Species‐specific mediation of temperature and community interactions by multiple foundation species

Foundation species can provide habitat that modify abiotic and biotic processes that contribute to ecosystem function. While many studies have focused on the processes and consequences of a focal foundation species, understanding the ecological equivalence of co‐occurring foundation species is important to identify key species responsible for ecosystem function. Here, we investigated the relative contributions of co‐occurring foundation species on abiotic (temperature) and biotic responses of invertebrate species (recruitment, persistence, growth and survival). In a series of experimental field studies, we manipulated foundation species to measure invertebrate recruitment, persistence, and predation. A laboratory experiment measured foundation species effects on herbivore growth. Results demonstrated that macroalgal (Fucus vesiculosus ecad and Ascophyllum nodosum ecad scorpioides) intermediate foundation species provide habitat, food, and alleviate abiotic stress for dominant littorinid herbivores that surpass that provided by the primary species (Spartina alterniflora). These foundation effects were species‐specific with F. vesiculosus ecad important for early life‐history stages (enhanced recruitment and early growth of littorinid snails) and A. nodosum ecad important later on as a refuge from predators (Carcinus meanas) and stressful temperature. Understanding of the different effects of co‐occurring foundation species on population and community processes is necessary for predicting community response to natural disturbance, species invasion, and ecosystem‐based management actions.     

DNA barcoding commercially important fish species of Turkey

DNA barcoding was used in the identification of 89 commercially important freshwater and marine fish species found in Turkish ichthyofauna. A total of 1765 DNA barcodes using a 654‐bp‐long fragment of the mitochondrial cytochrome c oxidase subunit I gene were generated for 89 commercially important freshwater and marine fish species found in Turkish ichthyofauna. These species belong to 70 genera, 40 families and 19 orders from class Actinopterygii, and all were associated with a distinct DNA barcode. Nine and 12 of the COI barcode clusters represent the first species records submitted to the BOLD and GenBank databases, respectively. All COI barcodes (except sequences of first species records) were matched with reference sequences of expected species, according to morphological identification. Average nucleotide frequencies of the data set were calculated as T = 29.7%, C = 28.2%, A = 23.6% and G = 18.6%. Average pairwise genetic distance among individuals were estimated as 0.32%, 9.62%, 17,90% and 22.40% for conspecific, congeneric, confamilial and within order, respectively. Kimura 2‐parameter genetic distance values were found to increase with taxonomic level. For most of the species analysed in our data set, there is a barcoding gap, and an overlap in the barcoding gap exists for only two genera. Neighbour‐joining trees were drawn based on DNA barcodes and all the specimens clustered in agreement with their taxonomic classification at species level. Results of this study supported DNA barcoding as an efficient molecular tool for a better monitoring, conservation and management of fisheries.     

New approaches for establishing conservation priorities for socio-economically important plant species

The establishment of priorities among species is a crucial step in any conservation strategy since financial resources are generally limited. Traditionally, priorities for conservation of plant species have been focused on endemicity, rarity and particularly on their threatened status. Crop wild relatives (CWR) and wild harvested plants (WHP) are important elements of biodiversity with actual or potential socio-economic value. In this study, eight prioritisation criteria were used along with different prioritisation systems and applied to the Portuguese CWR and WHP. The top 50 species obtained by each of these methods were identified. The final top CWR were those that occurred as a priority in most methods. Twenty CWR were identified as the highest priorities for conservation in Portugal and they include wild relatives of the crop genera Allium, Daucus, Dianthus, Epilobium, Festuca, Herniaria, Narcissus, Quercus, Plantago, Trifolium, and Vicia. Eighteen WHP were recognised as priorities for conservation and include several Narcissus and Thymus species, among others. The advantages, limitations and level of subjectivity of each of the methods used in this exercise are discussed.     

