DEF ‐C3 gene was expressed in petals and lip in the wild type but was ectopically expressed in sepal, petals, lip, leaf, root and bulb in ‘Hishou’. Sequence analysis of the Hr DEF ‐C3 loci revealed that the ‘Hishou’ genome harbored two types of Hr DEF ‐C3 genes: one identical to wild‐type Hr DEF ‐C3 and the other carrying a retrotransposon insertion in its promoter. Genetic linkage analysis of the progeny derived from an intraspecific cross between ‘Hishou’ and the wild type demonstrated that the mutant pseudopeloric trait was dominantly inherited and was linked to the Hr DEF ‐C3 gene carrying the retrotransposon. These results indicate that the pseudopeloric phenotype is caused by retrotransposon insertion in the Hr DEF ‐C3 promoter, resulting in the ectopic expression of Hr DEF ‐C3 . As the expression of Hr AGL 6‐C2 was limited to lateral sepals and lip, the overlapping expression of Hr DEF ‐C3 and Hr AGL 6‐C2 is likely to be responsible for the sepal to lip‐like identity in the lateral sepals of the ‘Hishou’ cultivar.     

Plastid phylogenetics of Oceania yams (Dioscorea spp., Dioscoreaceae) reveals natural interspecific hybridization of the greater yam (D. alata)

Phylogenetic relationships of Oceanian staple yams (species of Dioscorea section Enantiophyllum) were investigated using plastid trnL‐F and rpl32‐trnL^(UAG) sequences and nine nuclear co‐dominant microsatellites. Analysis of herbarium specimens, used as taxonomic references, allowed the comparison with samples collected in the field. It appears that D. alata, D. transversa and D. hastifolia are closely related species. This study does not support a direct ancestry from D. nummularia to D. alata as previously hypothesized. The dichotomy in D. nummularia previously described by farmers in semi‐perennial and annual types was reflected by molecular markers, but the genetic structure of D. nummularia appears more complex. Dioscorea nummularia displayed two haplotypes, each corresponding to a different genetic group. One, including a D. nummularia voucher from New Guinea, is closer to D. tranversa, D. alata and D. hastifolia and encompasses only semi‐perennial types. The second group is composed of semi‐perennial and annual yams. However, some of these annual yams also displayed D. alata haplotypes. Nuclear markers revealed that some annual yams shared alleles with D. alata and semi‐perennial D. nummularia, suggesting a hybrid origin, which may explain their intermediate morphotypes and the difficulty met in classifying them.     

Phylogeny of Gracilariaceae (Rhodophyta): evidence from plastid and mitochondrial nucleotide sequences

Gracilariaceae are mostly pantropical red algae and include ~230 species in seven genera. Infrafamilial classification of the group has long been based on reproductive characters, but previous phylogenies have shown that traditionally circumscribed groups are not monophyletic. We performed phylogenetic analyses using two plastid (universal plastid amplicon and rbcL) and one mitochondrial (cox1) loci from a greatly expanded number of taxa to better assess generic relationships and understand patterns of character distributions. Our analyses produce the most well‐supported phylogeny of the family to date, and indicate that key characteristics of spermatangia and cystocarp type do not delineate genera as commonly suggested. Our results further indicate that Hydropuntia is not monophyletic. Given their morphological overlap with closely related members of Gracilaria, we propose that Hydropuntia be synonymized with the former. Our results additionally expand the known ranges of several Gracilariaceae species to include Brazil. Lastly, we demonstrate that the recently described Gracilaria yoneshigueana should be synonymized as G. domingensis based on morphological and molecular characters. These results demonstrate the utility of DNA barcoding for understanding poorly known and fragmentary materials of cryptic red algae.     

