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Local canopy disturbance as an explanation for long-term increases in liana abundance

Canopy disturbance explains liana abundance and distribution within tropical forests and thus may also explain the widespread pattern of increasing liana abundance; however, this hypothesis remains untested. We used a 10-year study (2007 – 2017) of 117,100 rooted lianas in an old-growth Panamanian forest to test whether local canopy disturbance explains increasing liana abundance. We found that liana density increased 29.2% and basal area 12.5%. The vast majority of these increases were associated with clonal stem proliferation following canopy disturbance, particularly in liana-dense, low-canopy gaps, which had far greater liana increases than did undisturbed forest. Lianas may be ecological niche constructors; arresting tree regeneration in gaps and thus creating a high-light environment that favors sustained liana proliferation. Our findings demonstrate that liana abundance is increasing rapidly and their ability to proliferate via copious clonal stem production in canopy gaps explains much of their increase in this and possibly other tropical forests.

Population assignment tests uncover rare long-distance larval dispersal events

Long-distance dispersal (LDD) is consequential to metapopulation ecology and evolution. In systems where dispersal is undertaken by small propagules, such as larvae in the ocean, documenting LDD is especially challenging. Genetic parentage analysis has gained traction as a method for measuring larval dispersal, but such studies are generally spatially limited, leaving LDD understudied in marine species. We addressed this knowledge gap by uncovering LDD with population assignment tests in the coral reef fish Elacatinus lori—a species whose short-distance dispersal has been well-characterized by parentage analysis. When adults (n = 931) collected throughout the species' range were categorized into three source populations, assignment accuracy exceeded 99%, demonstrating low rates of connectivity between populations in the adult generation. After establishing high assignment confidence, we assigned settlers (n = 3,828) to source populations. Within the settler cohort, < 0.1% of individuals were identified as long-distance dispersers from other populations. These results demonstrate an exceptionally low level of connectivity between E. lori populations, despite the potential for ocean currents to facilitate LDD. More broadly, these findings illustrate the value of combining genetic parentage analysis and population assignment tests to uncover short- and long-distance dispersal, respectively.

Functional traits reveal the dominant drivers of long‐term community change across a North American Great Lake

The datasets here were used to determine annual sentinel fish species and trait composition in Lake Erie's western and central basins during 1969–2018 in relation to multiple anthropogenic stressors. Here, we provide three datasets, which are used in the paper by Sinclair et al. titled: "Functional traits reveal the dominant drivers of long-term community change across a North American Great Lake". Each dataset is provided as a separate tab in a single Excel worksheet. The first dataset ("Western basin") provides the annual catch-per-unit-effort (CPUE; individuals per trawl minute) for all sentinel fish species caught in Lake Erie's western basin during 1969–2018 in fall (September-October) trawl surveys conducted by the Ohio Department of Natural Resources - Division of Wildlife. The second dataset ("Central basin") provides the CPUE values for Lake Erie's central basin. The third dataset ("Environmental stressors") provides the annual values for nutrient inputs, water transparency, temperature, white perch abundances, and goby abundances for the western and central basins. A summary and explanation of each variable are also provided in the "Info" tab. Further information on how fish CPUE and stressor values were calculated is provided in the methods and supporting information of the associated article.

opencc-by-4.0Oct 2021View details →

The Complicated Case of δ Scuti Pulsations and Rotation in KIC 6951642; a long-orbit Single-lined Spectroscopic Binary Star

Abstract: More than four years of HERMES observations have confirmed KIC 6951642 is a very long orbit (≈1770 d) single-lined spectroscopic binary (F0-type) with a fast-rotating companion (vsin i = 123±3 Km/s). The Fourier spectrum of its four-year photometric observations includes plenty of significant frequencies (594) in low- and high-frequency regions. The high-frequency modes appear with various time-delay patterns. We detected several rotationally split 𝛿 Scuti pulsations centered at 13.96 per day (and average frequency spacing of Δ𝑓= 0.723±0.006 per day) for KIC 6951642. The detailed study of all significant low frequencies, extended from 0.72 to 3.60 per day, revealed that the two most dominant frequencies (with the same amplitude and larger than of p-modes) are a combina3on the lowest-frequency modes (𝑓3 = 𝑓< 0.17 per day), i.e. 𝑓orhrm + 𝑚𝑓orhrm (𝑚 = 12,14). We suggest the lowest-frequency modes are very large harmonics (orders of 10) of orbital frequency (≈0.0006 per day). We verified the other most dominant low-frequencies as harmonics of rotation frequency 0.721 per day and its combinations. Finally, we reject the probability of hybrid pulsations in the fast-rotating companion of KIC 6951642. We introduce it as a 𝛿 Scuti pulsator with a candidate rotation frequency of 0.721 per day.

Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies

Infections early in life can have enduring effects on an organism's development and immunity. In this study, we show that this equally applies to developing "superorganisms" – incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen's immune system to suppress pathogen proliferation. Early-life queen pathogen-exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen's pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism.

Labeled motor neurons following single and double nerve reinnervation of the long head of the biceps

We developed a novel rat model to investigate the neurophysiological effects of peripheral double nerve transfers to a single target muscle. In 62 male Sprague-Dawley rats the ulnar nerve of the antebrachium alone (n=30) or together with the anterior interosseus nerve (n=32) was transferred to reinnervate the long head of the biceps brachii. To further assess reinnervation, retrograde labeling was performed. Twelve weeks following surgery retrograde tracer dyes were injected in the long head of the biceps muscle to stain the reinnervating motoneurons. In 7 control animals, the number of innervating motorneurons was assessed by injecting retrograde tracer in the untreated long head of the biceps. The aim of this dataset was to compare the effects of single nerve transfer and double nerve transfer on motor neuron count.

opencc-by-4.0Oct 2022View details →

ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data (repository for simulated ONT RNA-seq data)

Simulated ONT direct RNA and 1D cDNA sequencing data of varying sequencing depths (0.5 million, 1 million, 3 million, and 5 million simulated reads) used for benchmark evaluations of transcript discovery and quantification in our paper "ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data". All details can be found in the Materials and Methods section of the paper.  HEK293T_DirectRNA.transcriptome_quantification.tsv and HEK293T_DirectRNA.transcriptome_quantification.tsv are tab-separated files containing estimated raw read counts and normalized abundance values (in TPM) of transcripts annotated in GENCODE v34lift37. Transcript quantification was done using NanoSim (version 3.1.0).  HEK293T_DirectRNA.NanoSim_500k.fastq.gz, HEK293T_DirectRNA.NanoSim_1M.fastq.gz, HEK293T_DirectRNA.NanoSim_3M.fastq.gz, and HEK293T_DirectRNA.NanoSim_5M.fastq.gz are gzip compressed FASTQ files containing 0.5 million, 1 million, 3 million, and 5 million simulated ONT direct RNA sequencing reads respectively.  HEK293T_1DcDNA.NanoSim_500k.fastq.gz, HEK293T_1DcDNA.NanoSim_1M.fastq.gz, HEK293T_1DcDNA.NanoSim_3M.fastq.gz, and HEK293T_1DcDNA.NanoSim_5M.fastq.gz are gzip compressed FASTQ files containing 0.5 million, 1 million, 3 million, and 5 million simulated ONT 1D cDNA sequencing reads respectively.

opencc-zeroOct 2022View details →

Data From: Long-term winter food supplementation shows no significant impact on reproductive performance in Mountain Chickadees in the Sierra Nevada Mountains

Supplemental feeding of wild animal populations is popular across many areas of the world and has long been considered beneficial, especially to avian taxa. Over four billion dollars are spent by hobby bird feeders in the United States each year alone. However, there is mixed evidence whether wildlife feeding is beneficial, including when it is implemented as a conservation management tool, a targeted experimental design, or an avocation. Much of the current evidence suggests that providing supplemental food is advantageous to the reproductive output and general survival of focal taxa. However, many of these studies are limited in scope and duration, leaving possible negative impacts unaddressed. This is particularly true regarding passive backyard feeding, which describes the majority of supplemental feeding, including the immense effort of millions of public enthusiasts. Here we show that winter supplemental feeding prior to reproduction had no significant impact on a range of reproductive parameters in a resident, montane passerine species, the Mountain Chickadee (Poecile gambeli). This population resides in an intact natural environment with no exposure to supplemental food beyond our experimental treatments, and individual birds were tracked across six years using radio frequency identification technology. Our results add to the growing evidence that supplemental feeding alone, isolated from the effects of urban environments, may have little to no impact on the population dynamics of some avian taxa.

