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Age-dependent timing and routes demonstrate developmental plasticity in a long-distance migratory bird

1. Longitudinal tracking studies have revealed consistent differences in the migration patterns of individuals from the same populations. The sources or processes causing this individual variation are largely unresolved. As a result, it is mostly unknown how much, how fast, and when animals can adjust their migrations to changing environments. 2. We studied the ontogeny of migration in a long-distance migratory shorebird, the black-tailed godwit (Limosa limosa limosa), a species known to exhibit marked individuality in the migratory routines of adults. By observing how and when these individual differences arise, we aimed to elucidate whether individual differences in migratory behaviour are inherited or emerge as a result of developmental plasticity. 3. We simultaneously tracked juvenile and adult godwits from the same breeding area on their south- and northward migrations. To determine how and when individual differences begin to arise, we related juvenile migration routes, timing, and mortality rates to hatch date and year of birth. Then, we compared adult and juvenile migration patterns to identify potential age-dependent differences. 4. In juveniles, the timing of their first southward departure was related to hatch date. However, their subsequent migration routes, orientation, destination, migratory duration, and likelihood of mortality were unrelated to the year or timing of migration, or their sex. Juveniles left the Netherlands after all tracked adults. They then flew non-stop to West Africa more often and incurred higher mortality rates than adults. Some juveniles also took routes and visited stopover sites far outside the well-documented adult migratory corridor. Such juveniles, however, were not more likely to die. 5. We found that juveniles exhibited different migratory patterns than adults, but no evidence that these behaviours are under natural selection. We thus eliminate the possibility that the individual differences observed among adult godwits are present at birth or during their first migration. This adds to the mounting evidence that animals possess the developmental plasticity to change their migration later in life in response to environmental conditions as those conditions are experienced.

opencc-by-4.0Dec 2021View details →

V838 Mon: a decade long waiting

V838 Mon was discovered in 2002 when it underwent a tremendous outburst. The remnants from this event are a cool supergiant embedded in an expanding molecular shell and a hot B3V secondary. After a few years of a relatively stable light curve, the system experienced a short term dimming in the bluer bands in the end of 2006. Right after recovering from the 70 days dimming, a deep eclipse started in early 2007 which took more than 2 years to reach the minimum light. As with the earlier short dimming, the eclipse is much more pronounced in the bluer bands, indicating that it is related to the hot B3V companion. Right after the onset of this eclipse, the hot companion disappeared completely from the spectrum. Our photometric monitoring of the light curve from the past 13 years implies that the eclipse is still on-going, although we record a steady increase in brightness in the blue bands. Moreover, our simultaneous spectral monitoring reveals a yet weak but steadily increasing H alpha emission, suggesting that the B3V companion is slowly recovering.

Data to support publication figures and animation scripts at GitHub: Modeling weather-driven long-distance dispersal of spruce budworm moths (Choristoneura fumiferana)

Long-term studies of insect populations in the North American boreal forest have shown the vital importance of long-distance dispersal to the maintenance and expansion of insect outbreaks. In this work, we extend several concepts established previously in an empirically-based dispersal flight model with recent work on the physiology and behavior of the adult eastern spruce budworm (SBW) moth, Choristoneura fumiferana (Clem.). An outbreak of defoliating SBW in Quebec, ongoing since the mid-2000s, already covers millions of hectares of forests in eastern Canada and threatens to spread into neighboring areas through annual summertime episodes of long-distance dispersal. Such flight events in favorable conditions frequently include billions of SBW moths dispersing in the warm atmospheric boundary layer, typically starting around sunset and often lasting through several hours of wind-driven transport over hundreds of kilometers. Successful SBW dispersal to possibly distant host forest areas depends acutely on the weather. Here we describe the components and results of SBW–pyATM, an open-source individual-based modeling framework developed in Python for the simulation of these weather-driven SBW dispersal events. Using seasonal SBW phenology results from BioSIM at known outbreak locations and high-resolution Weather Research and Forecasting (WRF) model output, we focus on modeling dispersal flights over two successive nights in July 2013 in southern Quebec. Our flight model closely reproduces the SBW spatial patterns and motions observed by weather surveillance radar over the St. Lawrence estuary. With SBW–pyATM we can estimate landing locations for both male and female SBW and the resulting spatial patterns of egg distribution, allowing us eventually to forecast future larval defoliation activity in new locations where immigration could help overcome local limitations on SBW populations. This information could then support forest management decisions where SBW outbreaks threaten valuable resources.