Comparative demography of commercially important parrotfish species from Micronesia

Fishery‐independent sampling was used to determine growth patterns, life span, mortality rates and timing of maturation and sex change in 12 common parrotfishes (Labridae: tribe Scarinae) from five genera (Calotomus, Cetoscarus, Chlorurus, Hipposcarus and Scarus) in Micronesia. Interspecific variation in life‐history traits was explored using multivariate analysis. All species displayed strong sex‐specific patterns of length‐at‐age among which males reached larger asymptotic lengths. There was a high level of correlation among life‐history traits across species. Relationships between length‐based and age‐based variables were weakest, with a tenuous link between maximum body size and life span. Cluster analysis based on similarities among life‐history traits demonstrated that species were significantly grouped at two major levels. The first grouping was driven by length‐based variables (lengths at maturity and sex change and maximum length) and separated the small‐ and large‐bodied species. Within these, species were grouped by age‐based variables (age at maturity, mortality and life span). Groupings based on demographic and life‐history features were independent of phylogenetic relationships at the given taxonomic level. The results reiterate that body size is an important characteristic differentiating species, but interspecific variation in age‐based traits complicates its use as a life‐history proxy. Detailed life‐history metrics should facilitate future quantitative assessments of vulnerability to overexploitation in multispecies fisheries.     

Comparative cytogenetics of three economically important Piper L. species from the Brazilian Amazon

The species Piper hispidinervum, Piper aduncum, and Piper affinis hispidinervum have essential oils with high levels of safrole, dillapiole, and sarisan, respectively. Safrole is important for pharmaceutical and chemical industries, while dillapiole and sarisan are promising compounds to control insects and fungi. These species are very similar morphologically and their taxonomy is controversial. Divergent hypotheses consider P. aduncum and P. hispidinervum either as a single species or as distinct taxa, while P. affinis hispidinervum is inferred to be a natural hybrid or a chemotype of P. hispidinervum. Delimiting the taxonomic boundaries would be helpful for germplasm conservation and breeding programs. This study aimed to undertake a detailed analysis of P. aduncum, P. hispidinervum, and P. affinis hispidinervum karyotype and rDNA sites. Genomic in situ hybridization (GISH) was used to establish genomic homology among species and to test the natural hybridization hypothesis for origin of P. affinis hispidinervum. Karyotype traits were similar for all three species: 2n = 26 small chromosomes, predominantly metacentric. All three species exhibited CMA+ bands on the secondary constriction of chromosome pair 4. A size-heteromorphic 35S rDNA site was co-localized with the CMA+ band. A 5S rDNA site was located in the proximal region of chromosome pair 7. The patterns of genomic hybridization revealed that the repetitive DNA fraction of the species is highly similar in terms of proportion of genome, sequence type, and distribution. Our findings did not allow us to differentiate the three species and point to the importance of deeper genomic studies to elucidate the taxonomic controversy.

     

Detrital traits affect substitutability of a range‐expanding foundation species across latitude

Climate‐driven range shifts of foundation species could alter ecosystem processes and community composition by providing different resources than resident foundation species. Along the US Atlantic coast, the northward expanding foundation species, black mangrove Avicennia germinans, is replacing the dominant salt marsh foundation species, marsh cordgrass Spartina alterniflora. These species have distinct detrital attributes that ostensibly provide different resources to epifauna. We experimentally examined how detritus of these species affects decomposition and community composition in different habitat contexts at regional and local scales. First, we manipulated detritus identity (Avicennia, Spartina) at 13 sites across a 5° latitudinal gradient spanning mangrove, mixed marsh‐mangrove and salt marsh habitats. Across latitude, we found that Avicennia detritus decomposed 2–4 times faster than Spartina detritus, suggesting that detrital turnover will increase with mangrove expansion. Epifaunal abundance and richness increased 2–7 times from south to north (mangrove to salt marsh) and were equivalent between Avicennia and Spartina detritus except for crabs, a dominant taxonomic group that preferred Spartina detritus. Second, to examine the whether changing habitat context affected regional patterns, we manipulated detritus identity and surrounding habitat type (mangrove, salt marsh) at a single mixed site, also including inert mimics to separate structural and nutritional roles of detritus. Epifaunal richness was similar between the two detrital types, but crabs were 2–7 times more abundant in Spartina detritus due to its structural attributes. Surrounding habitat type did not influence decomposition rate or community patterns, which suggests that latitudinal influences, not surrounding habitat, drove the regional community patterns in the first experiment. Overall, mangrove expansion could alter epifaunal communities due to the lower structural value and faster turnover of mangrove detritus. As species shift with changing climate, understanding foundation species substitutability is critical to predict community change, but we must account for concomitant environmental changes that also modify communities.     