Application of multigene phylogenetics and site‐stripping to resolve intraordinal relationships in the Rhodymeniales (Rhodophyta)

Previous molecular assessments of the red algal order Rhodymeniales have confirmed its monophyly and distinguished the six currently recognized families (viz. Champiaceae, Faucheaceae, Fryeellaceae, Hymenocladiaceae, Lomentariaceae, and Rhodymeniaceae); however, relationships among most of these families have remained unresolved possibly as a result of substitution saturation at deeper phylogenetic nodes. The objective of the current study was to improve rhodymenialean systematics by increasing taxonomic representation and using a more robust multigene dataset of mitochondrial (COB, COI/COI‐5P), nuclear (LSU, EF2) and plastid markers (psbA, rbcL). Additionally, we aimed to prevent phylogenetic inference problems associated with substitution saturation (particularly at the interfamilial nodes) by removing fast‐evolving sites and analyzing a series of progressively more conservative alignments. The Rhodymeniales was resolved as two major lineages: (i) the Fryeellaceae as sister to the Faucheaceae and Lomentariaceae; and (ii) the Rhodymeniaceae allied to the Champiaceae and Hymenocladiaceae. Support at the interfamilial nodes was highest when 20% of variable sites were removed. Inclusion of Binghamiopsis, Chamaebotrys, and Minium, which were absent in previous phylogenetic investigations, established their phylogenetic affinities while assessment of two genera consistently polyphyletic in phylogenetic analyses, Erythrymenia and Lomentaria, resulted in the proposition of the novel genera Perbella and Fushitsunagia. The taxonomic position of Drouetia was reinvestigated with re‐examination of holotype material of D. coalescens to clarify tetrasporangial development in this genus. In addition, we added three novel Australian species to Drouetia as a result of ongoing DNA barcoding assessments—D. aggregata sp. nov., D. scutellata sp. nov., and D. viridescens sp. nov.     

Classification of crucigenoid algae: phylogenetic position of the reinstated genus Lemmermannia,Tetrastrum spp. Crucigenia tetrapedia,and C. lauterbornii (Trebouxiophyceae,Chlorophyta)1

The subfamily Crucigenioideae was traditionally classified within the well‐characterized family Scenedesmaceae (Chlorophyceae). Several morpho‐logical revisions and questionable taxonomic changes hampered the correct classification of crucigenoid species resulting in a high number of synonymous genera. We used a molecular approach to determine the phylogenetic position of several Tetrastrum and Crucigenia species. The molecular results were correlated with morphological and ontogenetic characters. Phylogenetic analyses of the SSU rDNA gene resolved the position of Tetrastrum heteracanthum and T. staurogeniaeforme as a new lineage within the Oocystis clade of the Trebouxiophyceae. Crucigenia tetrapedia, T. triangulare, T. punctatum, and T. komarekii were shown to be closely related to Botryococcus (Trebouxiophyceae) and were transferred to Lemmer‐mannia. Crucigenia lauterbornii was not closely related to the other Crucigenia strains, but was recovered within the Chlorella clade of the Trebouxiophyceae.     

Phylogenetics of tribe Sabiceeae (Ixoroideae,Rubiaceae) revisited,with a new subgeneric classification for Sabicea

Tribe Sabiceeae (Ixoroideae, Rubiaceae) has undergone recent taxonomical changes with the incorporation of the related genera Ecpoma, Pseudosabicea and Stipularia into the type genus Sabicea. We use phylogenetic analysis and morphological data to verify the relationships among members of the tribe, including the most comprehensive taxon sampling of the tribe to date with 74 of 145 species. Sequence data from the nuclear internal transcribed spacer (ITS) and three plastid markers (petD, rps16, trnT–F) were used to infer relationships among the members of the tribe. Individual analyses using maximum likelihood, parsimony and Bayesian approaches reveal several supported clades: the former genus Stipularia is resolved as a monophyletic unit, but Ecpoma is monophyletic only if Sabicea urbaniana and Sabicea xanthotricha are included (corresponding to Sabicea subgenus Stipulariopsis sensu Wernham). Pseudosabicea is biphyletic, with one clade corresponding to section Anisophyllae of Hallé (1964) and the other one to the other sections (Floribundae and Sphaericae) of the genus. Eleven morphological characteristics were recorded for all species studied and seven have been mapped onto the phylogenetic tree to study their evolution in the group and assess their value for the classification of Sabicea s.l. Finally, our study shows that a combination of diagnostic characteristics should be used to differentiate each group and we propose to recognise four subgenera in Sabicea.     

