Filter Results
6319 results
1. Metabarcoding extra-organismal DNA from environmental samples is now a key technique in aquatic biomonitoring and ecosystem health assessment. However, choice of genetic marker and primer set is a critical consideration when designing experiments, especially so when developing community standards and legislative frameworks. Mitochondrial cytochrome c oxidase subunit I (COI), the standard DNA barcode marker for animals, with its extensive reference library, taxonomic discriminatory power, and predictable sequence variation, is the natural choice for many metabarcoding applications such as the bulk sequencing of invertebrates. However, the overall utility of COI for environmental sequencing of targeted taxonomic groups has yet to be fully scrutinised. 2. Here, by using a case study of marine and freshwater fishes from the British Isles, we quantify the in silico performance of twelve mitochondrial primer pairs from COI, cytochrome b, 12S and 16S, in terms of reference library coverage, taxonomic discriminatory power, and primer universality. We subsequently test in vitro three COI primer pairs and one 12S pair for their specificity, reproducibility, and congruence with independent datasets derived from traditional survey methods at five estuarine and coastal sites in the English Channel and North Sea coast. 3. Our results show that for aqueous extra-organismal DNA at low template concentrations, both metazoan and fish-targeted COI primers perform poorly in comparison to 12S, exhibiting low levels of reproducibility due to non-specific amplification of prokaryotic and non-target eukaryotic DNAs. 4. An ideal metabarcode would have an extensive reference library for which custom primer sets can be designed for either broad assessments of biodiversity or taxon specific surveys, but unfortunately, low primer specificity hinders the use of COI, while the paucity of reference sequences is problematic for 12S. The latter, however, can be mitigated by expanding the concept of DNA barcodes to include whole mitochondrial genomes generated by genome-skimming existing tissue collections.
Data Types:
  • Dataset
  • File Set
Phenological investigation can provide valuable insights into the ecological effects of climate change. Appropriate modelling of the time distribution of phenological events is key to determining the nature of any changes, as well as the driving mechanisms behind those changes. Here we present the nlstimedist R package, a distribution function and modelling framework that describes the temporal dynamics of unimodal phenological events. The distribution function is derived from first principles and generates three biologically interpretable parameters. Using seed germination at different temperatures as an example, we show how the influence of environmental factors on a phenological process can be determined from the quantitative model parameters. The value of this model is its ability to represent various unimodal temporal processes statistically. The three intuitively meaningful parameters of the model can make useful comparisons between different time periods, geographical locations or species’ populations, in turn allowing exploration of possible causes.
Data Types:
  • Other
  • Software/Code
  • Tabular Data
  • Dataset
Aim: Explore the spatial variation of the relationships between species richness (SR), phylogenetic diversity (PD) and environmental factors to infer the possible mechanisms underlying patterns of diversity in different regions of the globe. Location: Global. Time period: Present day. Major taxa studied: Terrestrial mammals. Methods: We used a hexagonal grid to map SR and PD of mammals and four environmental factors (temperature, productivity, elevation and climate-change velocity since the Last Glacial Maximum). We related those variables through direct and indirect pathways using a novel combination of Path Analysis and Geographically Weighted Regression to account for spatial non-stationarity of path coefficients. Results: SR, PD and environmental factors relate differently across the geographic space, with most relationships varying in both, magnitude and direction. Species richness is associated with lower phylogenetic diversity in much of the tropics and in the Americas, which reflects the tropical origin and the recent diversification of some mammalian clades in these regions. Environmental effects on PD are predominantly mediated by their effects on SR. But once richness is controlled for, the relationships between environmental factors and PD (i.e. PDSR) highlight environmentally driven changes in species composition. Environmental-PDSR relationships suggest that the relative importance of different mechanisms driving biodiversity shifts spatially. Across most of the globe, temperature and productivity are the strongest predictors of richness, while PDSR is best predicted by temperature. Main conclusions: Richness explains most spatial variation in PD, but both dimensions of biodiversity respond differently to environmental conditions across the globe, as indicated by the spatial mismatches in the relationships between environmental factors and these two types of diversity. We show that accounting for spatial non-stationarity and environmental effects on PD while controlling for richness uncovers a more complex scenario of drivers of biodiversity than previously observed.
