A new record for Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) species complex of Turkey

In this study, species complex of Turkish Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) populations was determined by PCR‐based DNA analysis. According to phylogenetic analyses, the B. tabaci samples have been identified within three generic groups. A major part of the samples belonged to two invasive species, either Middle East–Asia Minor 1 (MEAM1) or Mediterranean (MED). In addition to these two invasive species, several samples collected from greenhouses and cotton fields have been found to be related to Middle East–Asia Minor 2 (MEAM2), which is the first record of Turkish B. tabaci species complex.     

The impact of Broussonetia papyrifera (L.) vent. on community characteristics in the forest and forest–savannah transition ecosystems of Ghana

Following its introduction in the late 1960s, Broussonetia papyrifera L. Vent. Moraceae (paper mulberry) has emerged as a major exotic invasive species in Ghana's forest ecosystems. This study was carried out to assess the effects of B. papyrifera invasion on community composition in forest and forest–savannah transition ecosystems. Comparative and removal experiments were conducted in paired B. papyrifera invaded versus uninvaded plots. In the comparative assessment, species composition was found to be similar in both invaded and uninvaded plots. However, relative per cent cover of resident species and guilds including Chromolaena odorata, indigenous broadleaves and indigenous grasses were significantly lower in invaded plots. Seven months after B. papyrifera was experimentally removed from invaded stands, cover by indigenous broadleaves increased by 35%, as against only 5% in control plots at the forest site. However, at the transition site, the increase in per cent cover of indigenous broadleaves (18%) was not significantly different from control (2.5%) plots. We conclude that B. papyrifera has the capacity to reduce the abundance of indigenous broadleaf species, although its removal is more likely to favour regeneration in a forest than a forest–savannah transition ecosystem.     

A preliminary assessment of the response of a native reptile assemblage to spot‐spraying invasive Bitou Bush with glyphosate herbicide

During recent work examining the effects of Bitou Bush (Chrysanthemoides monilifera ssp. rotundata) invasion on native reptile assemblages in coastal heathland vegetation in Eastern Australia, unplanned spot‐spraying of glyphosate occurred at some of our experimental sites invaded by Bitou Bush. We used this unexpected herbicide application as an opportunity to provide a preliminary assessment of the short‐term impacts on reptiles of glyphosate spot‐spraying of Bitou Bush. Using an M‐BARCI design, we compared reptile assemblages among uninvaded (reference) sites, invaded (control) sites and invaded and sprayed (impact) sites before and after spraying. We found no significant short‐term (7 – 10 months) differences in reptile abundance, species richness or assemblage composition among invaded, uninvaded and sprayed sites before and after glyphosate application. We cautiously interpret our results to generate a preliminary finding that spot‐spraying of Bitou Bush with glyphosate appears not to have a deleterious effect on reptile assemblages at seven and ten months following herbicide application. While we would not recommend basing management decisions on the outcomes of our study alone, we suggest that our findings can be used to assist in the development of strategic analyses of glyphosate impacts on native flora and fauna.     

Climate and geochemistry as drivers of eucalypt diversification in Australia

Eucalypts cover most of Australia. Here, we investigate the relative contribution of climate and geochemistry to the distribution and diversity of eucalypts. Using geostatistics, we estimate major element concentrations, pH, and electrical conductivity at sites where eucalypts have been recorded. We compare the median predicted geochemistry and reported substrate for individual species that appear associated with extreme conditions; this provides a partial evaluation of the predictions. We generate a site‐by‐species matrix by aggregating observations to the centroids of 100‐km‐wide grid cells, calculate diversity indices, and use numerical ecology methods (ordination, variation partitioning) to investigate the ecology of eucalypts and their response to climatic and geochemical gradients. We find that β‐diversity coincides with variations in climatic and geochemical patterns. Climate and geochemistry together account for less than half of the variation in eucalypt species assemblages across Australia but for greater than 80% in areas of high species richness. Climate is more important than geochemistry in explaining eucalypts species distribution and change in assemblages across Australia as a whole but there are correlations between the two sets of environmental variables. Many individual eucalypt species and entire taxonomic sections (Aromatica, Longistylus of subgenus Eucalyptus, Dumaria, and Liberivalvae of subgenus Symphyomyrtus) have distributions affected strongly by geochemistry. We conclude that eucalypt diversity is driven by steep geochemical gradients that have arisen as climate patterns have fluctuated over Australia over the Cenozoic, generally aridifying since the Miocene. The diversification of eucalypts across Australia is thus an excellent example of co‐evolution of landscapes and biota in space and time and challenges accepted notions of macroecology.     

