Open AccessReview
Australian Tropical Marine Micromolluscs: An Overwhelming Bias
Diversity 2016, 8(3), 17; doi:10.3390/d8030017 -
Abstract
Assessing the marine biodiversity of the tropics can be overwhelming, especially for the Mollusca, one of the largest marine phyla in the sea. With a diversity that can exceed macrofaunal richness in many groups, the micro/meiofaunal component is one of most overlooked [...] Read more.
Assessing the marine biodiversity of the tropics can be overwhelming, especially for the Mollusca, one of the largest marine phyla in the sea. With a diversity that can exceed macrofaunal richness in many groups, the micro/meiofaunal component is one of most overlooked biotas in surveys due to the time-consuming nature of collecting, sorting, and identifying this assemblage. We review trends in micromollusc research highlighting the Australian perspective that reveals a dwindling taxonomic effort through time and discuss pervasive obstacles of relevance to the taxonomy of micromolluscs globally. Since a high during the 1970s, followed by a smaller peak in 2000, in 2010 we observe a low in micromolluscan collection activity in Australia not seen since the 1930s. Although challenging, considered planning at each step of the species identification pathway can reduce barriers to micromolluscan research (e.g., role of types, dedicated sampling, integration of microscopy and genetic methods). We discuss new initiatives to trial these methods in Western Australia, an understudied region with high biodiversity, and highlight why micromolluscs are worth the effort. A number of important fields that would benefit from increased focus on this group (e.g., ecological gaps) are considered. The methods and strategies for resolving systematic problems in micromolluscan taxonomy are available, only the desire and support to reverse the decline in knowledge remains to be found. Full article
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Open AccessArticle
Tropical Range Extension for the Temperate, Endemic South-Eastern Australian Nudibranch Goniobranchus splendidus (Angas, 1864)
Diversity 2016, 8(3), 16; doi:10.3390/d8030016 -
Abstract
In contrast to many tropical animals expanding southwards on the Australian coast concomitant with climate change, here we report a temperate endemic newly found in the tropics. Chromodorid nudibranchs are bright, colourful animals that rarely go unnoticed by divers and underwater photographers. [...] Read more.
In contrast to many tropical animals expanding southwards on the Australian coast concomitant with climate change, here we report a temperate endemic newly found in the tropics. Chromodorid nudibranchs are bright, colourful animals that rarely go unnoticed by divers and underwater photographers. The discovery of a new population, with divergent colouration is therefore significant. DNA sequencing confirms that despite departures from the known phenotypic variation, the specimen represents northern Goniobranchus splendidus and not an unknown close relative. Goniobranchus tinctorius represents the sister taxa to G. splendidus. With regard to secondary defences, the oxygenated terpenes found previously in this specimen are partially unique but also overlap with other G. splendidus from southern Queensland (QLD) and New South Wales (NSW). The tropical specimen from Mackay contains extracapsular yolk like other G. splendidus. This previously unknown tropical population may contribute selectively advantageous genes to cold-water species threatened by climate change. Competitive exclusion may explain why G. splendidus does not strongly overlap with its widespread sister taxon. Full article
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Open AccessArticle
Chemical Composition of the Essential Oil from Aerial Parts of Javanian Pimpinella pruatjan Molk. and Its Molecular Phylogeny
Diversity 2016, 8(3), 15; doi:10.3390/d8030015 -
Abstract
The species-rich and diverse genus Pimpinella is mainly distributed in Europe and Asia; a few species occur in Africa. Yet, the Javanian Pimpinella, P. pruatjan, which has been used as an aphrodisiac in Indonesian traditional medicine, was studied for the first [...] Read more.
