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opennotspecifiedApr 2020View details →

FIGURE 3. Median predorsal scales of Siphamia guttulata (A—paralectotype, AMS I.16306-001, 25.7 mm SL; B—CSIRO H 7457-01, 27 mm SL) and Siphamia tubifer (C—CSIRO H 6752-02, 31 mm SL). Scale bar = 0.5 mm. Yellow arrows point to first dorsal spine, numbers or pink arrows indicate median predorsal scales. Fifth median predorsal scale of Fig. C is a scale pocket as the scale has been lost. in Redescription and distributional range extension of the Speckled Siphonfish, Siphamia guttulata (Pisces: Apogonidae)

FIGURE 3. Median predorsal scales of Siphamia guttulata (A—paralectotype, AMS I.16306-001, 25.7 mm SL; B—CSIRO H 7457-01, 27 mm SL) and Siphamia tubifer (C—CSIRO H 6752-02, 31 mm SL). Scale bar = 0.5 mm. Yellow arrows point to first dorsal spine, numbers or pink arrows indicate median predorsal scales. Fifth median predorsal scale of Fig. C is a scale pocket as the scale has been lost.

opennotspecifiedMar 2006View details →

List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records in A new species of bat of the Hipposideros bicolor group (Chiroptera: Hipposideridae) from Central Laos, with evidence of convergent evolution with Sundaic taxa

List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records

opencc-zeroJul 2020View details →

Data from: Vestigial auriculomotor activity indicates the direction of auditory attention in humans

Unlike dogs and cats, people do not point their ears as they focus attention on novel, salient, or task-relevant stimuli. Our species may nevertheless have retained a vestigial pinna-orienting system that has persisted as a "neural fossil" within in the brain for about 25 million years. Consistent with this hypothesis, we demonstrate that the direction of auditory attention is reflected in sustained electrical activity of muscles within the vestigial auriculomotor system. Surface electromyograms (EMGs) were taken from muscles that either move the pinna or alter its shape. To assess reflexive, stimulus-driven attention we presented novel sounds from speakers at four different lateral locations while the participants silently read a boring text in front of them. To test voluntary, goal-directed attention we instructed participants to listen to a short story coming from one of these speakers, while ignoring a competing story from the corresponding speaker on the opposite side. In both experiments, EMG recordings showed larger activity at the ear on the side of the attended stimulus, but with slightly different patterns. Upward movement (perking) differed according to the lateral focus of attention only during voluntary orienting; rearward folding of the pinna's upper-lateral edge exhibited such differences only during reflexive orienting. The existence of a pinna-orienting system in humans, one that is experimentally accessible, offers opportunities for basic as well as applied science.

opencc-zeroSep 2020View details →

Data from: Phylotranscriptomics resolves interspecific relationships and indicates multiple historical out-of-North America dispersals through the Bering Land Bridge for the genus Picea (Pinaceae)

A robust phylogeny is prerequisite to understand the evolution and biogeography of organisms. However, ancient and recent evolutionary radiations occurred in many plant lineages, which pose great challenges for phylogenetic analysis, especially for conifers characterized by large effective population sizes and long generation times. Picea is an important component of the dark coniferous forests in the Northern Hemisphere. Previous studies improved our understanding of its evolutionary history, but its interspecific relationships and biogeographic history remain largely unresolved. In the present study, we reconstructed a well-resolved phylogeny of Picea by comparative transcriptomic analysis based on a complete species sampling. The phylogenetic analysis, together with molecular dating and ancestral area reconstruction, further supports the North American origin hypothesis for Picea, and indicates that this genus experienced multiple out-of-North America dispersals by the Bering Land Bridge. We also found that spruces in the Japanese Archipelago have multiple origins, and P. morrisonicola from the Taiwan Island has a close relationship with species from the Qinghai-Tibetan Plateau and adjacent regions. Our study provides the first complete phylogeny of Picea at the genomic level, which is important for future studies of this genus.

opencc-zeroOct 2020View details →

Red oak seedlings as indicators of deer browse pressure: gauging the outcome of different white-tailed deer management approaches