Cryptic speciation in the field vole: a multilocus approach confirms three highly divergent lineages in Eurasia

Species are generally described from morphological features, but there is growing recognition of sister forms that show substantial genetic differentiation without obvious morphological variation and may therefore be considered ‘cryptic species’. Here, we investigate the field vole (Microtus agrestis), a Eurasian mammal with little apparent morphological differentiation but which, on the basis of previous sex‐linked nuclear and mitochondrial DNA (mtDNA) analyses, is subdivided into a Northern and a Southern lineage, sufficiently divergent that they may represent two cryptic species. These earlier studies also provided limited evidence for two major mtDNA lineages within Iberia. In our present study, we extend these findings through a multilocus approach. We sampled 163 individuals from 46 localities, mainly in Iberia, and sequenced seven loci, maternally, paternally and biparentally inherited. Our results show that the mtDNA lineage identified in Portugal is indeed a distinct third lineage on the basis of other markers as well. In fact, multilocus coalescent‐based methods clearly support three separate evolutionary units that may represent cryptic species: Northern, Southern and Portuguese. Divergence among these units was inferred to have occurred during the last glacial period; the Portuguese lineage split occurred first (estimated at c. 70 000 bp ), and the Northern and Southern lineages separated at around the last glacial maximum (estimated at c. 18 500 bp ). Such recent formation of evolutionary units that might be considered species has repercussions in terms of understanding evolutionary processes and the diversity of small mammals in a European context.     

Seasonal changes in fish catch and environmental variables in a large Tropical Lake,Volta, Ghana

Fish species assemblage and selected environmental variables were monitored in Lake Volta from September 2014 to August 2016 to determine seasonal variability in species composition, catch and environmental variables that determine the structure of the fish community. A total of 1,557 individual fish belonging to 41 species, 25 genera and 13 families were recorded. The important fish species with respect to frequency of occurrence, abundance and weight, respectively, were as follows: Chrysichthys (100%; 43.03%; 17.93%), tilapias (100%; 28.97%; 17.86%), Alestes (100%; 14.13%; 32.10%) and Bagrus (91.67%; 5.65%; 12.80%) in that order. The composition of fish species and their temporal variation in experimental catches were similar to that of commercial catches. There were no significant differences (p > 0.05) in species abundance, weight and diversity indices between the dry and wet seasons. The modal class of length frequency distribution of the dominant species in the catch, Chrysichthys, reduced from 125 mm in 2006 to 95 mm in the current study indicating overfishing. Environmental variables considered showed little variation and within optimal ranges for fish survival and did not differ significantly between seasons. Canonical Correspondence Analysis showed that environmental variables explained 43.30% of the variation in species abundance with Lake water level, nitrite‐nitrogen and total dissolved solids being the main environmental factors influencing the structure of the fish community.     

Ditches as species‐rich secondary habitats and refuge for meadow species in agricultural marsh grasslands

Questions

Can drainage ditches in agricultural marsh grassland provide a suitable habitat for the persistence of fen meadow species? How does the ditch margin vegetation develop as a function of regular dredging? Is ornithologically oriented management also beneficial for plant biodiversity?

Location

Riparian marshes, Eider‐Treene‐Sorge lowland, Schleswig‐Holstein, Germany.

Methods

We performed vegetation surveys of drainage ditches along with their water body, slope and margin structures annually for 3 years. The data were analysed with respect to date and means of ditch dredging. In addition, we recorded vegetation of the surrounding agricultural grassland, measured nutrient status of the soil and the water body and sampled seed bank of the ditch slopes. We used ANOVA and multivariate methods to describe the development of the ditch vegetation and the persistence of target meadow species.