The species-rich and diverse genus Pimpinella is mainly distributed in Europe and Asia; a few species occur in Africa. Yet, the Javanian Pimpinella, P. pruatjan, which has been used as an aphrodisiac in Indonesian traditional medicine, was studied for the first time in the context of chemical composition, as well as phylogeny analysis and antimicrobial activity. We examined the chemical composition of the essential oil (EO) from aerial parts of P. pruatjan by gas liquid chromatography-mass spectrometry (GLC-MS). The main component of EO was (Z)-γ-bisabolene. Several oxygenated monoterpenes, oxygenated sesquiterpenes, and sesquiterpenes were also detected. The genetic relationship of Pimpinella pruatjan Molk. to other Pimpinella species was reconstructed using nucleotide sequences of the nuclear DNA marker ITS (Internal Transcribed Spacer). P. pruatjan clusters as a sister group to the African Pimpinella species. The EO did not exhibit an apparent antimicrobial activity. Full article
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Open AccessArticle
DNA-Based Identification and Chemical Characteristics of Hypnea musciformis from Coastal Sites in Ghana
Diversity 2016, 8(2), 14; doi:10.3390/d8020014 -
Abstract
This work reveals new, important insights about the influence of broad spatial variations on the phylogenetic relationship and chemical characteristics of Ghanaian Hypnea musciformis—a carrageenan-containing red seaweed. DNA barcoding techniques alleviate the difficulty for accurate morphological identification. COI barcode sequences of [...] Read more.
This work reveals new, important insights about the influence of broad spatial variations on the phylogenetic relationship and chemical characteristics of Ghanaian Hypnea musciformis—a carrageenan-containing red seaweed. DNA barcoding techniques alleviate the difficulty for accurate morphological identification. COI barcode sequences of the Ghanaian H. musciformis showed <0.7% intraspecies divergence, indicating no distinct phylogenetic variation, suggesting that they actually belong to the same species. Thus, the spatial distribution of the sampling sites along the coast of Ghana did not influence the phylogenetic characteristics of H. musciformis in the region. The data also showed that the Ghanaian Hypnea sp. examined in this work should be regarded as the same species as the H. musciformis collected in Brazilian Sao Paulo (KP725276) with only 0.8%–1.3% intraspecies divergence. However, the comparison of COI sequences of Ghanaian H. musciformis with the available COI sequence of H. musciformis from other countries showed intraspecies divergences of 0%–6.9% indicating that the COI sequences for H. musciformis in the GenBank may include different subspecies. Although samples did not differ phylogenetically, the chemical characteristics of the H. musciformis differed significantly between different sampling locations in Ghana. The levels of the monosaccharides, notably galactose (20%–30% dw) and glucose (10%–18% dw), as well as the seawater inorganic salt concentration (21–32 mg/L) and ash content (19%–33% dw), varied between H. musciformis collected at different coastal locations in Ghana. The current work demonstrated that DNA-based identification allowed a detailed understanding of H. musciformis phylogenetic characteristics and revealed that chemical compositional differences of H. musciformis occur along the Ghanaian coast which are not coupled with genetic variations among those samples. Full article
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Open AccessArticle
Structure of Fungal Communities in Sub-Irrigated Agricultural Soil from Cerrado Floodplains
Diversity 2016, 8(2), 13; doi:10.3390/d8020013 -
Abstract
This study aimed to evaluate the influence of soybean cultivation on the fungal community structure in a tropical floodplain area. Soil samples were collected from two different soybean cropland sites and a control area under native vegetation. The soil samples were collected [...] Read more.
This study aimed to evaluate the influence of soybean cultivation on the fungal community structure in a tropical floodplain area. Soil samples were collected from two different soybean cropland sites and a control area under native vegetation. The soil samples were collected at a depth of 0–10 cm soil during the off-season in July 2013. The genetic structure of the soil fungal microbial community was analyzed using the automated ribosomal intergenic spacer analysis (ARISA) technique. Among the 26 phylotypes with abundance levels higher than 1% detected in the control area, five were also detected in the area cultivated for five years, and none of them was shared between the control area and the area cultivated for eight years. Analysis of similarity (ANOSIM) revealed differences in fungal community structure between the control area and the soybean cropland sites, and also between the soybean cropland sites. ANOSIM results were confirmed by multivariate statistics, which additionally revealed a nutrient-dependent relation for the fungal community structure in agricultural soil managed for eight consecutive years. The results indicated that land use affects soil chemical properties and richness and structure of the soil fungal microbial community in a tropical floodplain agricultural area, and the effects became more evident to the extent that soil was cultivated for soybean for more time. Full article
Open AccessReview
Recent Advances in Understanding the Effects of Climate Change on Coral Reefs
Diversity 2016, 8(2), 12; doi:10.3390/d8020012 -
Abstract
Climate change is one of the greatest threats to the persistence of coral reefs. Sustained and ongoing increases in ocean temperatures and acidification are altering the structure and function of reefs globally. Here, we summarise recent advances in our understanding of the [...] Read more.