Tspe_v1 (Telopea speciosissima) genome supplementary files for: Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C

Telopea speciosissima, the New South Wales waratah, is an Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Here, we report the first chromosome-level genome for T. speciosissima. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8 % of Embryophyta BUSCOs 'Complete'. We present a new method in Diploidocus (<a href="https://github.com/slimsuite/diploidocus">https://github.com/slimsuite/diploidocus</a>) for classifying, curating and QC-filtering scaffolds, which combines read depths, k-mer frequencies and BUSCO predictions. We also present a new tool, DepthSizer (<a href="https://github.com/slimsuite/depthsizer">https://github.com/slimsuite/depthsizer</a>), for genome size estimation from the read depth of single-copy orthologues and estimate the genome size to be approximately 900 Mb. The largest 11 scaffolds contained 94.1 % of the assembly, conforming to the expected number of chromosomes (2n = 22). Genome annotation predicted 40,158<code> </code>protein-coding genes, 351 rRNAs and 728 tRNAs. We investigated CYCLOIDEA (CYC) genes, which have a role in determination of floral symmetry, and confirm the presence of two copies in the genome. Read depth analysis of 180 'Duplicated' BUSCO genes using a new tool, DepthKopy (<a href="https://github.com/slimsuite/depthkopy">https://github.com/slimsuite/depthkopy</a>), suggests almost all are real duplications, increasing confidence in the annotation and highlighting a possible need to revise the BUSCO set for this lineage. The chromosome-level T. speciosissima reference genome (Tspe_v1) provides an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.

Long-term study shows that increasing body size in response to warmer summers is associated with a higher mortality risk in a long-lived bat species

Change in body size is one of the universal responses to global warming, with most species becoming smaller. While small size in most species corresponds to low individual fitness, small species typically show high population growth rates in cross-species comparisons. It is unclear, there- fore, how climate-induced changes in body size ultimately affect population persistence. Unravelling the relationship between body size, ambient temperature and individual survival is especially important for the conservation of endangered long-lived mammals such as bats. Using an individual-based 24-year dataset from four free-ranging Bechstein'sbat colonies (Myotis bechsteinii), we show for the first time a link between warmer summer temperatures, larger body sizes and increased mortality risk. Our data reveal a crucial time window in June–July, when juveniles grow to larger body sizes in warmer conditions. Body size is also affected by colony size, with larger colonies raising larger offspring. At the same time, larger bats have higher mortality risks throughout their lives. Our results highlight the importance of understanding the link between warmer weather and body size as a fitness-relevant trait for predicting species-specific extinction risks as consequences of global warming.

Long-distance dependencies in birdsong syntax

Songbird syntax is generally thought to be simple, lacking in particular long-distance dependencies in which one element affects choice of another occurring considerably later in the sequence. Here we test for long-distance dependencies in the sequences of songs produced by song sparrows (Melospiza melodia). Song sparrows sing with eventual variety, repeating each song type in a consecutive series termed a "bout." We show that in switching between song types, song sparrows follow a "cycling rule," cycling through their repertoires in close to the minimum possible number of bouts. Song sparrows do not cycle in a set order but rather vary the order of song types from cycle to cycle. Cycling in a variable order strongly implies long-distance dependencies: choice of the next type must depend on the song types sung over the past cycle, in the range of 9-10 bouts. Song sparrows also follow a "bout length rule," whereby the number of repetitions of a song type in a bout is positively associated with the length of the interval until that type recurs. This rule requires even longer-distance dependencies that cross one another; such dependencies are characteristic of more complex levels of syntax than previously attributed to non-human animals.

Coastal squeeze on temperate reefs: long-term shifts in salinity, water quality, and oyster-associated communities

Foundation species such as mangroves, saltmarshes, kelps, seagrasses, and oysters thrive within suitable environmental envelopes as narrow ribbons along the land-sea margin. Therefore, these habitat-forming species and resident fauna are sensitive to modified environmental gradients. For oysters, many estuaries impacted by sea-level rise, channelization, and municipal infrastructure are experiencing saltwater intrusion and water-quality degradation that may alter reef distributions, functions, and services. To explore decadal-scale oyster-reef community patterns across a temperate estuary in response to environmental change, we resampled reefs in the Newport River Estuary (NRE) during 2013-2015 that were previously studied during 1955-1956. We also coalesced historical NRE reef distribution (1880s-2015), salinity (1913-2015), and water-quality driven shellfish closure boundary (1970s-2015) data to document environmental trends that could influence reef ecology and service delivery. Over the last 60-120 years, the entire NRE has shifted toward higher salinities. Consequently, oyster-reef communities have become less distinct across the estuary, manifest by 20-27% lower species turnover and decreased faunal richness among NRE reefs in the 2010s relative to the 1950s. During the 2010s, NRE oyster-reef communities tended to cluster around a euhaline, intertidal-reef type more so than during the 1950s. This followed from faunal expansions farther up-estuary and biological degradation of subtidal reefs as NRE conditions became more marine and favorable for aggressive, reef-destroying taxa. In addition to these biological shifts, the area of suitable bottom on which subtidal-reefs persist (ultimately regulated by up-estuary intrusion of marine waters) and support human harvest (driven by water quality, eroding from up-estuary) has decreased by >75% since the natural history of NRE reefs was first explored. This "coastal squeeze" on harvestable subtidal oysters (reduced from a 4.5-km to a 0.75-km envelope along the NRE's main axis) will likely have consequences regarding the economic incentives for future oyster conservation, as well as the suite of services delivered by remaining shellfish reefs (e.g., biodiversity maintenance, seafood supply). More broadly, these findings exemplify how "squeeze" may be a pervasive concern for biogenic habitats along terrestrial or marine ecotones during an era of intense global change.