Genetic structuring of important medicinal species of genus Warburgia as revealed by AFLP analysis

The genus Warburgia (Canellaceae) contains four tree species that are of valuable medicinal importance and are all found in Africa. Genetic diversity present in wild populations of these species is under great threat due to unsustainable harvesting for medicines and indiscriminate felling for timber and agricultural expansion. There is therefore an urgent need for conservation of these species. Some authors disagree about the taxonomy of the genus and list different species as synonyms. Amplified fragment length polymorphism (AFLP) technique was used to determine the genetic relationships between three species to resolve the taxonomic confusion. The amount of genetic variation within and among populations was assessed to guide strategies for their conservation and sustainable utilization. Four AFLP primer pairs (EcoRI/MseI) generated a total of 185 amplification products. Analysis of molecular variance revealed most variation among individuals within populations (63%, P < 0.0001), but variation among populations (37%, P < 0.0001) was highly significant as well. Constrained analysis of principal coordinates based on the Jaccard distance confirmed the separation among populations (38.2%, P < 0.0001). A phenetic tree and ordination graphs showed a clear distinction of W. ugandensis from W. salutaris and W. stuhlmannii. W. ugandensis populations from Uganda and western Kenya formed a subgroup that clustered away from the rest of the W. ugandensis populations. W. salutaris and W. stuhlmannii populations showed little genetic differentiation. An implication of the data to genetic management and taxonomic clarification is discussed.     

Salt effects on functional traits in model and in economically important Lotus species

A common stress on plants is NaCl‐derived soil salinity. Genus Lotus comprises model and economically important species, which have been studied regarding physiological responses to salinity. Leaf area ratio (LAR), root length ratio (RLR) and their components, specific leaf area (SLA) and leaf mass fraction (LMF) and specific root length (SRL) and root mass fraction (RMF) might be affected by high soil salinity. We characterised L. tenuis, L. corniculatus, L. filicaulis, L. creticus, L. burtii and L. japonicus grown under different salt concentrations (0, 50, 100 and 150 mm NaCl) on the basis of SLA, LMF, SRL and RMF using PCA. We also assessed effects of different salt concentrations on LAR and RLR in each species, and explored whether changes in these traits provide fitness benefit. Salinity (150 mm NaCl) increased LAR in L. burtii and L. corniculatus, but not in the remaining species. The highest salt concentration caused a decrease of RLR in L. japonicus Gifu, but not in the remaining species. Changes in LAR and RLR would not be adaptive, according to adaptiveness analysis, with the exception of SLA changes in L. corniculatus. PCA revealed that under favourable conditions plants optimise surfaces for light and nutrient acquisition (SLA and SRL), whereas at higher salt concentrations they favour carbon allocation to leaves and roots (LMF and RMF) in detriment to their surfaces. PCA also showed that L. creticus subjected to saline treatment was distinguished from the remaining Lotus species. We suggest that augmented carbon partitioning to leaves and roots could constitute a salt‐alleviating mechanism through toxic ion dilution.     

Footprint tunnels are effective for detecting dormouse species

Glirids are arboreal rodents that are difficult to monitor due to their nocturnal activity and their relatively low density. We compared results from footprint tunnels with those from two other monitoring methods (nest boxes and nesting tubes) for three dormouse species in an occupancy framework. Footprint tunnels performed better than the other two methods for the hazel dormouse Muscardinus avellanarius and the edible dormouse Glis glis, and were the only method which detected the garden dormouse Eliomys quercinus. Our findings provide evidence to support the effectiveness of footprint tunnels in monitoring the occurrence of dormouse species in comparison with other methods.     