Climate change is one of the greatest threats to the persistence of coral reefs. Sustained and ongoing increases in ocean temperatures and acidification are altering the structure and function of reefs globally. Here, we summarise recent advances in our understanding of the effects of climate change on scleractinian corals and reef fish. Although there is considerable among-species variability in responses to increasing temperature and seawater chemistry, changing temperature regimes are likely to have the greatest influence on the structure of coral and fish assemblages, at least over short–medium timeframes. Recent evidence of increases in coral bleaching thresholds, local genetic adaptation and inheritance of heat tolerance suggest that coral populations may have some capacity to respond to warming, although the extent to which these changes can keep pace with changing environmental conditions is unknown. For coral reef fishes, current evidence indicates increasing seawater temperature will be a major determinant of future assemblages, through both habitat degradation and direct effects on physiology and behaviour. The effects of climate change are, however, being compounded by a range of anthropogenic disturbances, which may undermine the capacity of coral reef organisms to acclimate and/or adapt to specific changes in environmental conditions. Full article
Open AccessArticle
Prevalence and Incidence of Black Band Disease of Scleractinian Corals in the Kepulauan Seribu Region of Indonesia
Diversity 2016, 8(2), 11; doi:10.3390/d8020011 -
Abstract
Black band disease (BBD) is the oldest recognised disease associated with scleractinian corals. However, despite this, few BBD surveys have been conducted in the Indonesian archipelago, one of the world’s hot spots for coral diversity. In this study, we show that BBD [...] Read more.
Black band disease (BBD) is the oldest recognised disease associated with scleractinian corals. However, despite this, few BBD surveys have been conducted in the Indonesian archipelago, one of the world’s hot spots for coral diversity. In this study, we show that BBD was recorded in the reefs of Kepulauan Seribu, Indonesia, at the time of surveying. The disease was found to mainly infect corals of the genus Montipora. In some instances, upwards of 177 colonies (31.64%) were found to be infected at specific sites. Prevalence of the disease ranged from 0.31% to 31.64% of Montipora sp. colonies throughout the archipelago. Although BBD was found at all sites, lower frequencies were associated with sites closest to the mainland (17.99 km), as well as those that were furthest away (63.65 km). Despite there being no linear relationship between distance from major population centers and BBD incidence, high incidences of this disease were associated with sites characterized by higher levels of light intensity. Furthermore, surveys revealed that outbreaks peaked during the transitional period between the dry and rainy seasons. Therefore, we suggest that future surveys for disease prevalence in this region of Indonesia should focus on these transitory periods. Full article
Open AccessArticle
Genetic Diversity in Apple Fruit Moth Indicate Different Clusters in the Two Most Important Apple Growing Regions of Norway
Diversity 2016, 8(2), 10; doi:10.3390/d8020010 -
Abstract
The apple fruit moth (Argyresthia conjugella (A. conjugella)) in Norway was first identified as a pest in apple production in 1899. We here report the first genetic analysis of A. conjugella using molecular markers. Amplified fragment length polymorphism (AFLP) [...] Read more.
