Rapid radiation of Southern Ocean shags in response to receding sea ice

ABSTRACTAimUnderstanding how wild populations respond to climatic shifts is a fundamental goal of biological research in a fast-changing world. The Southern Ocean represents a fascinating system for assessing large-scale climate-driven biological change, as it contains extremely isolated island groups within a predominantly westerly, circumpolar wind and current system. The blue-eyed shags (Leucocarbo spp.) represent a paradoxical Southern Ocean seabird radiation; a circumpolar distribution implies strong dispersal capacity yet their speciose nature suggests local adaptation and isolation. Here we use genetic tools in an attempt to resolve this paradox.LocationSouthern Ocean.Taxa17 species and subspecies of blue-eyed shags (Leucocarbo spp.) across the geographical distribution of the genus.MethodsHere we use mitochondrial and nuclear sequence data to conduct the first global genetic analysis of this group using a temporal phylogenetic framework to test for rapid speciation.ResultsOur analysis reveals remarkably shallow evolutionary histories among island-endemic lineages, consistent with a recent high-latitude circumpolar radiation. This rapid sub-Antarctic expansion contrasts with significantly deeper lineages detected in more temperate regions such as South America and New Zealand that may have acted as glacial refugia. The dynamic history of high-latitude expansions is further supported by ancestral demographic and biogeographic reconstructions.Main conclusionsThe circumpolar distribution of blue-eyed shags, and their highly dynamic evolutionary history, potentially make Leucocarbo a strong sentinel of past and ongoing Southern Ocean ecosystem change given their sensitivity to climatic impacts.

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A novel high-accuracy genome assembly method utilizing a high-throughput workflow

10.1101/2020.11.26.400507 ◽

2020 ◽

Author(s):

Qingdong Zeng ◽

Wenjin Cao ◽

Liping Xing ◽

Guowei Qin ◽

Jianhui Wu ◽

...

Keyword(s):

High Throughput ◽

Genome Assembly ◽

Large Scale ◽

Sequence Data ◽

Physical Map ◽

Bac Library ◽

High Accuracy ◽

Biological Research ◽

Bac Clone ◽

Assembly Method

AbstractAcross domains of biological research using genome sequence data, high-quality reference genome sequences are essential for characterizing genetic variation and understanding the genetic basis of phenotypes. However, the construction of genome assemblies for various species is often hampered by complexities of genome organization, especially repetitive and complex sequences, leading to mis-assembly and missing regions. Here, we describe a high-throughput gold standard genome assembly workflow using a large-scale bacterial artificial chromosome (BAC) library with a refined two-step pooling strategy and the Lamp assembler algorithm. This strategy minimizes the laborious processes of physical map construction and clone-by-clone sequencing, enabling inexpensive sequencing of several thousand BAC clones. By applying this strategy with a minimum tiling path BAC clone library for the short arm of chromosome 2D (2DS) of bread wheat, 98% of BAC sequences, covering 92.7% of the 2DS chromosome, were assembled correctly for this species with a highly complex and repetitive genome. We also identified 48 large mis-assemblies in the reference wheat genome assembly (IWGSC RefSeq v1.0) and corrected these large mis-assemblies in addition to filling 92.2% of the gaps in RefSeq v1.0. Our 2DS assembly represents a new benchmark for the assembly of complex genomes with both high accuracy and efficiency.

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Large-scale spatial variabilities in the humpback whale acoustic presence in the Atlantic sector of the Southern Ocean

Royal Society Open Science ◽

10.1098/rsos.201347 ◽

2020 ◽

Vol 7 (12) ◽

pp. 201347

Author(s):

Elena Schall ◽

Karolin Thomisch ◽

Olaf Boebel ◽

Gabriele Gerlach ◽

Stefanie Spiesecke ◽

...