After decades of high deer populations, North America forests have lost much of their previous biodiversity. Any landscape-level recovery requires substantial reductions in deer herds, but modern societies and wildlife management agencies appear unable to devise appropriate solutions to this chronic ecological and human health crisis. We evaluated the effectiveness of fertility control hunting in reducing deer impacts at Cornell University. We estimated spring deer populations and planted Quercus rubra seedlings to assess deer browse pressure, rodent attack, and other factors compromising seedling performance. Oak seedlings protected in cages grew well, but deer annually browsed ≥ 60% of unprotected seedlings. Despite female sterilization rates of > 90%, the deer population remained stable. Neither sterilization nor recreational hunting reduced deer browse rates and neither appears able to achieve reductions in deer populations or their impacts. We eliminated deer sterilization and recreational hunting in a core management area in favor of allowing volunteer archers to shoot deer over bait, including at night. This resulted in a substantial reduction in the deer population and a linear decline in browse rates as a function of the spring deer abundance. Public trust stewardship of North American landscapes will require a fundamental overhaul in deer management to may provide for a brighter future, and oak sentinels may be a promising metric to assess changes. These changes will require intense public debate and may require new approaches such as regulated commercial hunting and the natural dispersal or intentional release of important deer predators (e.g., wolves and mountain lions). Such drastic changes in deer management will be highly controversial, and at present, likely difficult to implement in North America. However, the future of our forest ecosystems and associated biodiversity will depend on evidence and guided change in landscape management and stewardship.

openother-openOct 2020View details →

Utility of acoustic indices for ecological monitoring in complex sonic environments

Abstract With the continued adoption of passive acoustic monitoring as a tool for rapid and high-resolution ecosystem monitoring, ecologists are increasingly making use of a suite of acoustic indices to summarise the sonic environment. Though these indices are often reported to well represent some aspect of the biology of an ecosystem, the degree to which they are confounded by various extraneous sonic conditions is largely unknown. We conducted an aural inventory across 23 field sites in Okinawa to identify the number of unique animal sounds present in recordings. Using these values of ‘measured richness’, we then examined how the performance of 11 commonly-used acoustic indices varied across a range of sonic conditions (including in the presence and absence of insect stridulations, audible wind or rain, and human-related sounds). Our analysis identified both well- and poor-performing acoustic indices, as well as those that were particularly sensitive to sonic conditions. Only two indices reflected measured richness across the full range of sonic conditions examined. A few indices were relatively insensitive to extraneous sonic conditions, but no index correlated with measured richness when masked by sound from broadband stridulating insects. Our results demonstrate considerable sensitivity of most commonly used acoustic indices to confounding sonic conditions, highlighting the challenges of working with large acoustic datasets collected in the field. We make practical recommendations for acoustic index use based on study design, with the aim of identifying the suite of acoustic indices with greatest utility as indicators for rapid biodiversity monitoring and management of the world’s natural soundscapes. Methods The dataset contains the names of audio files collected across 23 field sites between April 2017 and January 2018 as part of the OKEON-Churamori project on the island of Okinawa, Japan. We conducted an aural inventory, manually counting and recording the number of unique biotic sounds (approximately corresponding to species richness) and noting the presence or absence of three potentially confounding sonic conditions: audible geophony (wind, rain etc.), anthropophony (human-related sounds), and broadband sounds produced by stridulating insect (e.g. cicadas, orthopterans). We then calculated 11 commonly used acoustic indices from the literature and compared their performance (correlation with richness) in the presence vs absence of each sonic condition. Our dataset also contains time and date information for each recording, and the mean site-level richness (i.e. across multiple recordings) for each site and for each unique site-by-season combination. See Table A2 and Methods section in the associated manuscript for details on data processing and the calculation of acoustic indices. Usage notes See readme file for descriptions of data table structure.

opencc-zeroOct 2020View details →

Acoustic indices perform better when applied at ecologically meaningful time and frequency scales

Abstract: 1. Acoustic indices are increasingly employed in the analysis of soundscapes to ascertain biodiversity value. However, conflicting results and lack of consensus on best practices for their usage has hindered their application in conservation and land-use management contexts. Here we propose that the sensitivity of acoustic indices to ecological change and fidelity of acoustic indices to ecological communities are severely impacted by signal masking. Signal masking can occur when acoustic responses sensitive to the effect being monitored are masked by less sensitive acoustic groups, or target taxa sonification is masked by non-target noise. We argue that by calculating acoustic indices at ecologically appropriate time and frequency bins, masking effects can be reduced and the efficacy of indices increased. 2. We test this on a large acoustic dataset collected in Eastern Amazonia spanning a disturbance gradient including undisturbed, logged, burned, logged-and-burned, and secondary forests. We calculated values for two acoustic indices: the Acoustic Complexity Index and the Bioacoustic Index, across the entire frequency spectrum (0-22.1 kHz), and four narrower subsets of the frequency spectrum; at dawn, day, dusk and night. 3. We show that signal masking has a large impact on the sensitivity of acoustic indices to forest disturbance classes. Calculating acoustic indices at a range of narrower time-frequency bins substantially increases the classification accuracy of forest classes by random forest models. Furthermore, signal masking led to highly misleading correlations, including spurious inverse correlations, between biodiversity indicator metrics and acoustic index values compared to correlations derived from manual sampling of the audio data. 4. Consequently, we recommend that acoustic indices are calculated either at a range of time and frequency bins, or at a single narrow bin, predetermined by a priori ecological understanding of the soundscape.