The apple fruit moth (Argyresthia conjugella (A. conjugella)) in Norway was first identified as a pest in apple production in 1899. We here report the first genetic analysis of A. conjugella using molecular markers. Amplified fragment length polymorphism (AFLP) analysis was applied to 95 individuals from six different locations in the two most important apple-growing regions of Norway. Five AFLP primer combinations gave 410 clear polymorphic bands that distinguished all the individuals. Further genetic analysis using the Dice coefficient, Principal Coordinate analysis (PCO) and Bayesian analyses suggested clustering of the individuals into two main groups showing substantial genetic distance. Analysis of molecular variance (AMOVA) revealed greater variation among populations (77.94%) than within populations (22.06%) and significant and high FST values were determined between the two major regions (Distance = 230 km, FST = 0.780). AFLP analysis revealed low to moderate genetic diversity in our population sample from Norway (Average: 0.31 expected heterozygosity). The positive significant correlation between the geographic and the molecular data (r2 = 0.6700) indicate that genetic differences between the two major regions may be due to geographical barriers such as high mountain plateaus (Hardangervidda) in addition to isolation by distance (IBD). Full article
Open AccessArticle
Detection of a High-Density Brachiolaria-Stage Larval Population of Crown-of-Thorns Sea Star (Acanthaster planci) in Sekisei Lagoon (Okinawa, Japan)
Diversity 2016, 8(2), 9; doi:10.3390/d8020009 -
Abstract
Outbreaks of the crown-of-thorns sea star (Acanthaster planci) are likely to be strongly associated with drastic changes in larval survival influenced by food availability. However, no quantitative or qualitative data are available on the distribution of A. planci larvae in [...] Read more.
Outbreaks of the crown-of-thorns sea star (Acanthaster planci) are likely to be strongly associated with drastic changes in larval survival influenced by food availability. However, no quantitative or qualitative data are available on the distribution of A. planci larvae in the field nor on the environmental factors that influence their survivorship. Here we use a DNA barcoding approach to describe the distribution of A. planci larvae in Sekisei Lagoon, Ryukyu Archipelago, Japan after conducting three days of high-intensity sampling. High densities (53.3 individuals/m3) of A. planci larvae were found outside of Yonara Channel, which is the largest reef channel in this lagoon. Surprisingly, most (94%) of the aggregated larvae were advanced-stage brachiolaria. Considering that it takes several days to develop to this stage, this result demonstrates that A. planci larvae were floating for some time and maintaining a high-density population. However, this dense larval cloud disappeared immediately after a typhoon. No spatial correlation was found between larval density and either nutrient or chlorophyll a concentrations, suggesting that A. planci larvae do not necessarily aggregate in nutrient-rich water. These data suggest that some high-density populations of late developmental stage A. planci larvae were produced under a low phytoplankton concentration and could potentially trigger an adult outbreak. Consequently, our data suggest that adult outbreaks may not necessarily be triggered by food availability alone. Full article
Open AccessArticle
Genetic Diversity Assessment of Portuguese Cultivated Vicia faba L. through IRAP Markers
Diversity 2016, 8(2), 8; doi:10.3390/d8020008 -
Abstract
Faba bean have been grown in Portugal for a long time and locally adapted populations are still maintained on farm. The genetic diversity of four Portuguese faba bean populations that are still cultivated in some regions of the country was evaluated [...] Read more.
Faba bean have been grown in Portugal for a long time and locally adapted populations are still maintained on farm. The genetic diversity of four Portuguese faba bean populations that are still cultivated in some regions of the country was evaluated using the Inter Retrotransposons Amplified Polymorphism (IRAP) technique. It was shown that molecular markers based on retrotransposons previously identified in other species can be efficiently used in the genetic variability assessment of Vicia faba. The IRAP experiment targeting Athila yielded the most informative banding patterns. Cluster analysis using the neighbor-joining algorithm generated a dendrogram that clearly shows the distribution pattern of V. faba samples. The four equina accessions are separated from each other and form two distinct clades while the two major faba bean accessions are not unequivocally separated by the IRAP. Fluorescent In Situ Hybridization (FISH) analysis of sequences amplified by IRAP Athila revealed a wide distribution throughout V. faba chromosomes, confirming the whole-genome coverage of this molecular marker. Morphological characteristics were also assessed through cluster analysis of seed characters using the unweighted pair group method arithmetic average (UPGMA) and principal component analysis (PCA), showing a clear discrimination between faba bean major and equina groups. It was also found that the seed character most relevant to distinguish accessions was 100 seed weight. Seed morphological traits and IRAP evaluation give similar results supporting the potential of IRAP analysis for genetic diversity studies. Full article
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Open AccessArticle
Marine Biodiversity in Temperate Western Australia: Multi-Taxon Surveys of Minden and Roe Reefs
Diversity 2016, 8(2), 7; doi:10.3390/d8020007 -
Abstract
A growing body of evidence indicates that temperate marine ecosystems are being tropicalised due to the poleward extension of tropical species. Such climate mediated changes in species distribution patterns have the potential to profoundly alter temperate communities, as this advance can serve [...] Read more.