Keyword(s):

Southern Ocean ◽

High Latitude ◽

Large Scale ◽

Austral Summer ◽

Humpback Whale ◽

Humpback Whales ◽

Stock Management ◽

Atlantic Sector ◽

Acoustic Activity ◽

Passive Acoustic

Southern Hemisphere humpback whales ( Megaptera novaeangliae ) inhabit a wide variety of ecosystems including both low- and high-latitude areas. Understanding the habitat selection of humpback whale populations is key for humpback whale stock management and general ecosystem management. In the Atlantic sector of the Southern Ocean ( ASSO ), the investigation of baleen whale distribution by sighting surveys is temporally restricted to the austral summer. The implementation of autonomous passive acoustic monitoring, in turn, allows the study of vocal baleen whales year-round. This study describes the results of analysing passive acoustic data spanning 12 recording positions throughout the ASSO applying a combination of automatic and manual analysis methods to register humpback whale acoustic activity. Humpback whales were present at nine recording positions with higher acoustic activities towards lower latitudes and the eastern and western edges of the ASSO . During all months, except December (the month with the fewest recordings), humpback whale acoustic activity was registered in the ASSO . The acoustic presence of humpback whales at various locations in the ASSO confirms previous observations that part of the population remains in high-latitude waters beyond austral summer, presumably to feed. The spatial and temporal extent of humpback whale presence in the ASSO suggests that this area may be used by multiple humpback whale breeding populations as a feeding ground.

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annonex2embl: automatic preparation of annotated DNA sequences for bulk submissions to ENA

Bioinformatics ◽

10.1093/bioinformatics/btaa209 ◽

2020 ◽

Vol 36 (12) ◽

pp. 3841-3848

Author(s):

Michael Gruenstaeudl

Keyword(s):

Dna Sequences ◽

Large Scale ◽

Sequence Data ◽

Complete Sequence ◽

Supplementary Information ◽

Biological Research ◽

Sequence Alignments ◽

Easy Integration ◽

Central Pillar ◽

Python Package

Abstract Motivation The submission of annotated sequence data to public sequence databases constitutes a central pillar in biological research. The surge of novel DNA sequences awaiting database submission due to the application of next-generation sequencing has increased the need for software tools that facilitate bulk submissions. This need has yet to be met with the concurrent development of tools to automate the preparatory work preceding such submissions. Results The author introduce annonex2embl, a Python package that automates the preparation of complete sequence flatfiles for large-scale sequence submissions to the European Nucleotide Archive. The tool enables the conversion of DNA sequence alignments that are co-supplied with sequence annotations and metadata to submission-ready flatfiles. Among other features, the software automatically accounts for length differences among the input sequences while maintaining correct annotations, automatically interlaces metadata to each record and displays a design suitable for easy integration into bioinformatic workflows. As proof of its utility, annonex2embl is employed in preparing a dataset of more than 1500 fungal DNA sequences for database submission. Availability and implementation annonex2embl is freely available via the Python package index at http://pypi.python.org/pypi/annonex2embl. Supplementary information Supplementary data are available at Bioinformatics online.

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annonex2embl: automatic preparation of annotated DNA sequences for bulk submissions to ENA

10.1101/820480 ◽

2019 ◽

Cited By ~ 3

Author(s):

Michael Gruenstaeudl

Keyword(s):

Dna Sequences ◽

Large Scale ◽

Sequence Data ◽

Complete Sequence ◽

Biological Research ◽

Sequence Alignments ◽

European Nucleotide Archive ◽

Concurrent Development ◽

Easy Integration ◽

Central Pillar

ABSTRACTMotivationThe submission of annotated sequence data to public sequence databases constitutes a central pillar in biological research. The surge of novel DNA sequences awaiting database submission due to the application of next-generation sequencing has increased the need for software tools that facilitate bulk submissions. This need has yet to be met with a concurrent development of tools to automate the preparatory work preceding such submissions.ResultsI introduce annonex2embl, a Python package that automates the preparation of complete sequence flatfiles for large-scale sequence submissions to the European Nucleotide Archive. The tool enables the conversion of DNA sequence alignments that are co-supplied with sequence annotations and metadata to submission-ready flatfiles. Among other features, the software automatically accounts for length differences among the input sequences while maintaining correct annotations, automatically interlaces metadata to each record, and displays a design suitable for easy integration into bioinformatic workflows. As proof of its utility, annonex2embl is employed in preparing a dataset of more than 1,500 fungal DNA sequences for database submission.