opencc-by-4.0Jan 2022View details →

Data for the article entitled "ENVIRONMENTAL AND SOCIAL CORRELATES, AND ENERGETIC CONSEQUENCES OF FITNESS MAXIMISATION ON DIFFERENT MIGRATORY BEHAVIOURS IN A LONG-LIVED SCAVENGER"

Data used in the statistical analyses of the article entitled "ENVIRONMENTAL AND SOCIAL CORRELATES, AND ENERGETIC CONSEQUENCES OF FITNESS MAXIMISATION ON DIFFERENT MIGRATORY BEHAVIOURS IN A LONG-LIVED SCAVENGER"

opencc-by-4.0Jun 2019View details →

Supporting Documents for "The DESC Catchments: Long-term Monitoring of Inland Precambrian Shield Catchment Streamflow and Water Chemistry in Central Ontario, Canada"

Supporting documents for "The DESC Catchments: Long-term Monitoring of Inland Precambrian Shield Catchment Streamflow and Water Chemistry in Central Ontario, Canada"  that are otherwise not readily accessible.  These include historical government reports and relevant laboratory method descriptions from the Ontario Ministry of Environment (Canada). Reports List includes a listing of the 14 documents.

Shearwaters sometimes take long homing detours when denied natural outward journey information

The cognitive processes (learning and processing of information) underpinning long-distance navigation of birds are poorly understood. Here, we utilised the homing motivation of the Manx shearwater to investigate navigational decision making in a wild bird by displacing them 294km to the far side of a large island (the Island of Ireland). Since shearwaters are reluctant to fly over land, the island blocked the direct route home, forcing a navigational decision. Further still, on the far side of the obstacle, we chose a release site where use of local knowledge could facilitate a 20% improvement in route efficiency if shearwaters were able to anticipate and avoid a large inlet giving the appearance of open water in the home direction. We found that no shearwater took the most efficient initial route home, but instead oriented in the home direction (even once the obstacle became visible). Upon reaching the obstacle, four shearwaters subsequently circumnavigated the land mass via the long route, travelling a further 900km as a result. Hence, despite readily orienting homewards immediately after displacement, shearwaters seem unaware of the scale of the obstacle formed by a large land mass despite this being a prominent feature of their regular foraging environment.

Muscle mass of the long head of the biceps following single and double nerve transfer

The aim of this dataset was to compare the effects of single nerve transfer and double nerve transfer on muscle mass. 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, muscle mass was analyzed. Twelve weeks following surgery, after successful reinnervation was confirmed by muscle response to nerve crush and neurotomy, the long head of the biceps muscles were harvested and weighed. To provide internal control, the untreated contralateral muscle heads were also harvested and weighed.

opencc-by-4.0Feb 2022View details →

Data supporting "Can Long-Term Experiments Predict Real Field N and P Balance and System Sustainability? Results from Maize, Winter Wheat, and Soybean Trials Using Mineral and Organic Fertilisers"

Data supporting "Can Long-Term Experiments Predict Real Field N and P Balance and System Sustainability? Results from Maize, Winter Wheat, and Soybean Trials Using Mineral and Organic Fertilisers" by Piccoli et al. (2021) Agronomy 2021, 11, 1472. https://doi.org/10.3390/agronomy11081472

opencc-by-4.0Feb 2022View details →

Supplemental Data for "Plus and minus ends of microtubule respond asymmetrically to kinesin binding by a long range directionally driven allosteric mechanism"

This is raw data set associated with all the figures in the article "Plus and minus ends of microtubule respond asymmetrically to kinesin binding by a long range directionally driven allosteric mechanism" published in Science Advances by Huong T Vu, Zhechun Zhang, Riina Tehver and D. Thirumalai.