A growing body of evidence indicates that temperate marine ecosystems are being tropicalised due to the poleward extension of tropical species. Such climate mediated changes in species distribution patterns have the potential to profoundly alter temperate communities, as this advance can serve to push temperate taxa, many of which are southern Australian endemics, southward. These changes can lead to cascading effects for the biodiversity and function of coastal ecosystems, including contraction of ranges/habitats of sensitive cool water species. Hence there is growing concern for the future of Australia’s temperate marine biodiversity. Here we examine the diversity and abundance of marine flora and fauna at two reefs near Perth’s metropolitan area—Minden Reef and Roe Reef. We report the presence of 427 species of marine flora and fauna from eight taxon groups occurring in the Perth metropolitan area; at least three species of which appear to be new to science. Our data also extends the known range of 15 species, and in numerous instances, thousands of kilometres south from the Kimberley or Pilbara and verifies that tropicalisation of reef communities in the Perth metropolitan area is occurring. We report the presence of 24 species endemic to south-west Australia that may be at risk of range contractions with continued ocean warming. The results of these surveys add to our knowledge of local nearshore marine environments in the Perth metropolitan area and support the growing body of evidence that indicates a diverse and regionally significant marine fauna occurs in temperate Western Australia. Regular, repeated survey work across seasons is important in order to thoroughly document the status of marine biodiversity in this significant transition zone. Full article
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Open AccessReview
Update of “Biodiversity of the Hypersaline Urmia Lake National Park (NW Iran)”
Diversity 2016, 8(1), 6; doi:10.3390/d8010006 -
Abstract
Urmia Lake, an endorheic salt lake in northwestern Iran, was registered in the Ramsar Convention on Wetlands as a wetland of international importance, also a UNESCO biosphere reserve. In this review, we have updated our last checklist in 2014 with available information [...] Read more.
Urmia Lake, an endorheic salt lake in northwestern Iran, was registered in the Ramsar Convention on Wetlands as a wetland of international importance, also a UNESCO biosphere reserve. In this review, we have updated our last checklist in 2014 with available information on the biodiversity of the lake. Full article
Open AccessArticle
Building a Plant DNA Barcode Reference Library for a Diverse Tropical Flora: An Example from Queensland, Australia
Diversity 2016, 8(1), 5; doi:10.3390/d8010005 -
Abstract
A foundation for a DNA barcode reference library for the tropical plants of Australia is presented here. A total of 1572 DNA barcode sequences are compiled from 848 tropical Queensland species. The dataset represents 35% of the total flora of Queensland’s Wet [...] Read more.
A foundation for a DNA barcode reference library for the tropical plants of Australia is presented here. A total of 1572 DNA barcode sequences are compiled from 848 tropical Queensland species. The dataset represents 35% of the total flora of Queensland’s Wet Tropics Bioregion, 57% of its tree species and 28% of the shrub species. For approximately half of the sampled species, we investigated the occurrence of infraspecific molecular variation in DNA barcode loci rbcLa, matK, and the trnH-psbA intergenic spacer region across previously recognized biogeographic barriers. We found preliminary support for the notion that DNA barcode reference libraries can be used as a tool for inferring biogeographic patterns at regional scales. It is expected that this dataset will find applications in taxonomic, ecological, and applied conservation research. Full article
Open AccessEditorial
Acknowledgement to Reviewers of Diversity in 2015
Diversity 2016, 8(1), 4; doi:10.3390/d8010004 -
Abstract The editors of Diversity would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2015. [...] Full article
Open AccessArticle
Identification and Density Estimation of American Martens (Martes americana) Using a Novel Camera-Trap Method
Diversity 2016, 8(1), 3; doi:10.3390/d8010003 -
Abstract
Camera-traps are increasingly used to estimate wildlife abundance, yet few studies exist for small-sized carnivores or comparing efficacy against traditional methods. We developed a camera-trap to identify the unique ventral patches of American martens (Martes americana). Our method was designed [...] Read more.