Results

Vegetation re‐development of ditch margins proceeds quite rapidly after disturbance from dredging. Dominance of mudbank species was observed only in the first year, followed by an increase of reed species and reduction of phytodiversity. Target species of wet meadow communities reach highest abundance in the second and third year and build a significant seed bank before being suppressed by reeds.

Conclusions

In heavily eutrophicated, intensively used marsh grassland, regularly disturbed ditch margins are important secondary habitats for pioneer and subdominant wetland species, which have nearly disappeared in a larger area. Current management cycles of ditch dredging every 3–4 years comply with the successional development, allowing the mudbank and wet meadow species to persist in the vegetation and seed bank. In contrast to the frequency, the form of dredging (ditch profile), which is crucial for bird protection, plays a minor role for plants. We recommend moderate disturbance (mowing of ditch margins) to suppress strong competitors in the years between dredging for additional support to target plant species.     

Bayesian species identification under the multispecies coalescent provides significant improvements to DNA barcoding analyses

DNA barcoding methods use a single locus (usually the mitochondrial COI gene) to assign unidentified specimens to known species in a library based on a genetic distance threshold that distinguishes between‐species divergence from within‐species diversity. Recently developed species delimitation methods based on the multispecies coalescent (MSC) model offer an alternative approach to individual assignment using either single‐locus or multiloci sequence data. Here, we use simulations to demonstrate three features of an MSC method implemented in the program bpp . First, we show that with one locus, MSC can accurately assign individuals to species without the need for arbitrarily determined distance thresholds (as required for barcoding methods). We provide an example in which no single threshold or barcoding gap exists that can be used to assign all specimens without incurring high error rates. Second, we show that bpp can identify cryptic species that may be misidentified as a single species within the library, potentially improving the accuracy of barcoding libraries. Third, we show that taxon rarity does not present any particular problems for species assignments using bpp and that accurate assignments can be achieved even when only one or a few loci are available. Thus, concerns that have been raised that MSC methods may have problems analysing rare taxa (singletons) are unfounded. Currently, barcoding methods enjoy a huge computational advantage over MSC methods and may be the only approach feasible for massively large data sets, but MSC methods may offer a more stringent test for species that are tentatively assigned by barcoding.     

Relationships between the density of two potential restoration tree species and plant species abundance and richness in a degraded Afromontane forest of Kenya

In recent years, there have been considerable efforts to restore degraded tropical montane forests through active restoration using indigenous tree species. However, little is known about how these species used for restoration influence other species. In this study, two potential restoration species, Albizia gummifera and Neoboutonia macrocalyx, are investigated with regard to the relationship between their density and the abundance and richness of other plant species. The study was conducted in a degraded forest consisting of disturbed transition zones and secondary forest. Our results show positive relationships between the density of A. gummifera and the abundance of tree seedling and sapling richness in the transition zones and in the secondary forest. Shrub richness was negatively related to the density of A. gummifera. Abundance and richness of tree saplings and shrubs were positively related to N. macrocalyx density both in the transition zones and in the secondary forest. Herb species richness declined with N. macrocalyx density in the transition zones but increased with N. macrocalyx density in the secondary forest. The positive relationships between the density of the two tree species and species richness of other woody species suggest that both A. gummifera and N. macrocalyx can be suitable for active restoration of degraded mountain forests within their natural range.     