opencc-by-4.0Nov 2020View details →

The last interglacial sea-level record of the Israeli coastline - WALIS database of sea-level indicators

This file is a record of relative sea level proxies of the last Interglacial sea-level along the Israeli coastline. It has been exported from the World Atlas of Last Interglacial Shorelines - WALIS

opencc-by-4.0Mar 2020View details →

Annexes to the European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2017/2018

Version 2 - changes as compared to version 1 The following revisions were applied to the file EUSR AMR2018_Annexes A-F.docx in the section Annex F: - in Table 6B, pages 119-120, the footnotes (e) to (p) were re-attributed in the table, so as to match the table footnotes; - in Table 31 on page 123,  'LA' was replaced with 'HA' for Belgium data in the column titled 'LA, CA or HA'. Light formatting has been applied on pages 121 and 122, Tables 7a and 7b, changed from portrait to landscape orientation, as well as to footers and headers that were made consistent throughout the document. --------- Version 1  All tables produced for the European Union Summary Report on Antimicrobial Resistance in Zoonotic and Indicator Bacteria from Humans, Animals and Food in 2018 : - Campylobacter - E. coli - MRSA -Salmonella - ESBL Annexes A to F are also included.

Data from: Life-history dimensions indicate non-random assembly processes in tropical island tree communities

Community assembly processes on islands are often non-random. The mechanisms behind non-random assembly, however, are generally difficult to disentangle. Functional diversity in combination with a null model approach that accounts for differences in species richness among islands can be used to test for non-random assembly processes, but has been applied rarely to island communities. By linking functional diversity of trees on islands with a null model approach, we bridge this gap and test for the role of stochastic vs. non-random trait-mediated assembly processes in shaping communities by studying functional diversity-area relationships. We measured 11 plant functional traits linked to species dispersal and resource acquisition strategies of 57 tree species on 40 tropical islands. We grouped traits into four life-history dimensions representing (i) dispersal ability, (ii) growth strategy, (iii) light acquisition, and (iv) nutrient acquisition. To test for non-random assembly processes, we used null models that account for differences in species richness among the islands. Our results reveal contrasting responses of the four life-history dimensions to island area. The dispersal and the growth strategy dimensions were underdispersed on smaller islands, whereas the light acquisition dimension was overdispersed. The nutrient acquisition dimension did not deviate from null expectations. With increasing island area, shifts in the strength of non-random assembly processes increased the diversity of dispersal and acquisition strategies in island communities. Our results suggest that smaller islands may be more difficult to colonize and provide more limited niche space compared to larger islands, whose tree communities are likely determined by stochastic processes and higher niche diversity. Our null model approach highlights that analysing the functional diversity of different life-history dimensions provides a powerful framework to unravel community assembly processes on islands. These complex, non-random assembly processes are masked by measures of functional diversity that do not account for differences in species richness between islands.

Data from: A review of seascape complexity indices and their performance in coral and rocky reefs

Seascape complexity is an important driver of ecological processes in marine systems. Today, high resolution, multiscale bathymetric data is being collected due to rapid advances in marine technologies and image processing, drastically improving the detailed mapping of the physical structure of the seascape. However, these data are rarely synthesized to create comprehensive complexity estimates, and complexity is still mostly measured using a small set of simple indices. The aims of this study are to: (1) review existing seascape complexity indices and propose innovative indices designed to capture the marine organism perspective, (2) quantify the interrelationships among these complexity indices; (3) test the performance of these indices in explaining fish assemblage structure; and (4) provide R code to easily reproduce the indices. Seascape bottom topography for this study was quantified using digital depth recordings along transects in Mediterranean subtropical rocky reefs and Red Sea tropical coral reefs. These were used to generate complexity indices that were then compared to visually surveyed fish assemblages. We found that several common indices captured similar complexity facets, while an innovative family of structural diversity indices, representing the diversity of physical elements, captured distinct complexity facets not represented by existing indices. No single index was consistently superior; however, vertical relief was consistently included as a top predictor of fish assemblage structure. Interestingly, the most commonly used index, rugosity, was a poor predictor. We suggest a new, distinct set of structural diversity indices that may explain considerable variation in fish assemblages. The results suggest that several indices may need to be combined to capture the full influence of complexity on marine diversity and caution against the use of a single 'universal' index. While bathymetric data is increasingly being collected at high resolutions and increasing scales, synthesizing this data requires the use of appropriate complexity indices. The guidelines and recommendations presented here, along with the <a href="https://doi.org/10.5281/zenodo.4393340">supplemental R code</a>, will facilitate progress towards a more complete representation of different complexity facets.