Microsatellite allele sizes alone are insufficient to delineate species boundaries in Symbiodinium

Symbiodinium are a diverse group of unicellular dinoflagellates that are important nutritional symbionts of reef‐building corals. Symbiodinium putative species (‘types’) are commonly identified with genetic markers, mostly nuclear and chloroplast encoded ribosomal DNA regions. Population genetic analyses using microsatellite loci have provided insights into Symbiodinium biogeography, connectivity and phenotypic plasticity, but are complicated by: (i) a lack of consensus criteria used to delineate inter‐ vs. intragenomic variation within species; and (ii) the high density of Symbiodinium in host tissues, which results in single samples comprising thousands of individuals. To address this problem, Wham & LaJeunesse (2016) present a method for identifying cryptic Symbiodinium species from microsatellite data based on correlations between allele size distributions and nongeographic genetic structure. Multilocus genotypes that potentially do not recombine in sympatry are interpreted as secondary ‘species’ to be discarded from downstream population genetic analyses. However, Symbiodinium species delineations should ideally incorporate multiple physiological, ecological and molecular criteria. This is because recombination tests may be a poor indicator of species boundaries in Symbiodinium due to their predominantly asexual mode of reproduction. Furthermore, discontinuous microsatellite allele sizes in sympatry may be explained by secondary contact between previously isolated populations and by mutations that occur in a nonstepwise manner. Limitations of using microsatellites alone to delineate species are highlighted in earlier studies that demonstrate occasional bimodal distributions of allele sizes within Symbiodinium species and considerable allele size sharing among Symbiodinium species. We outline these issues and discuss the validity of reinterpretations of our previously published microsatellite data from Symbiodinium populations on the Great Barrier Reef (Howells et al. 2013).     

Biological criteria for the exploitation of the commercially important species of Gelidium in Spain

Exploitation of the commercially-important species of Gelidium in Spain (G. sesquipedale and G. latifolium) and development of the industry occurred after World War II, as a consequence of their use as resources for the extraction of agar. This resulted in the implementation of several harvesting methods, the most important of which is the gathering of cast seaweeds, both from the shore and the sea. From the very beginning, direct exploitation of these species (i.e. plucking) was controversial because of possible adverse ecological effects. Consequently, several biological and ecological studies of both species of Gelidium were begun. This included such aspects as growth, biomass production, productivity, reproduction, regeneration capacity and agar yield. Recently, the growing interest in using and conserving this resource has led to increased knowledge of the biology and ecology of these species. In this paper, we provide an overview of the research carried out by different Spanish groups and suggest guidelines for rational management of these resources.     

Egg identification of three economical important fish species using DNA barcoding in comparison to a morphological determination

Accurate identification of fish eggs to species level is a challenging task as many species have similar egg sizes and morphology. The results of egg determination of three economically important fish species are presented by using DNA barcoding in comparison to the classical morphological determination. About 500 fish eggs from the Celtic Sea were collected, morphologically identified and used for DNA analysis. In total, DNA barcodes were successfully obtained from 98% of the investigated eggs, including 167 DNA barcodes from 169 morphologically identified fish eggs of Merluccius merluccius (98.8%), 257 of 262 Scomber scombrus (98.1%), and 47 from 50 Trachurus trachurus (94%). Overall, species identification with DNA barcodes showed a congruence of 96.2% to identification by morphology, whereas 3.8% (n = 18) of the analyzed eggs were morphologically assigned to the wrong species. The highest number of incorrect identified eggs was for S. scombrus (n = 15). Our study highlights the usefulness of DNA barcoding for valid fish egg identification but also indicates the robustness of the classical morphology‐based approach.     