Data Types:
  • Other
  • Dataset
  • File Set
Metatranscriptomics is a powerful method for studying the composition and function of complex microbial communities. The application of metatranscriptomics to multi-species parasite infections is of particular interest, as research on parasite evolution and diversification has been hampered by technical challenges to genome-scale DNA sequencing. In particular, blood parasites of vertebrates are abundant and diverse though they often occur at low infection intensities and exist as multi-species infections, rendering the isolation of genomic sequence data challenging. Here, we use birds and their diverse haemosporidian parasites to illustrate the potential for metatranscriptome sequencing to generate large quantities of genome-wide sequence data from multiple blood parasite species simultaneously. We used RNA-Seq on 24 blood samples from songbirds in North America to show that metatranscriptomes can yield large proportions of haemosporidian protein-coding gene repertoires even when infections are low-intensity (<0.1% red blood cells infected) and consist of multiple parasite taxa. By bioinformatically separating host and parasite transcripts and assigning them to the haemosporidian genus of origin, we found that transcriptomes detected ~23% more total parasite infections across all samples than were identified using microscopy and DNA barcoding. For single-species infections, we obtained data for upwards of 1,300 loci from samples with as low as 0.03% parasitemia, with the number of loci increasing with infection intensity. In total, we provide data for 1,502 single-copy orthologous loci from a phylogenetically-diverse set of 33 haemosporidian mitochondrial lineages. The metatranscriptomic approach described here has the potential to accelerate ecological and evolutionary research on haemosporidians and other diverse parasites.
Data Types:
  • Other
  • Dataset
  • File Set
1. Long-term pathogen control or eradication in wildlife is rare and represents a major challenge in conservation. Control is particularly difficult for environmentally transmitted pathogens, including some of the most conservation-critical wildlife diseases. 2. We undertook a treatment program aimed at population-scale eradication of the environmentally transmitted Sarcoptes scabiei mite (causative agent of sarcoptic mange) during an epizootic in bare-nosed wombats (Vombatus ursinus). Field trial results were used to parameterize a mechanistic host-disease model that explicitly described indirect-transmission, host behaviour, and viable disease intervention methods. 3. Model analysis shows that elimination of S. scabiei in the wild is most sensitive to the success of treatment delivery, and duration of the program. In addition, we found the frequency that wombats switch burrows was an important positive driver of mite persistence. 4. Synthesis and applications: This research emphasises the utility of applying model-guided management techniques in order to achieve practical solutions in the field. Our approach and findings have applicability to other species affected by S. scabiei (e.g., wolves, red foxes, Spanish ibex, and American black bear), as well as other conservation-critical systems involving environmental transmission (e.g., bat white-nose syndrome and amphibian chytridiomycosis).
Data Types:
  • Software/Code
  • Tabular Data
  • Dataset
A comparative study of the closely related species of the genus Gastridium (Poaceae, Tribe: Poeae, Subtribe: Agrostidinae), G. ventricosum, G. phleoides, and G. scabrum was assessed based on a critical examination of both fresh and dried specimens, including relevant material, and a morphometric analysis of herbarium specimens collected in Italy. The study aimed to provide new diagnostic tools to improve the taxonomy of the genus and confirm species delimitation. Thus, variation in floral morphology in the three species was further explored using seven quantitative and ten qualitative characters measured on 318 spikelets, both awned and unawned. Statistical methods, including principal components analysis (PCA) and non‐metric multidimensional scaling (NMDS), were used. Numerical analyses showed a general distinctness of spikelets and florets, consistent with the three studied species, and revealed among and within species variation patterns in between‐ both spikelet types. Accordingly, the most informative quantitative characters appeared to be the width and length of glumes and the length of awns, useful to distinguish G. phleoides with the substantially narrowest glumes and the significantly higher length of awns from the others, especially from G. scabrum, in which the width of glumes reaches the highest value. The most informative qualitative characters appeared to be the presence/absence of thick hairs or minute tubercles on the upper side of the lemma. The autonomy of the three studied species was confirmed. The taxonomic significance of the results was briefly discussed, and notes on the species dispersal were added. Some nomenclatural and taxonomic notes on G. scabrum, of which literature still showed evidence of a general unawareness, were given.
Data Types:
  • Dataset
  • File Set
Rainforests on Borneo support exceptional concentrations of endemic insect biodiversity, but many of these forest-dependent species are threatened by land-use change. Totally protected areas (TPAs) of forest are key for conserving biodiversity, and we examined the effectiveness of the current TPA network for conserving range-restricted butterflies in Sabah (Malaysian Borneo). We found that mean diurnal temperature range and precipitation of the wettest quarter of the year were the most important predictors of butterfly distributions (N = 77 range-restricted species), and that species richness increased with elevation and aboveground forest carbon. On average across all species, TPAs were effective at conserving ~43% of species’ ranges, but encompassed only ~40% of areas with high species richness (i.e. containing at least 50% of our study species). The TPA network also included only 33-40% of areas identified as high priority for conserving range-restricted species, as determined by a systematic conservation prioritization analysis. Hence, the current TPA network is reasonably effective at conserving range-restricted butterflies, although considerable areas of high species richness (6565 km2) and high conservation priority (11,152-12,531 km2) are not currently protected. Sabah’s remaining forests, and the range-restricted species they support, are under continued threat from agricultural expansion and urban development, and our study highlights important areas of rainforest that require enhanced protection.