Automated flow control of a multi-lane swimming chamber for small fishes indicates species-specific sensitivity to experimental protocols

In fishes, swimming performance is considered an important metric to measure fitness, dispersal, and migratory abilities. Swimming performance of individual larval fishes is often integrated into models to make inferences on how environmental parameters affect population-level dynamics (e.g., connectivity). However, little information exists regarding how experimental protocols affect the swimming performance of marine fish larvae. In addition, the technical setups used to measure larval fish swimming performance often lack automation and accurate control of water quality parameters and flow velocity. In this study, we automated the control of multi-lane swimming chambers for small fishes by developing an open-source algorithm. This automation allowed us to execute repeatable flow scenarios and reduce operator interference and inaccuracies in flow velocity typically associated with manual control. Furthermore, we made structural modifications to a prior design to reduce areas of lower flow velocity. We then validated the flow dynamics of the new chambers using computational fluid dynamics and particle tracking software. The algorithm provided accurate alignment between set and measured flow velocities and we used it to test whether faster critical swimming speed (Ucrit) protocols (i.e., shorter time intervals and higher velocity increments) would increase Ucrit of early life stages of two tropical fish species (4-10 mm standard length). The Ucrit of barramundi (Lates calcarifer) and cinnamon anemonefish (Amphiprion melanopus) increased linearly with fish length, but in cinnamon anemonefish, Ucrit started to decrease upon metamorphosis. Swimming protocols using longer time intervals (>2.5 times increase) negatively affected Ucrit in cinnamon anemonefish but not in barramundi. These species-specific differences in swimming performance highlight the importance of testing suitable Ucrit protocols prior to experimentation. Automated control of flow velocity will create more accurate and repeatable data on swimming performance of larval fishes. Integrating refined measurements into individual-based models will support future research on the effects of environmental change.

Most cultural importance indices do not predict species cultural keystone status

The use of quantitative indices to quantify the importance of a plant species to human societies is widespread. While quantifi- cation may yield support for standardized methodologies and facilitate generalizations, it is important to examine the potential limitations of these indices. Moreover, because these indices are calculated at the species level, failure to control for phylogenetic relatedness in predictive models may yield misleading conclusions. We test if commonly used cultural importance indices predict species cultural keystone status among the Shipibo-Konibo community of Paoyhan in the Peruvian Amazon. Eleven of the 12 indices were correlated with each other indicating most cultural importance indices are redundant. Most indices did not predict species cultural keystone status. Phylogenetic control improved our models indicating a significant part of the predictive power of even the best index was explained by species shared evolutionary history. Our findings highlight the need for the cautious use of cultural importance indices to infer species cultural keystone status. Newly developed indices should be tested for correlation with existing indices to avoid redundancy.

opencc-by-4.0Jan 2021View details →

Habitus of an Agonum specimen, arrow indicates labrum

Habitus of an Agonum specimen, arrow indicates labrum, png file

opencc-by-4.0Jan 2021View details →

Determination of complex refractive indices and optical properties of volcanic ashes in the thermal infrared based on generic petrological compositions: supplementary material

This dataset contains supplementary material to the paper "Determination of complex refractive indices and optical properties of volcanic ashes in the thermal infrared based on generic petrological compositions", doi: 10.1016/j.jvolgeores.2021.107174 It contains a set of volcanic ash refractive indices and optical properties derived for certain microphysical properties. For more information please consider the manuscript or contact the authors.

opencc-zeroDec 2018View details →

Data from: Cats under cover: habitat models indicate a high dependency on woodlands by Atlantic Forest felids

Four Neotropical small and medium felids—the ocelot, jaguarundi, margay and southern tiger cat—have overlapping geographic distributions in the endangered Atlantic Forest. Local studies show that these felids avoid areas with high human impact, but the three smaller ones use human-modified areas more frequently than do ocelots. To understand how landscape changes affect the habitat distribution of these four felids in the Atlantic Forest of Argentina, we used maximum entropy models to analyze the effect of environmental and anthropogenic factors. We estimated niche breadth and overlap among these felids. The conversion of the native forest to land uses without trees was the most important variable that determined the habitat distribution of the four species. For all four species the optimal habitat covered less than 1/3 of the study area and corresponds mainly to the native forest areas. Nearly 50 percent of these areas had some level of protection. The niche width was higher for the small felids than for ocelots. Niche overlap was high for all species pairs, but higher among the small felids and lower for each of these with the ocelot. The four felids were negatively affected by native forest loss, with ocelots being more sensitive than the smaller felids. The conversion of unprotected forest areas to other types of land uses would imply a greater habitat loss for these felids. The protection of current remnants of Atlantic Forest in Argentina is important for the long-term conservation of the four felids.