Bacterial communities in predatory mites are associated with species and diet types

The symbiotic bacterial communities of phytophagous arthropods are affected by host species and feeding habits, but such effects have been poorly studied in natural enemies. Here, we investigated the entire bacterial microbiome of two species of predatory mites, Neoseiulus californicus and Neoseiulus barkeri, feeding on three types of diets (artificial diet, pollen and their natural prey, the spider mite Tetranychus urticae) by high-throughput sequencing of the 16S rRNA gene. We found that the bacterial diversity of predatory mites feeding on artificial diet was significantly different from pollen and spider mite feeding groups in both N. californicus and N. barkeri, while bacterial diversity also differed strikingly between the two species even when feeding on the same artificial diet. This finding suggests that the bacterial community of predatory mites is determined by both species and diet. Alphaproteobacteria and Gammaproteobacteria were the two dominant bacterial classes in both predatory mite species, except for N. californicus feeding on artificial diet. The bacterium Bosea sp. was detected in all samples as the core microbial species in predatory mites. Additionally, we discuss whether Bradyrhizobiaceae and Rhodobacteraceae bacteria could be used as probiotics in the artificial diet of N. californicus for better mass rearing.

     

Primer design for identifying economically important Liriomyza species (Diptera: Agromyzidae) by multiplex PCR

Leafminer flies, especially, Liriomyza huidobrensis, Liriomyza sativae and Liriomyza trifolii, are quarantine species in many countries. Their morphological similarity makes identification difficult. To develop a rapid, reliable, sensitive and simple molecular identification method using multiplex PCR, we newly sequenced the mitochondrial cytochrome oxidase I (COI) genes of Liriomyza bryoniae, Liriomyza chinensis, L. huidobrensis, L. sativae, L. trifolii, Chromatomyia horticola and four parasitoid species. We aligned them with all the COI sequences of the leafminer flies found in the international DNA nucleotide sequence databases (DDBJ/EMBL/GenBank). We then designed species‐specific primers to allow us to differentiate between L. bryoniae, L. chinensis, L. huidobrensis, L. sativae, and L. trifolii.     

Genetic variation in agronomically important species of Stylosanthes determined using random amplified polymorphic DNA markers

Summary Random amplified polymorphic DNA (RAPD) markers were generated from 20 cultivars and accessions representing four agronomically important species of Stylosanthes, S. scabra, S. hamata, S. guianensis, and S. humilis. Approximately 200 fragments generated by 22 primers of arbitrary sequence were used to assess the level of DNA variation. Relatively low levels of polymorphism (0–16% of total bands in pairwise comparisons) were found within each species, while polymorphisms between the species were much higher (up to 46%). Very few polymorphisms (0–2%) were detected between the individuals of the same cultivar or accession. A phenogram of relationships among the species was constructed based on band sharing. Four main clusters corresponding to each species were readily distinguished on this phenogram. The allotetraploid species S. hamata and its putative diploid progenitor, S. humilis, were more similar to each other than to S. scabra and S. guianensis. No variation in RAPD markers was found between the two commercial S. hamata cvs Verano and Amiga. Cultivar Oxley in S. guianensis was considerably different from the other cultivars and accessions of this species. The phylogenetic distinctions obtained with RAPDs were in agreement with other studies from morphology, cytology, and enzyme electrophoresis. The low level of polymorphisms observed within each species suggested that interspecific crosses may be a better vehicle for the construction of RAPD linkage maps in Stylosanthes.     

Two sympatric spotted gum species are molecularly homogeneous

Large fruited spotted gum eucalypt Corymbia henryi occurs sympatrically with small fruited spotted gum Corymbia citriodora subspecies variegata over a large portion of its range on the east coast of Australia. The two taxa are interfertile, have overlapping flowering times and share a common set of insect and vertebrate pollinators. Previous genetic analysis of both taxa from two geographically remote sites suggested that the two were morphotypes rather than genetically distinct species. In this study we further explore this hypothesis of genic species by expanding sampling broadly through their sympatric locations and examine local-scale spatial genetic structure in stands that differ in species and age composition. Delineation of populations at five microsatellite loci, using an individual-based approach and Bayesian modelling, as well as clustering of individuals based on allele frequencies showed the two species to be molecularly homogeneous. Genetic structure aligned largely with geographic areas of origin, and followed an isolation-by-distance model, where proximal populations were generally less differentiated than more distant ones. At the stand level, spotted gums also generally showed little structure consistent with the high levels of gene flow inferred across the species range. Disturbances in the uniformity of structuring were detected, however, and attributed to localised events giving rise to even aged stands, probably due to regeneration from a few individuals following fire.     