Detection of major loci associated with the variation of 18 important agronomic traits between Solanum pimpinellifolium and cultivated tomatoes

Wild species can be used to improve various agronomic traits in cultivars; however, a limited understanding of the genetic basis underlying the morphological differences between wild and cultivated species hinders the integration of beneficial traits from wild species. In the present study, we generated and sequenced recombinant inbred lines (RILs, 201 F₁₀ lines) derived from a cross between Solanum pimpinellifolium and Solanum lycopersicum tomatoes. Based on a high‐resolution recombination bin map to uncover major loci determining the phenotypic variance between wild and cultivated tomatoes, 104 significantly associated loci were identified for 18 agronomic traits. On average, these loci explained ~39% of the phenotypic variance of the RILs. We further generated near‐isogenic lines (NILs) for four identified loci, and the lines exhibited significant differences for the associated traits. We found that two loci could improve the flower number and inflorescence architecture in the cultivar following introgression of the wild‐species alleles. These findings allowed us to construct a trait–locus network to help explain the correlations among different traits based on the pleiotropic or linked loci. Our results provide insights into the morphological changes between wild and cultivated tomatoes, and will help to identify key genes governing important agronomic traits for the molecular selection of elite tomato varieties.     

Toward an inordinate fondness for stars,beetles and Lobophora? Species diversity of the genus Lobophora (Dictyotales,Phaeophyceae) in New Caledonia

Until the recent use of molecular markers, species diversity of Lobophora, an ecologically important brown algal genus with a worldwide distribution in temperate and tropical seas, has been critically underestimated. Using a DNA‐based taxonomic approach, we re‐examined diversity of the genus from New Caledonia in the Southwest Pacific Ocean. First, species were delineated using general mixed Yule coalescent‐based and barcoding gap approaches applied to a mitochondrial cox3 data set. Results were subsequently confirmed using chloroplast psbA and rbcL data sets. Species delimitation analyses agreed well across markers and delimitation algorithms, with the barcoding gap approach being slightly more conservative. Analyses of the cox3 data set resulted in 31–39 molecular operational taxonomic units (MOTUs), four of which are previously described species (L. asiatica, L. crassa, L. nigrescens s.l., L. pachyventera). Of the remaining MOTUs for which we obtained a representative number of sequences and results are corroborated across analyses and genes, we described 10 species de novo: L. abaculusa, L. abscondita, L. densa, L. dimorpha, L. gibbera, L. hederacea, L. monticola, L. petila, L. rosacea, and L. undulata. Our study presents an excellent case of how a traditional morphology‐based taxonomy fails to provide accurate estimates of algal diversity. Furthermore, the level of Lobophora diversity unveiled from a single locality in the Pacific Ocean raises important questions with respect to the global diversity of the genus, the distributions and range sizes of the individual species, as well as the mechanisms facilitating coexistence.     

One species in eight: DNA barcodes from type specimens resolve a taxonomic quagmire

Each holotype specimen provides the only objective link to a particular Linnean binomen. Sequence information from them is increasingly valuable due to the growing usage of DNA barcodes in taxonomy. As type specimens are often old, it may only be possible to recover fragmentary sequence information from them. We tested the efficacy of short sequences from type specimens in the resolution of a challenging taxonomic puzzle: the Elachista dispunctella complex which includes 64 described species with minuscule morphological differences. We applied a multistep procedure to resolve the taxonomy of this species complex. First, we sequenced a large number of newly collected specimens and as many holotypes as possible. Second, we used all >400 bp examine species boundaries. We employed three unsupervised methods (BIN, ABGD, GMYC) with specified criteria on how to handle discordant results and examined diagnostic bases from each delineated putative species (operational taxonomic units, OTUs). Third, we evaluated the morphological characters of each OTU. Finally, we associated short barcodes from types with the delineated OTUs. In this step, we employed various supervised methods, including distance‐based, tree‐based and character‐based. We recovered 658 bp barcode sequences from 194 of 215 fresh specimens and recovered an average of 141 bp from 33 of 42 holotypes. We observed strong congruence among all methods and good correspondence with morphology. We demonstrate potential pitfalls with tree‐, distance‐ and character‐based approaches when associating sequences of varied length. Our results suggest that sequences as short as 56 bp can often provide valuable taxonomic information. The results support significant taxonomic oversplitting of species in the Elachista dispunctella complex.     