opencc-zeroOct 2022View details →

Long-term fire and vegetation change in northwestern Amazonia

Amazonian forest plots are used to quantify biodiversity and carbon sequestration, and provide the foundation for much of what is known about tropical ecology. Many plots are assumed to be undisturbed, but recent work suggests that past fire, forest openings, and cultivation created vegetation changes that have persisted for decades to centuries (ecological legacies). The Yasuní Forest Dynamics plot is one of the most biodiverse places on earth, yet its human history remains unknown. Here, we use charcoal and phytolith analysis to investigate the fire and vegetation history of the Yasuní forest plot, and compare results with nearby forest plots in Colombia (Amacayacu) and Peru (Medio Putumayo-Algodón (MPA)) to explore the spatial variability of past disturbances and ecological legacies in northwestern Amazonia. Three 14C dated charcoal fragments provided evidence for a modern (1956 CE) and a past fire event ca. 750 years ago at Yasuní, compared with fire ages of 1000-1600 years ago documented at Amacayacu and MPA. Small-scale disturbances and localized canopy-openings also occurred in the Yasuní plot. Phytolith assemblages from Yasuní and Amacayacu showed more variability in past vegetation change than MPA. Low-intensity, non-continuous disturbances occurred at all three plots in the past, and our results highlight the variability of past human activities both in space and time in northwestern Amazonia. Our data also suggest that post-Columbian human disturbances from the Rubber Boom (AD 1850-1920) and subsequent oil exploration have likely left stronger ecological legacies than those left by pre-Columbian peoples in our studied regions.

opencc-by-4.0Oct 2022View details →

Long-Term Survival and Curative-Intent Treatment in Hepatitis B or C Virus-Associated Hepatocellular Carcinoma Patients Diagnosed during Screening

We uploaded the image of the mansucript Long-Term Survival and Curative-Intent Treatment in Hepatitis B or C Virus-Associated Hepatocellular Carcinoma Patients Diagnosed during Screening accepted on Biology.

opencc-zeroOct 2022View details →

Resistance of termite mounds to variation in long-term fire regimes across semi-arid African savannas

1. Fire regimes are expected to change with climate change, resulting in a crucial need to understand the specific ways in which variable fire regimes impact important contributors to ecosystem functioning, such as mound-building termites. Termite mounds and fire are both important agents of savanna ecosystem heterogeneity and functioning, but there is little understanding of how they interact across savanna types. 2. We used very high-resolution LiDAR remote sensing to measure the size, density, and distribution of termite mounds across approximately 1,300 ha of experimental burn plots in four South African savanna landscapes representing a wide range of fire treatments differing in seasonality and frequency of burning. 3. In nutrient-poor granitic savannas, fire had no impact on termite mound size, densities, and spatial distributions. In nutrient-rich basaltic savannas with high mammalian herbivore abundance and intermediate rainfall, very frequent fires caused a decrease in termite mound size, whereas in arid nutrient-rich basaltic savannas, fires that occurred at intermediate frequencies and in transitional seasons (i.e., late dry season and late wet season) decreased the degree of spatial overdispersal exhibited by mounds. 4. Overall, our results suggest that termite mounds are resistant to variation in fire seasonality and frequency, likely indicating that ecosystem services provided by mound-building termites will be unaffected by changing fire regimes. However, consideration of changes to termite mound size and distribution could be necessary for land managers in specific savanna types, such as nutrient-rich soils with high mammalian herbivore abundance.

