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  • 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.
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  • 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.
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  • Oryctocephalid trilobites are seldom abundant and often tectonically deformed, creating problems for robust species delimitation and compromising their utility in biostratigraphic and evolutionary studies. By studying more than 140 specimens recovered from the upper portion of the Combined Metals Member (Pioche Formation, Nevada; Cambrian Stage 4, Series 2), we exploit a rare opportunity to explore how morphological variation among oryctocephalid specimens is partitioned into intraspecific variation versus interspecific disparity. Qualitative and quantitative analyses reveal that two species are represented: Oryctocephalites palmeri Sundberg and McCollum, 1997 and Oryctocephalites sp. A, the latter known from a single cranidium stratigraphically below all occurrences of the former. In contrast to the conclusions of a previous study, there is no evidence of cranidial dimorphism in O. palmeri. However, that species exhibits considerable variation in cranidial shape and pygidial spine arrangement and number. Cranidial shape variation within O. palmeri is approximately one-half of the among-species disparity within the genus. Comparison of cranidial shape between noncompacted and compacted samples reveals that compaction causes significant change in mean shape and an increase in shape variation; such changes are interpretable in terms of observed fracture patterns. Nontaphonomic variation is partitioned into ontogenetic and nonallometric components. Those components share similar structure with each other and with interspecific disparity, suggesting that ontogenetic shape change might be an important source of variation available for selection. This highlights the importance of ontogenetic and taphonomic sources of variation with respect to species delimitation, morphospace occupation, and investigation of evolutionary patterns and processes.
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  • 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.
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  • 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).
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  • Aim: Understanding how landscape features affect gene flow is critical to connectivity conservation and restoration management. Here, we examined the relationship between functional connectivity (gene flow) and structural connectivity (area and spatial configuration of habitats) in three co-occurring short-range plant taxa in an ancient terrestrial island system. Location: Low altitude mountain ranges south-western Australia Methods: We analysed spatial patterns of genetic differentiation at nuclear microsatellite loci using Bayesian clustering. Circuit theory modelling was used to generate all possible pathways that connect populations as resistance distance matrices based on two surfaces for each taxon. The first surface assumes a flat terrain and tests whether genetic similarity declines only with distance – isolation by distance (IBD). The second surface is habitat suitability based on species distribution modelling (SDM), which tests whether genetic similarity is a function of connected and suitable habitat. Multiple matrix regression with randomisation was used to test the significance of the resistance distance matrices at predicting two metrics of genetic differentiation (FST and DEST). Variance explained was partitioned using redundancy analysis. Results: Genetic structure for the insect-pollinated taxa - Acacia adinophylla, and Tetratheca aphylla subsp. aphylla was at similar spatial scales. Unexpectedly, a higher level of genetic structure was found in the wind-pollinated Lepidosperma bungalbin. IBD best explained the gene flow of A. adinophylla (R2 = 0.41-0.43) with partial support provided by habitat suitability (R2 = 0.04-0.07). In contrast, connectivity by habitat suitability was highest for T. aphylla subsp. aphylla (R2 = 0.56-0.59). Drivers of L. bungalbin connectivity were inconsistent between the two measures of genetic differentiation. Main conclusions: Gene flow is facilitated by different factors for the three taxa. Habitat fragmentation would most strongly impede gene flow for T. aphylla subsp. aphylla. Geographic distance cannot be assumed as the sole or best determinant of gene flow among populations, nor can findings be generalised to coexisting taxa.
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  • 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.
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  • 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.
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  • 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.
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  • Aim. Understanding the forces that drive range shifts in forest landscapes is imperative for predicting species distributions under anthropogenic climate and land use change. However, empirical studies exploring how these components jointly influence critical early-life stages of mountain tree species across environmental gradients are scarce. We used the high-mountain tree Polylepis australis as model species to investigate the relative importance of altitude and associated climatic conditions, land use for livestock and microsite characteristics on early-life performance. Location. Córdoba Sierras, central Argentina. Methods. We set up an extensive in situ sowing experiment with a robust split-plot design that integrated spatial scales ranging from 0.4 m2 subplots at the microsite level (associated with vegetative and micro-topographic structures), to livestock exclosure and enclosure plots of several hectares, to an altitudinal gradient of 1000 m. Components of early-life performance were monitored across two subsequent growing seasons. Results. Microsite characteristics played a fundamental role in P. australis establishment, whereby interactions with altitude and/or land use suggested alternate mechanisms: facilitation (likely reduced desiccation) dominated at low altitude while at high altitude abiotic stress (likely intensive frost and radiation) overruled any microsite effects. At mid altitude benefits of competition release prevailed over facilitation and microsite effects gained importance under livestock presence. Inconsistencies between pre- and post- emergence responses illustrated potential tradeoffs between beneficial and detrimental effects of microsite conditions upon performance throughout early life: a favorable location for seeds may abruptly turn adverse for seedlings. Main conclusions. We unravel how changes in altitude, anthropogenic disturbances and microsite characteristics jointly modulate P. australis performance across stages of early establishment. Such information is fundamental when categorizing specific microhabitats as “safe sites” for tree regeneration especially in mountain environments with high spatiotemporal heterogeneity.
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