Camera-traps are increasingly used to estimate wildlife abundance, yet few studies exist for small-sized carnivores or comparing efficacy against traditional methods. We developed a camera-trap to identify the unique ventral patches of American martens (Martes americana). Our method was designed to: (1) determine the optimal trap configuration to photograph ventral patches; (2) evaluate the use of temporally clustered photographs to determine independence and improve identification; and (3) determine factors that influence identification probability. We tested our method by comparing camera- and live-trap density estimates using spatial capture–recapture (SCR) models. The ventral patches of radio-collared martens were most visible when traps were placed 15–20 cm above a feeding platform. Radio-collared martens (n = 14) visited camera-traps for long periods (median = 7 min) with long intervals between visits (median = 419 min), and visits by different martens at the same trap <15 min apart was infrequent (n = 3) during both years. Similarly, there was complete agreement among observers that clustered photos of un-collared martens were always of the same individual. Pairwise agreement was high between observers; eight un-collared martens were identifiable by consensus on 90% (54 of 60) of recorded visits. Factors influencing identification probability were directly related to the time martens spent feeding at traps (β = 0.143, P = 0.01) and inversely proportional to the time that elapsed since traps were baited (β = −0.344, P = 0.006). Density estimates were higher and more precise for camera-trapping (0.60, 0.35–1.01 martens/km2) than live-trapping (0.45, 0.16–1.22 martens/km2), providing evidence that SCR density estimates may be biased when capture heterogeneity is present, yet cannot be accounted for due to small sample size. Our camera-trap method provides a minimally invasive and accurate tool for monitoring marten populations. Full article
Open AccessArticle
Can Theory Improve the Scope of Quantitative Metazoan Metabarcoding?
Diversity 2016, 8(1), 1; doi:10.3390/d8010001 -
Abstract
Using high-throughput sequencing approaches to quantify biodiversity has a number of hurdles, in particular that the number of reads for a given taxon may not be proportional to the number of individuals of that taxon in a sample. Here, we consider whether [...] Read more.
Using high-throughput sequencing approaches to quantify biodiversity has a number of hurdles, in particular that the number of reads for a given taxon may not be proportional to the number of individuals of that taxon in a sample. Here, we consider whether summary statistics generated in the course of population genetic analyses (such as estimates of haplotype diversity and mutation rate) may be useful in reverse inference of the number of individuals input to an assay. Although our results show that these statistics—combined with the observed number of segregating sites and number of haplotypes in the assay—may be informative, there remain significant concerns about the ability to “metabarcode” a sample and infer relative species abundance. Full article
Open AccessReview
DNA Barcoding as a Molecular Tool to Track Down Mislabeling and Food Piracy
Diversity 2016, 8(1), 2; doi:10.3390/d8010002 -
Abstract
DNA barcoding is a molecular technology that allows the identification of any biological species by amplifying, sequencing and querying the information from genic and/or intergenic standardized target regions belonging to the extranuclear genomes. Although these sequences represent a small fraction of the [...] Read more.
DNA barcoding is a molecular technology that allows the identification of any biological species by amplifying, sequencing and querying the information from genic and/or intergenic standardized target regions belonging to the extranuclear genomes. Although these sequences represent a small fraction of the total DNA of a cell, both chloroplast and mitochondrial barcodes chosen for identifying plant and animal species, respectively, have shown sufficient nucleotide diversity to assess the taxonomic identity of the vast majority of organisms used in agriculture. Consequently, cpDNA and mtDNA barcoding protocols are being used more and more in the food industry and food supply chains for food labeling, not only to support food safety but also to uncover food piracy in freshly commercialized and technologically processed products. Since the extranuclear genomes are present in many copies within each cell, this technology is being more easily exploited to recover information even in degraded samples or transformed materials deriving from crop varieties and livestock species. The strong standardization that characterizes protocols used worldwide for DNA barcoding makes this technology particularly suitable for routine analyses required by agencies to safeguard food safety and quality. Here we conduct a critical review of the potentials of DNA barcoding for food labeling along with the main findings in the area of food piracy, with particular reference to agrifood and livestock foodstuffs. Full article
Open AccessArticle
FactorsR: An RWizard Application for Identifying the Most Likely Causal Factors in Controlling Species Richness
Diversity 2015, 7(4), 385-396; doi:10.3390/d7040385 -
Abstract
We herein present FactorsR, an RWizard application which provides tools for the identification of the most likely causal factors significantly correlated with species richness, and for depicting on a map the species richness predicted by a Support Vector Machine (SVM) model. As [...] Read more.