Chronic Ca2+ imaging of cortical neurons with long-term expression of GCaMP-X

Dynamic Ca2+ signals reflect acute changes in membrane excitability and also mediate signaling cascades in chronic processes. In both cases, chronic Ca2+ imaging is often desired but challenged by the cytotoxicity intrinsic to calmodulin (CaM)-based GCaMP, a series of genetically-encoded Ca2+ indicators that have been widely applied. Here, we demonstrate the performance of GCaMP-X in chronic Ca2+ imaging of cortical neurons, where GCaMP-X by design is to eliminate the unwanted interactions between the conventional GCaMP and endogenous (apo)CaM-binding proteins. By expressing in adult mice at high levels over an extended time frame, GCaMP-X showed less damage and improved performance in two-photon imaging of sensory (whisker-deflection) responses or spontaneous Ca2+ fluctuations, in comparison with GCaMP. Chronic Ca2+ imaging of one month or longer was conducted for cultured cortical neurons expressing GCaMP-X, unveiling that spontaneous/local Ca2+ transients progressively developed into autonomous/global Ca2+ oscillations. Along with the morphological indices of neurite length and soma size, the major metrics of oscillatory Ca2+, including rate, amplitude and synchrony were also examined. Dysregulations of both neuritogenesis and Ca2+ oscillations became discernible around 2–3 weeks after virus injection or drug induction to express GCaMP in newborn or mature neurons, which were exacerbated by stronger or prolonged expression of GCaMP. In contrast, neurons expressing GCaMP-X were significantly less damaged or perturbed, altogether highlighting the unique importance of oscillatory Ca2+ to neural development and neuronal health. In summary, GCaMP-X provides a viable solution for Ca2+ imaging applications involving long-time and/or high-level expression of Ca2+ probes.

Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms

Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful but nevertheless produced substantial datasets. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (> 515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (> 11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2,000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in mollusks, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off-target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non-model organisms.

Data for: Ectoparasite population dynamics affected by host body size but not host density or water temperature in a 32-year long time series

Host density, host body size, and ambient temperature have all been positively associated with increases in parasite infection. However, the relative importance of these factors in shaping long-term parasite population dynamics in wild host populations is unknown due to the absence of long-term studies. Here, we examine long-term drivers of gill lice (Copepoda) infections in Arctic charr (Salmonidae) over 32 years. We predicted that host density and body size and water temperature would all positively affect parasite population size and population growth rate. Our results show that fish size was the main driver of gill lice infections in Arctic charr. In addition, Arctic charr became infected at smaller sizes and with more parasites in years of higher brown trout population size. Negative intraguild interactions between brown trout and Arctic charr appear to drive smaller Arctic charr to seek refuge in deeper areas of the lake, thus increasing infection risk. There was no effect of host density on the force of infection, and the relationship between Arctic charr density and parasite mean abundance was negative, possibly due to an encounter-dilution effect. The population densities of host and parasite fluctuated independently of one another. Water temperature had negligible effects on the temporal dynamics of the gill lice population. Understanding long-term drivers of parasite population dynamics is key for research and management. In fish farms, artificially high densities of hosts lead to vast increases in the transmission of parasitic copepods. However, in wild fish populations fluctuating at natural densities, the surface area available for copepodid attachment might be more important than the density of available hosts.

Data for: Using a demographic model to project the long-term effects of fire management on tree biomass in Australian savannas

Tropical savannas are characterised by high primary productivity and high fire frequency, such that much of the carbon captured by vegetation is rapidly returned to the atmosphere. Hence, there have been suggestions that management-driven reductions in savanna fire frequency and/or severity could significantly reduce greenhouse gas emissions and sequester carbon in tree biomass. However, a key knowledge gap is the extent to which savanna tree biomass will respond to modest shifts in fire regimes due to plausible, large-scale management interventions. Here, we: (1) characterise relationships between the frequency and severity of fires and key demographic rates of savanna trees, based on long-term observations in vegetation monitoring plots across northern Australia; (2) use these relationships to develop a process-explicit demographic model describing the effects of fire on savanna tree populations; and (3) use the demographic model to address the question: to what extent is it feasible, through the strategic application of prescribed burning, to increase tree biomass in Australian tropical savannas? Our long-term tree monitoring dataset included observations of 12,344 tagged trees in 236 plots, monitored for between 3 and 24 years. Analysis of this dataset showed that frequent high-severity fires significantly reduced savanna tree recruitment, survival and growth. Our demographic model suggested that: (1) despite the negative effects of frequent high-severity fires on demographic rates, savanna tree biomass appears to be suppressed by only a relatively small amount by contemporary fire regimes, characterised by a mix of low- to high-severity fires; and (2) plausible, management-driven reductions in the frequency of high-severity fires are likely to lead to increases in tree biomass of about 11.0 t DM ha–1 (95% confidence interval: -1.2–20.8) over a century. Accounting for this increase in carbon storage could generate significant carbon credits, worth on average three times those generated annually by current greenhouse gas (methane and nitrous oxide) abatement projects, and has the potential to significantly increase the economic viability of fire/carbon projects, thereby promoting ecologically sustainable management of tropical savannas in Australia and elsewhere. This growing industry has the potential to bring much-needed economic activity to savanna landscapes, without compromising important natural and cultural values.