Bulb and Root Rot in Lily (Lilium longiflorum) and Onion (Allium cepa) in Israel

In the past 10 years, there has been a substantial increase in reports, from growers and extension personnel, on bulb and root rots in lily (Lilium longiflorum) in Israel. Rot in these plants, when grown as cut flowers, caused serious economic damage expressed in reduction in yield and quality. In lily, the fungal pathogens involved in the rot were characterized as binucleate Rhizoctonia AG‐A, Rhizoctonia solani, Pythium oligandrum, Fusarium proliferatum (white and purple isolates) and F. oxysporum, using morphological and molecular criteria. These fungi were the prevalent pathogens in diseased plants collected from commercial greenhouses. Pathogenicity trials were conducted on lily bulbs and onion seedlings under controlled conditions in a greenhouse to complete Koch's postulates. Disease symptoms on lily were most severe in treatments inoculated with binucleate Rhizoctonia AG‐A, P. oligandrum and F. proliferatum. Plant height was lower in the above treatments compared with the control plants. The least aggressive fungus was R. solani. In artificial inoculations of onion, seedling survival was significantly affected by all fungi. The most pathogenic fungus was F. proliferatum w and the least were isolates of F. oxysporum (II and III). All fungi were successfully re‐isolated from the inoculated plants.     

Validation of a cheap and simple nondestructive method for obtaining AFLPs and DNA sequences (mitochondrial and nuclear) in amphibians

The use of nondestructive methods for obtaining DNA from amphibians (e.g. buccal swabs) allows genetic studies to be performed without affecting the survival of the studied individuals. In this study, we compared two methods of nondestructive DNA sampling, buccal swabs and interdigital membrane or toe‐clipping, in several amphibian species of different size: Rhinella spinulosa, R. atacamensis, six species of the genus Telmatobius and Pleurodema thaul. We evaluated the integrity of the DNA extracted by sequencing fragments of mitochondrial and nuclear genes and by generating amplified fragment length polymorphisms markers (AFLPs). In all cases, we obtained an adequate amount of DNA (mean range 55–298 ng/μL). We obtained identical DNA sequences from buccal swab and interdigital membrane/toe‐clip for all individuals. The differences in the coding of AFLP markers between the tissues were similar to those reported for replicas of the same type of sample in similar analyses in other species of amphibians. In conclusion, the use of buccal swabs is a trustworthy and inexpensive method to obtain DNA for mitochondrial and nuclear sequencing and AFLP analyses. Given the types of markers evaluated, buccal swabs may be used for phylogenetic, phylogeographic and population genetic studies, even in small amphibians (<33 mm).     

Cranial morphology and taxonomic resolution of some dolphin taxa (Delphinidae) in Australian waters,with a focus on the genus Tursiops

Phylogenetic relationships in the family Delphinidae have been widely debated. We examined 347 skulls of Tursiops, Stenella, Delphinus, Steno, Lagenodelphis, and Sousa in order to resolve the phylogenetic position of Australian species of Tursiops. Five Tursiops type specimens were included. Cranial morphology was described using 2‐dimensional (2‐D) and 3‐dimensional geometric morphometrics (3‐GM), counts and categorical data. Analyses showed a clear morphological separation of Tursiops, including type specimens, from other genera. The three Stenella species did not cluster together. Stenella attenuata clustered with Delphinus delphis, and Stenella coeruleoalba with Lagenodelphis hosei. Length and width of the skull and rostrum were important discriminators in both methods. For 3‐D data, round vs. angular posterior skull shape distinguished some genera. Taxa that overlapped in the multivariate analyses had different mean tooth counts. Our study challenges genetic studies that identified Tursiops as polyphyletic, with T. aduncus closer to S. attenuata.     

Length‐weight relationships of Barilius barila (Hamilton, 1822), Opsarius tileo (Hamilton, 1822) and Cyprinion semiplotum (McClelland, 1839) collected from Manas River in Assam,India

Length‐weight relationships (LWRs) are presented for three hill stream fish species belonging to the family Cyprinidae namely, Barilius barila (Hamilton, 1822), Opsarius tileo (Hamilton, 1822) and Cyprinion semiplotum (McClelland, 1839). Fishes were collected on a monthly basis from January 2016 to December 2017 with the help of cast net (270 cm length, 1.2 cm mesh size) and gillnet (7,500 cm length × 130 cm depth, 5 cm mesh size) from the Manas river in Assam, India.. A new length record for the FishBase LWR database was observed in B. barila.