opencc-zeroDec 2011View details →

Data from: Genetic analysis of the peatmoss Sphagnum cribrosum (Sphagnaceae) indicates independent origins of an extreme infra-specific morphology shift

Within Sphagnum cribrosum, a dioicous aquatic peatmoss, a unique morphological variant (the "waveform"), found at only two lakes in North Carolina, has a branching architecture that is extremely differentiated from anything otherwise known in Sphagnum, though the plants are microscopically indistinguishable from S. cribrosum. At one site where the two morphologies co-occur, sixty years of field observations demonstrate the persistence of each morphology, even where the two forms grow intermixed. We conducted a reciprocal transplant experiment in which waveform and normal plants maintained their divergent morphologies for eight months. We sampled populations throughout the range and conducted genetic and phylogenetic analyses with microsatellite markers and DNA sequences to investigate the genetic context of the waveform morphology within S. cribrosum. Haplotype networks from DNA sequences showed the two waveform populations are separated by 11 substitutions across three loci. Microsatellite analyses using non-parametric clustering and admixture models also indicated genetic dissimilarity between genotypes with waveform morphology at the two lakes. Both molecular datasets suggest that the waveform morphology had at least two independent origins despite proximity of the two lakes where it uniquely occurs. Given the clonal nature of the waveform, it is unlikely to form a cohesive evolutionary lineage deserving of taxonomic status. The analysis also revealed a genetically diverse population in Georgia as the potential source of variation found in all other populations of S. cribrosum.

opencc-zeroDec 2015View details →

Data from: Telomere length reflects reproductive effort indicated by corticosterone levels in a long-lived seabird

Telomere length (TL) is a candidate biomarker of ageing and phenotypic quality, but little is known of the (physiological) causes of TL variation. We previously showed that individual common terns Sterna hirundo with high reproductive success had short telomeres independent of age, and this pattern was particularly strong in the longer telomeres of the within-individual TL distribution. To test whether this relation can be attributed to effects of reproductive effort, we investigated baseline corticosterone in relation to reproductive success (number of fledglings) and TL. In this context, we assume that variation in baseline corticosterone can be interpreted as index of energy expenditure and allostatic load. Males with higher corticosterone levels during incubation, compared between and within individuals, achieved higher reproductive success and had shorter telomeres. The effect on telomeres was more pronounced in corticosterone measured later in incubation and in the longer telomeres of the within-individual TL distribution. Female corticosterone level during incubation was neither related to reproductive success nor to TL. That we observed these effects only in males mirrors different parental roles during reproduction in the common tern, where males do most of the chick provisioning. The negative association between reproductive success and TL suggests individual differences in reproductive effort as reflected in, or mediated by, baseline corticosterone. We see this result as a promising step towards unravelling the physiological causes of variation in TL and the costs of reproduction.

opencc-zeroDec 2014View details →

Data from: Exaggerated sexual swellings and male mate choice in primates: testing the reliable indicator hypothesis in the Amboseli baboons

The paradigm of competitive males vying to influence female mate choice has been repeatedly upheld, but, increasingly, studies also report competitive females and choosy males. One female trait that is commonly proposed to influence male mate choice is the exaggerated sexual swelling displayed by females of many Old World primate species. The reliable indicator hypothesis posits that females use the exaggerated swellings to compete for access to mates, and that the swellings advertise variation in female fitness. We tested the two main predictions of this hypothesis in a wild population of baboons (Papio cynocephalus). First, we examined the effect of swelling size on the probability of mate guarding ('consortship') by the highest-ranking male and the behaviour of those males that trailed consortships ('follower males'). Second, we asked whether a female's swelling size predicted several fitness measures. We found that high-ranking males did not prefer females with larger swellings (when controlling for cycle number and conception) and that females with larger swellings did not have higher reproductive success. Our study, the only complete test of the reliable indicator hypothesis in a primate population, rejects the idea that female baboons compete for mates by advertising heritable fitness differences. Furthermore, we found unambiguous evidence that males biased their mating decisions in favour of females who had experienced more sexual cycles since their most recent pregnancy. Thus, rather than tracking the potential differences in fitness between females, male baboons appear to track and target the potential for a given reproductive opportunity to result in fertilization.