Data for: Grazing effects of wintering geese on grassland yield: A long-term study from NW-Germany

Conflicts between grassland farming and wintering geese stimulated a long-term study on goose-dependent yield losses. In the period 1996-2018 the loss of dry biomass of the first harvest increased from ca. 15 % to 50 % which corresponds with changes in the number and migratory behaviour of the barnacle goose. In contrast we found no decline in grassland yields with increasing number of greater white-fronted geese. The second harvest was not affected by wintering geese. The present study forms the basis for a fair and comprehensible system of compensation payments fo affected farmers.

opencc-by-4.0Nov 2022View details →

Supporting data for the manuscript entitled: Long-term biodegradation of oil under Arctic Conditions: the Baffin Island Oil Spill (BIOS) revisited after almost four decades.

The potential of an unintentional oil spill from ships or upcoming oil development is rising as the Arctic warms up more. It is crucial to understand how oil behaves in this setting and what influences oil biodegradation in the Arctic. On Baffin Island in the Canadian High Arctic, the Baffin Island Oil Spill (BIOS) project staged a number of simulated oil spills on the backshore zone of beaches in the 1980s. Two BIOS sites were revisited in 2019, about 40 years after the first oil pollution, providing a unique chance to research the long-term weathering of crude oil in Arctic conditions. Here, we demonstrate that even after over 40 years, residual oil is still detectable at these locations. Oil at both locations seems to deteriorate relatively slowly, with estimated loss rates ranging from 1.8 to 2.7% annually and appearing to vary across the two locations. We also demonstrate how the locations' sediment microbial communities are still severely impacted by leftover oil, as seen by a decline in diversity, variations in microbial load, and an enrichment of reported oil-degrading bacteria in contaminated sediments. The most enriched putative oil degraders were found in non-oiled control sediments as well, indicating that these degraders are a normal component of the Arctic sediment microbiome even in the absence of oil. Reconstructed genomes of putative oil degraders indicate that only a portion of these degraders have unique adaptations for growth in psychrothermic environments. This study's findings taken together demonstrate that oil spills in the Arctic can linger and have a lasting, major impact on the environment for decades.

opencc-by-4.0Dec 2022View details →

Global long-term (2010-2020) daily seamless fused XCO2 and XCH4 from GOSAT, OCO-2, and CAMS-EGG4

A novel spatiotemporally self-supervised fusion method is proposed to establish long-term daily seamless XCO2 and XCH4 products from 2010 to 2020 over the globe at grids of 0.25°. More details are provided in https://doi.org/10.5194/essd-2023-28.

Long-term spatially-replicated data show no physical cost to a benefactor species in a facilitative plant-plant interaction

Facilitation is an interaction where one species (the benefactor) positively impacts another (the beneficiary). However, the reciprocal effects of beneficiaries on their benefactors are typically only documented using short-term datasets. We use Azorella selago, a cushion plant species and benefactor, and a co-occurring grass species, Agrostis magellanica, on sub-Antarctic Marion Island, comparing cushion plants and the grasses growing on them over a 13-year period using a correlative approach. We additionally compare the feedback effect of A. magellanica on A. selago identified using our long-term dataset with data collected from a single time period. We hypothesized that A. selago size and vitality would be negatively affected by A. magellanica cover and that the effect of A. magellanica on A. selago would become more negative with increasing beneficiary cover and abiotic-severity, due to, e.g., more intense competition for resources. We additionally hypothesized that A. magellanica cover would increase more on cushion plants with greater dead stem cover, since dead stems do not inhibit grass colonization or growth. The relationship between A. magellanica cover and A. selago size and vitality was not significant in the long-term dataset, and the feedback effect of A. magellanica on A. selago did not vary significantly with altitude or aspect; however, data from a single time period did not consistently identify this same lack of correlation. Moreover, A. selago dead stem cover was not significantly related to an increase in A. magellanica cover over the long term; however, we observed contrasting results from short-term datasets. Long-term datasets may, therefore, be more robust (and practical) for assessing beneficiary feedback effects than conventional approaches, particularly when benefactors are slow-growing. For the first time using a long-term dataset, we show a lack of physical cost to a benefactor species in a facilitative interaction, in contrast to the majority of short-term studies.