Data Types:
  • Dataset
  • File Set
Aim: Bees play an important role in natural ecosystems and the world’s food supply. In the past decades, bee abundance and diversity have declined globally. This has resulted in decreased pollination services for natural ecosystems and the agricultural sector at the field scale. One of the causes of the decline in bee abundance and diversity is the use of pesticides. Linking pesticide use, land use and bee presence could provide crucial insights into areas and pesticides that pose a significant threat to the abundance and diversity of bees. Obtaining actual figures of farmer pesticide use is rarely possible. Therefore, we designed a method to study the effects of potential pesticide use on the survival and distribution of honey- and bumblebees. Location: The Netherlands. Methods: A pesticide risk model was implemented incorporating a hazard quotient as the risk assessment. The number of allowed pesticide active ingredients per crop that could pose a risk to honeybees and bumblebees were linked to the Dutch crop parcel locations for 2015 and 2016. The potential pesticide risk maps were analyzed using honeybee colony survival and bumblebee presence data. Results: Non-significant negative effects of potential pesticide risk on honeybee colony survival and bumblebee presence were found. A significant negative effect of greenhouses was identified for both honeybees and bumblebees. The most important factors in the models predicting honeybee colony survival and bumblebee presence were urban land areas and natural grasslands respectively, both showing a positive effect. Main conclusions: Here, the first attempt to estimate and map pesticide risk to bees in the Netherlands in a country-wide manner is presented. The results could provide crucial high-resolution insights for bee conservation action and facilitate the increase of pollination services in natural ecosystems and the agricultural sector on a local and country-wide scale.
Data Types:
  • Dataset
  • File Set
Acer (the maple genus) is one of the diverse tree genera in the Northern Hemisphere with about152 species, most of which are in eastern Asia. There are roughly a dozen of species in Europe/western Asia and a dozen in North America. Several phylogenetic studies of Acer have been conducted since 1998, but none have provided a satisfactory resolution for basal relationships among sections of Acer. Here we report the first well-resolved phylogeny of Acer based on DNA sequences of over 500 nuclear loci generated using the anchored hybrid enrichment method and explore the implications of the robust phylogeny for Acer systematics and biogeography. Our phylogenetic results support the most recent taxonomic treatment of Acer by de Jong with some modifications; section Pentaphylla may be expanded to include section Trifoliata, and A. yangbiense may be included in section Lithocarpa. Sections Spicata, Negundo, Arguta, and Palmata form a clade sister to the rest of the genus where sections Glabra and Parviflora comprise the first clade followed by section Macrantha, sections Ginnala, Lithocarpa, Indivisa, sections Platanoidea and Macrophylla, section Rubra, section Acer, and section Pentaphylla. Monotypic sections Glabra and Macrophylla in North America are sister to the Japanese section Parviflora and Eurasian section Platanoidea, respectively. Ancestral area inferences using S-DIVA (statistical dispersal and vicariance analysis) and DEC (dispersal and extinction cladogenesis) methods suggest that Asia might be the most likely ancestral area of Acer as proposed by Wolfe and Tanai and molecular dating using BEAST (Bayesian evolutionary analysis by sampling trees) indicate that section diversifications of Acer might have completed largely in the late Eocene and the intercontinental disjunctions of Acer between eastern Asia and eastern North America formed mostly in the Miocene.
Data Types:
  • Software/Code
  • Dataset
Premise of the research. The disjunct distribution of plant genera between eastern Asia (EA) and eastern North America (ENA) has long attracted the attention of biologists and biogeographers. For most genera that have been studied, there are more species in EA than ENA and the diversity anomaly may have resulted from the greater physiographical heterogeneity in conjunction with climate and sea level changes in EA than in ENA. However, few empirical studies have explicitly tested the association between species diversity and allopatric speciation events. The genus Stewartia (Theaceae) displays this diversity anomaly with two species in ENA and 21 species in EA, but the phylogeny of this group has not been resolved due to insufficient data. Methodology. Here, we sampled 15 species of Stewartia (65%) and generated data from over 500 nuclear loci using the anchored phylogenomic approach to produce a robust phylogeny of Stewartia. In addition, biogeographical analyses were performed to elucidate the natural history of Stewartia including estimated times of divergence, ancestral areas, and speciation patterns. Pivotal results. Our parsimony, Bayesian, and species tree analyses produced congruent phylogenies with high resolution of the interspecific relationships within Stewartia. Speciation in Asia was mostly allopatric between the Japanese islands and the Asian continent during the Miocene and early Pliocene, while the two ENA species represent lineages from different times with S. malacodendron being the first lineage to split off from the remaining species and S. ovata coming later sister to the deciduous species of Asian Stewartia. Conclusions. The results provide direct evidence for the importance of allopatry in the differential diversity between EA and ENA.
Data Types:
  • Software/Code
  • Dataset
5