opencc-zeroFeb 2022View details →

Empirical tests of habitat selection theory reveal that conspecific density and patch quality, but not habitat amount, drive long-distance immigration in a wild bird

Individuals that disperse long distances from their natal site must select breeding patches with no prior knowledge of patch suitability. Despite decades of theoretical studies examining which cues dispersing individuals should use to select breeding patches, few empirical studies have tested the predictions of these theories at spatial scales relevant to long-distance dispersal in wild animal populations. Here, we use a novel assignment model based on multiple intrinsic markers to quantify natal dispersal distances of Wood Thrush (Hylocichla mustelina) breeding in forest fragments. We show that long-distance natal dispersal in this species is more frequent than commonly assumed for songbirds and that habitat selection by these individuals is driven by density-dependence and patch quality but not the amount of habitat surrounding breeding patches. These results represent an important contribution to understanding habitat selection by dispersing individuals, especially with regards to long-distance dispersal.

opencc-by-4.0Feb 2022View details →

Supplemetary data for the paper "Knockdown of circular RNA hsa_circ_0003307 inhibits synovial inflammation in ankylosing spondylitis by regulating the PI3K/AKT pathway" by Yanyan Fang, Jian Liu*, Yan Long, Jianting Wen, Dan Huang, Ling Xin

Statistical analyses and graphs were performed using Prism 8 software (GraphPad, La Jolla, USA). Age was analyzed using Student's t test (Supplementary Table 1A,B). Expression of circRNA_0003307 in PBMCs was analyzed using Welch's t-test (Supplementary Table 2A,B). CircRNA_0003307 expression in AS-FLS was analyzed using a one-way analysis of variance, then Games-Howell test (Supplementary Table 4A–C). The p-PI3K protein expression in AS-FLS was analyzed using a one-way analysis of variance, then Games-Howell test (Supplementary Table 5A–C). The p-AKT protein expression in AS-FLS was analyzed using a one-way analysis of variance, then Games-Howell test (Supplementary Table 6A–C). The TNF-α levels in AS-FLS was analyzed using a one-way analysis of variance, then Games-Howell test (Supplementary Table 7A–C). The TNFAIP2 levels in AS-FLS was analyzed using a one-way analysis of variance, then Games-Howell test (Supplementary Table 8A–C). Categorical variables were compared using chi-square test. Correlations were assessed using Spearman’s analysis because clinical characteristics were not normally distributed (Supplementary Table 3). A receiver operating characteristic (ROC) curve analysis was performed to judge whether circRNA_0003307 can be used as a diagnostic indicator for AS. P <0.05 indicates that the difference was statistically significant.

opencc-by-4.0Aug 2022View details →

Long-read DNA-Seq of SmAP1 knockout strains

Halobacterium salinarum knockout strains (delta-Ura3: control; delta-Ura3/delta-SmAP1: SmAP1 knockout) were cultured in uracil-supplemented (50 μg/mL) complex medium (CM) until mid-exponential phase (OD600nm = 0.5). The cultures were grown at 37C, under light exposure, and with constant agitation (125 RPM). We collected 2 mL samples and submitted them to DNA extraction using the DNeasy Blood & Tissue kit (QIAGEN), according to the manufacturer's instructions for Gram-negative bacteria. We tested DNA samples for purity and quantity using spectrophotometric and fluorimetric methods, respectively. The samples were prepared for long-read sequencing following the 1D native barcoding genomic DNA protocol using SQK-LSK108 and EXP-NBD103 (Oxford Nanopore Technologies). The equimolar pool of barcoded samples was sequenced using a MinION Mk1B instrument (Oxford Nanopore Technologies) in an FLO-MIN106 flow cell for 24 hours. Three biological replicates were sequenced for each one of the strains (control and SmAP1 knockout). This repository stores the partitioned (eleven parts: aa-ak) compressed directory (tar.gz) containing all the raw reads (fast5 format) output by the MinKNOW software. Experimental design: <table> <tbody> <tr> <td>Barcode</td> <td>Description</td> </tr> <tr> <td>Barcode 01</td> <td>Control, biological replicate 1</td> </tr> <tr> <td>Barcode 02</td> <td>Control, biological replicate 2</td> </tr> <tr> <td>Barcode 03</td> <td>Control, biological replicate 3</td> </tr> <tr> <td>Barcode 04</td> <td>SmAP1 knockout, biological replicate 1</td> </tr> <tr> <td>Barcode 05</td> <td>SmAP1 knockout, biological replicate 2</td> </tr> <tr> <td>Barcode 06</td> <td>SmAP1 knockout, biological replicate 3</td> </tr> </tbody> </table> Instructions to merge files and extract: 1. Download all the files available in this Zenodo entry (smap1_ko_exp_fast5.tar.gz.part_a*; from aa to ak; eleven files) to your preferred directory; 2. Execute the following commands using a Linux or OSX terminal: <pre><code class="language-bash"># concatenate all the files into a single one cat smap1_ko_exp_fast5.tar.gz.part_a* > smap1_ko_exp_fast5.tar.gz # extract the merged file tar zxvf smap1_ko_exp_fast5.tar.gz</code></pre>