We herein present FactorsR, an RWizard application which provides tools for the identification of the most likely causal factors significantly correlated with species richness, and for depicting on a map the species richness predicted by a Support Vector Machine (SVM) model. As a demonstration of FactorsR, we used an assessment using a database incorporating all species of terrestrial carnivores, a total of 249 species, distributed across 12 families. The model performed with SVM explained 91.9% of the variance observed in the species richness of terrestrial carnivores. Species richness was higher in areas with both higher vegetation index and patch index, i.e., containing higher numbers of species whose range distribution is less fragmented. Lower species richness than expected was observed in Chile, Madagascar, Sumatra, Taiwan, and Sulawesi. Full article
Open AccessArticle
SSR Markers for Trichoderma virens: Their Evaluation and Application to Identify and Quantify Root-Endophytic Strains
Diversity 2015, 7(4), 360-384; doi:10.3390/d7040360 -
Abstract
Using biological fertilizers and pesticides based on beneficial soil microbes in order to reduce mineral fertilizers and chemical pesticides in conventional agriculture is still a matter of debate. In this regard, a European research project seeks to elucidate the role of root-endophytic [...] Read more.
Using biological fertilizers and pesticides based on beneficial soil microbes in order to reduce mineral fertilizers and chemical pesticides in conventional agriculture is still a matter of debate. In this regard, a European research project seeks to elucidate the role of root-endophytic fungi and to develop molecular tools to trace and quantify these fungi in the rhizosphere and root tissue. To do this, the draft genome sequence of the biocontrol fungus Trichoderma virens (T. virens) was screened for simple sequence repeats (SSRs) and primers were developed for 12 distinct loci. Primers were evaluated using a global collection of ten isolates where an average of 7.42 alleles per locus was detected. Nei’s standard genetic distance ranged from 0.18 to 0.27 among the isolates, and the grand mean of haploid diversity in AMOVA analysis was 0.693 ± 0.019. Roots of tomato plants were inoculated with different strains and harvested six weeks later. Subsequent PCR amplification identified root-endophytic strains and co-colonization of roots by different strains. Markers were applied to qPCR to quantify T. virens strains in root tissue and to determine their identity using allele-specific melting curve analysis. Thus, the root-endophytic lifestyle of T. virens was confirmed, strains in roots were quantified and simultaneous colonization of roots by different strains was observed. Full article
Open AccessArticle
Predicting Future European Breeding Distributions of British Seabird Species under Climate Change and Unlimited/No Dispersal Scenarios
Diversity 2015, 7(4), 342-359; doi:10.3390/d7040342 -
Abstract
Understanding which traits make species vulnerable to climatic change and predicting future distributions permits conservation efforts to be focused on the most vulnerable species and the most appropriate sites. Here, we combine climate envelope models with predicted bioclimatic data from two emission [...] Read more.
Understanding which traits make species vulnerable to climatic change and predicting future distributions permits conservation efforts to be focused on the most vulnerable species and the most appropriate sites. Here, we combine climate envelope models with predicted bioclimatic data from two emission scenarios leading up to 2100, to predict European breeding distributions of 23 seabird species that currently breed in the British Isles. Assuming unlimited dispersal, some species would be “winners” (increase the size of their range), but over 65% would lose range, some by up to 80%. These “losers” have a high vulnerability to low prey availability, and a northerly distribution meaning they would lack space to move into. Under the worst-case scenario of no dispersal, species are predicted to lose between 25% and 100% of their range, so dispersal ability is a key constraint on future range sizes. More globally, the results indicate, based on foraging ecology, which seabird species are likely to be most affected by climatic change. Neither of the emissions scenarios used in this study is extreme, yet they generate very different predictions for some species, illustrating that even small decreases in emissions could yield large benefits for conservation. Full article