Dictyota cyanoloma (Dictyotales,Phaeophyceae), a Newly Introduced Brown Algal Species in California

Here, we report for the first time the presence of Dictyota cyanoloma in southern California. Dictyota cyanoloma is conspicuous in harbors and bays by its distinctive bright blue‐iridescent margins. This species was originally described from Europe, but subsequent studies have revealed that it represented an introduction from Australia. The current distribution of D. cyanoloma comprises southern Australia and the North East Atlantic, including the Mediterranean Sea and the Macaronesian islands. The presence of D. cyanoloma in southern California is supported by molecular cox1 and psbA gene sequences. A reconstruction of the invasive history based on nine polymorphic microsatellite markers reveals a close affinity of the Californian specimens with European populations. Dictyota cyanoloma in the United States appears to be (so far) restricted to the Californian coast from San Diego Bay in the south to Santa Catalina Island and Long Beach Harbor in the north. A correlative species distribution model suggests gradually declining habitat suitability north of the Southern Californian Bight and high suitability in Baja California, including the Gulf of California. Finally, its widespread abundance in bays and harbors suggests shipping is a likely transport mechanism.     

Altitude affects the distribution and abundance of two non‐native insect pests of the common walnut

The leaf miner Coptodisca lucifluella and the carpophagous Rhagoletis completa, of American origin, are two non‐native walnut (Juglans spp.) pests in Italy. For the Friuli Venezia Giulia region (FVG) (N‐E Italy), C. lucifluella is not yet listed, while R. completa has been present for over 25 years. During 2015, samples of leaves and fruits were collected from 219 single old common walnut trees (Juglans regia) placed at different altitudes (0–1,073 m a.s.l.) in FVG to detect the distribution and abundance of both pests. Samples of leaf miner larvae and their parasitoids were subjected to mitochondrial DNA analysis for identification. C. lucifluella has been found in 55 out of 219 sites. The species has been identified by typical leaf symptoms and by its DNA barcode. This is the first report of the species for FVG. The leaf miner distribution was negatively correlated with altitude. The species has not been observed at sites over 600 m a.s.l. Larvae were parasitized by native parasitoids identified as belonging to the genus Chrysocharis by morphological features and by DNA barcode. R. completa has been found in 89 out of 165 sites on walnut trees with fruits. The infestation level was very high in lowland localities. At sites over 700 m a.s.l., no infestation was found. Both species are widespread in the region, and their occurrence is significantly affected by altitude. Data suggest that walnut trees could be cultivated in some mountain areas without the need to control R. completa with insecticides.     

Occurrence of an invasive coral in the southwest Atlantic and comparison with a congener suggest potential niche expansion

Tubastraea tagusensis, a coral native to the Galapagos Archipelago, has successfully established and invaded the Brazilian coast where it modifies native tropical rocky shore and coral reef communities. In order to understand the processes underlying the establishment of T. tagusensis, we tested whether Maxent, a tool for species distribution modeling, based on the native range of T. tagusensis correctly forecasted the invasion range of this species in Brazil. The Maxent algorithm was unable to predict the Brazilian coast as a suitable environment for the establishment of T. tagusensis. A comparison between these models and a principal component analysis (PCA) allowed us to examine the environmental dissimilarity between the two occupied regions (native and invaded) and to assess the species' occupied niche breadth. According to the PCA results, lower levels of chlorophyll‐a and nitrate on the Atlantic coast segregate the Brazilian and Galapagos environments, implying that T. tagusensis may have expanded its realized niche during the invasion process. We tested the possible realized niche expansion in T. tagusensis by assuming that Tubastraea spp. have similar fundamental niches, which was supported by exploring the environmental space of T. coccinea, a tropical‐cosmopolitan congener of T. tagusensis. We believe that the usage of Maxent should be treated with caution, especially when applied to biological invasion (or climate change) scenarios where the target species has a highly localized native (original) distribution, which may represent only a small portion of its fundamental niche, and therefore a violation of a SDM assumption.     