opencc-zeroMar 2022View details →

Why the long teeth? Morphometric analysis suggests different selective pressures on functional occlusal traits in Plio-Pleistocene African suids

Neogene and Pleistocene African suids displayed convergent evolutionary trends in the third molar (M3) morphology, with increasingly elongated and higher crowns through time. While these features can prevent premature loss of masticatory functionality and potentially increase long-term reproductive success, changes in dental occlusal traits such as enamel complexity and thickness can also improve chewing efficiency and increase short-term energetic return. While both long-term and short-term benefits can contribute to the thriving of a lineage, the selective pressures associated with each category can be different. To examine how crown elongation correlates with these functional occlusal traits, we selected M3s of Kolpochoerus, Notochoerus, and Metridiochoerus from Kenya and South Africa, dated between 3.0 Ma and 0.4 Ma. To account for dental wear, we used micro-CT imaging of unworn/slightly worn M3s to simulate wear progression within each tooth. We compared morphometric representatives of occlusal enamel complexity and thickness among the specimens following their respective wear trajectories. We found that M3 elongation correlates with higher occlusal complexity and thinner enamel in Notochoerus and Metridiochoerus lineages through time. In Kolpochoerus, enamel complexity and thickness were generally maintained through time, despite M3 elongation. The differences in M3 morphometric trends suggest that Kolpochoerus likely experienced a different set of selective pressures on functional occlusal traits compared to Notochoerus and Metridiochoerus. The shared evolutionary trends of M3 specialization among Notochoerus and Metridiochoerus suggest similar selective pressures on their chewing efficiency and the possibility of a dietary niche overlap in more xeric habitats.

opencc-by-4.0Dec 2020View details →

Long-wave infrared super-resolution wide-field microscopy by sum-frequency generation - experimental data

Experimental Data for "Long-wave infrared super-resolution wide-field microscopy by sum-frequency generation", under consideration at APL, preprint: <a href="https://doi.org/10.48550/arXiv.2112.08112">https://doi.org/10.48550/arXiv.2112.08112</a> Files: readme.txt: explanation of the content SFGmicroscope.h5: microscope data APL_test_script.m: matlab test script generating the relevant figures from the data For more information, please contact Richarda Niemann (niemann@fhi-berlin.mpg.de) or Alex Paarmann (alexander.paarmann@fhi-berlin.mpg.de).

opencc-zeroMar 2022View details →

Dataset for: Short flowers for long tongues: functional specialization in a nocturnal pollination network of an asclepiad in long-tongued hawkmoths (Biotropica)

Since Darwin, very long and narrow floral tubes have been known to represent the main floral morphological feature for specialized long-tongued hawkmoth pollination. However, specialization may be driven by other contrivances instead of floral tube morphology. Asclepiads are plants with a complex floral morphology where primary hawkmoth pollination had never been described. We detailed here the intricate pollination mechanism of the South American asclepiad Schubertia grandiflora, where functional specialization on long-tongued hawkmoth pollinators occurs despite the short floral tube of this species. We studied two plant populations in the Brazilian Cerrado and recorded floral visitors using different approaches, such as light-trapped hawkmoths for pollen analysis, direct field observations, and IR motion-activated cameras. Finally, using a community-level approach we applied an ecological network analysis to identify the realized pollinator niche of S. grandiflora among the available niches in the pollinator community. Throughout a period of 17 years, long-tongued hawkmoths were consistently recorded as the main floral visitors and the only effective pollinators of S. grandiflora. Flowers rely on highly modified corona and gynostegium, and enlarged nectar chambers, to drive visitors and pollination mechanism. Despite relatively short-tube, network analysis placed S. grandiflora in the module including exclusively long-tongued hawkmoth pollinators and the most phenotypically specialized sphingophilous plants in the community. These results represent the first example of functional specialization in long-tongued hawkmoths in an asclepiad species. However, this specialization is uncoupled from the long floral tubes historically associated with the sphingophily syndrome.