Temperature‐dependant development of Nasonia vitripennis on five forensically important carrion fly species

The effects of temperature and host species on the development of Nasonia vitripennis Walker (Hymenoptera: Pteromalidae), a forensically important parasitoid of carrion flies, were studied under laboratory conditions. Development time of N. vitripennis on five species of Calliphoridae (Diptera), Calliphora albifrontalis Malloch, Calliphora dubia Macquart, Lucilia sericata Meigen, Chrysomya rufifacies Macquart, and Chrysomya megacephala Fabricius, were determined under eight constant temperatures (15, 18, 21, 24, 27, 30, 33, and 36 °C). Thermal requirements for development (developmental thresholds, thermal constant, and optimum temperature) of N. vitripennis in each host species were estimated using linear and nonlinear models. Upper and lower developmental thresholds ranged between 36.6–38.4 and 9.6–11.1 °C, respectively. The optimum temperature for development was estimated at between 30.6 and 31.8 °C. Statistical differences in the development time of N. vitripennis on the various calliphorid host species were evident within all temperature treatments, particularly at the upper and lower temperature range investigated. As such, it is recommended that insect‐based estimates of time since death in forensic investigations relying on parasitoid evidence should use host‐specific development data where available.     

Temperature‐dependent development of the parasitoid Tachinaephagus zealandicus on five forensically important carrion fly species

The influences of temperature and host species on the development of the forensically important parasitoid Tachinaephagus zealandicus Ashmead (Hymenoptera: Encyrtidae) were studied at six constant temperatures in the range of 15–30°C. T. zealandicus completed development successfully between 15°C and 27°C on five species of Calliphoridae, Calliphora albifrontalis Malloch, Calliphora dubia Macquart, Lucilia sericata Meigen, Chrysomya rufifacies Macquart and Chrysomya megacephala Fabricius. No adult parasitoids emerged from any of the host species reared at 30°C. Temperature and host species significantly influenced development time, emergence success and progeny size. Development was significantly longer on Ch. megacephala and Ch. rufifacies at 18–24°C and significantly longer on Ch. rufifacies and C. albifrontalis at 15°C and 27°C. Parasitoid emergence success was greatest at 21°C, declined at the temperature extremes (15°C and 27°C) and was significantly lower on Ch. megacephala and Ch. rufifacies than on the three other host species. Progeny numbers per host pupa were highest at 21–24°C, declined on either side of this temperature range and were significantly lower on L. sericata, Ch. rufifacies and Ch. megacephala than on either C. dubia or C. albifrontalis. An effect of host species on sex ratio was only observed at 27°C, at which a higher proportion of T. zealandicus females emerged from Ch. megacephala and Ch. rufifacies than from the other host species. The thermal requirements for development (developmental thresholds, thermal constant, optimum temperature) of T. zealandicus in each host species were estimated using linear and non‐linear models. Upper and lower developmental thresholds ranged between 29.90°C and 31.73°C, and 9.73°C and 10.08°C, respectively. The optimum temperature for development was estimated at between 25.81°C and 27.05°C. Given the significant effect of host species on development time, the use of parasitoid–host‐specific developmental data in forensic application is recommended.     

Ceratocystis species, including two new species associated with nitidulid beetles, on eucalypts in Australia

The genus Ceratocystis includes important fungal pathogens of trees, including Eucalyptus spp. Ironically, very little is known regarding the diversity or biology of Ceratocystis species on Eucalyptus species in Australia, where most of these trees are native. The aim of this study was to survey for Ceratocystis spp., and their possible insect associates, on eucalypts in Australia and thus to establish a foundation of knowledge regarding these fungi on the continent. Collections were made in three states of Australia from wounds on trees, as well as from nitidulid beetles associated with these wounds. Ceratocystis spp. were identified based on morphology and multigene sequence comparisons. Of the 54 isolates obtained, two previously unknown species of Ceratocystis were found and these are described here as Ceratocystis corymbiicola sp. nov. and Ceratocystis tyalla sp. nov. Furthermore, the distribution of Ceratocystis pirilliformis is expanded to include Eucalyptus spp. in Tasmania.