Identification of Belgian mosquito species (Diptera: Culicidae) by DNA barcoding

Since its introduction in 2003, DNA barcoding has proven to be a promising method for the identification of many taxa, including mosquitoes (Diptera: Culicidae). Many mosquito species are potential vectors of pathogens, and correct identification in all life stages is essential for effective mosquito monitoring and control. To use DNA barcoding for species identification, a reliable and comprehensive reference database of verified DNA sequences is required. Hence, DNA sequence diversity of mosquitoes in Belgium was assessed using a 658 bp fragment of the mitochondrial cytochrome oxidase I (COI) gene, and a reference data set was established. Most species appeared as well‐supported clusters. Intraspecific Kimura 2‐parameter (K2P) distances averaged 0.7%, and the maximum observed K2P distance was 6.2% for Aedes koreicus. A small overlap between intra‐ and interspecific K2P distances for congeneric sequences was observed. Overall, the identification success using best match and the best close match criteria were high, that is above 98%. No clear genetic division was found between the closely related species Aedes annulipes and Aedes cantans, which can be confused using morphological identification only. The members of the Anopheles maculipennis complex, that is Anopheles maculipennis s.s. and An. messeae, were weakly supported as monophyletic taxa. This study showed that DNA barcoding offers a reliable framework for mosquito species identification in Belgium except for some closely related species.     

Mutualism fails when climate response differs between interacting species

Successful species interactions require that both partners share a similar cue. For many species, spring warming acts as a shared signal to synchronize mutualist behaviors. Spring flowering plants and the ants that disperse their seeds respond to warming temperatures so that ants forage when plants drop seeds. However, where warm‐adapted ants replace cold‐adapted ants, changes in this timing might leave early seeds stranded without a disperser. We investigate plant seed dispersal south and north of a distinct boundary between warm‐ and cold‐adapted ants to determine if changes in the ant species influence local plant dispersal. The warm‐adapted ants forage much later than the cold‐adapted ants, and so we first assess natural populations of early and late blooming plants. We then transplant these plants south and north of the ant boundary to test whether distinct ant climate requirements disrupt the ant–plant mutualism. Whereas the early blooming plant's inability to synchronize with the warm‐adapted ant leaves its populations clumped and patchy and its seedlings clustered around the parents in natural populations, when transplanted into the range of the cold‐adapted ant, effective seed dispersal recovers. In contrast, the mutualism persists for the later blooming plant regardless of location because it sets seed later in spring when both warm‐ and cold‐adapted ant species forage, resulting in effective seed dispersal. These results indicate that the climate response of species interactions, not just the species themselves, is integral in understanding ecological responses to a changing climate. Data linking phenological synchrony and dispersal are rare, and these results suggest a viable mechanism by which a species' range is limited more by biotic than abiotic interactions – despite the general assumption that biotic influences are buried within larger climate drivers. These results show that biotic partner can be as fundamental a niche requirement as abiotic resources.     

Existence of species complex largely reduced barcoding success for invasive species of Tephritidae: a case study in Bactrocera spp.

Fruit flies in the family Tephritidae are the economically important pests that have many species complexes. DNA barcoding has gradually been verified as an effective tool for identifying species in a wide range of taxonomic groups, and there are several publications on rapid and accurate identification of fruit flies based on this technique; however, comprehensive analyses of large and new taxa for the effectiveness of DNA barcoding for fruit flies identification have been rare. In this study, we evaluated the COI barcode sequences for the diagnosis of fruit flies using 1426 sequences for 73 species of Bactrocera distributed worldwide. Tree‐based [neighbour‐joining (NJ)]; distance‐based, such as Best Match (BM), Best Close Match (BCM) and Minimum Distance (MD); and character‐based methods were used to evaluate the barcoding success rates obtained with maintaining the species complex in the data set, treating a species complex as a single taxon unit, and removing the species complex. Our results indicate that the average divergence between species was 14.04% (0.00–25.16%), whereas within a species this was 0.81% (0.00–9.71%); the existence of species complexes largely reduced the barcoding success for Tephritidae, for example relatively low success rates (74.4% based on BM and BCM and 84.8% based on MD) were obtained when the sequences from species complexes were included in the analysis, whereas significantly higher success rates were achieved if the species complexes were treated as a single taxon or removed from the data set – BM (98.9%), BCM (98.5%) and MD (97.5%), or BM (98.1%), BCM (97.4%) and MD (98.2%).