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DMSP/SSUSI observations of the high-latitude dayside aurora (HiLDA

10.5194/egusphere-egu2020-12369 ◽

2020 ◽

Author(s):

Lei Cai ◽

Anita Kullen ◽

Yongliang Zhang ◽

Tomas Karlsson ◽

Andris Vaivads

Keyword(s):

Southern Hemisphere ◽

High Latitude ◽

Large Scale ◽

Current System ◽

Potential Drop ◽

Particle Spectrum ◽

Northern Summer ◽

Open Field Line ◽

Polar Rain ◽

Auroral Emissions

High-latitude dayside aurora (HiLDA) are large-scale discrete arcs or spot-like aurora poleward of the cusp, observed previously in the northern hemisphere by the Viking UV imager [Murphree et al., 1990] and by the IMAGE FUV [Frey et al., 2003]. The particular interest on HiLDA is to understand its formation related to the dayside reconnection and the resulted field-aligned currents (FACs) configuration in the polar cap (open field line region). In addition, the occurrence of HiLDA in the southern hemisphere is not well known.In this study, we investigate the properties of HiLDA using DMSP/SSUSI images from the satellites F16, F17, F18, and F19. The combined data with auroral images from DMSP/SSUSI, ion drift velocity from SSIES, magnetic field perturbations from SSM, and energetic particle spectrum from SSJ make it possible to study the electrodynamics in the vicinity of the HiLDA and its connection the dayside cusp. HiLDA is formed due to monoenergetic electron precipitation (inverted-V structures) with the absence of ion precipitation. The field-aligned potential drop can be up to tens of keV. Applying the current-voltage relation, we suggest accelerated polar rain as the source of HiLDA, indirectly controlled by the solar wind/magnetosheath plasma population. The upward field-aligned current associated with the potential drop is a part of the cusp current system, produced by the dayside reconnection. Both lobe reconnection and reconnection on the duskside flanks play a role in the formation of HiLDA.The occurrence of HiLDA is highly associated with the sunlit hemisphere and IMF By dominated conditions. Our results agree with previous observations, which show that HiLDA occurs during positive By dominated conditions in the northern summer hemisphere. We also confirmed that HiLDA occurs during negative By dominated conditions in the southern hemisphere. In addition, the fine structures of HiLDA are studied.ReferencesMurphree, J. S., Elphinstone, R. D., Hearn, D., and Cogger, L. L. ( 1990), Large&#8208;scale high&#8208;latitude dayside auroral emissions, J. Geophys. Res., 95( A3), 2345&#8211; 2354, doi:.Frey, H. U., Immel, T. J., Lu, G., Bonnell, J., Fuselier, S. A., Mende, S. B., Hubert, B., &#216;stgaard, N., and Le, G. ( 2003), Properties of localized, high latitude, dayside aurora, J. Geophys. Res., 108, 8008, doi:, A4.

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Spacecraft Charging at Geosynchronous Orbit and Large Scale Electric Fields in the High Latitude Ionosphere.

10.21236/ada132031 ◽

1981 ◽

Author(s):

Joan Feynman ◽

William J. Burke

Keyword(s):

Electric Fields ◽

High Latitude ◽

Large Scale ◽

Geosynchronous Orbit ◽

Spacecraft Charging ◽

High Latitude Ionosphere

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Next-Generation Sequencing: An Emerging Tool for Drug Designing

Current Pharmaceutical Design ◽

10.2174/1381612825666190911155508 ◽

2019 ◽

Vol 25 (31) ◽

pp. 3350-3357 ◽

Cited By ~ 1

Author(s):

Pooja Tripathi ◽

Jyotsna Singh ◽

Jonathan A. Lal ◽

Vijay Tripathi

Keyword(s):

Next Generation Sequencing ◽

High Throughput ◽

Large Scale ◽

Massively Parallel Sequencing ◽

Genomic Research ◽

Biological Research ◽

Next Generation ◽

Human Welfare ◽

Drug Designing ◽

Generation Sequencing

Background: With the outbreak of high throughput next-generation sequencing (NGS), the biological research of drug discovery has been directed towards the oncology and infectious disease therapeutic areas, with extensive use in biopharmaceutical development and vaccine production. Method: In this review, an effort was made to address the basic background of NGS technologies, potential applications of NGS in drug designing. Our purpose is also to provide a brief introduction of various Nextgeneration sequencing techniques. Discussions: The high-throughput methods execute Large-scale Unbiased Sequencing (LUS) which comprises of Massively Parallel Sequencing (MPS) or NGS technologies. The Next geneinvolved necessarily executes Largescale Unbiased Sequencing (LUS) which comprises of MPS or NGS technologies. These are related terms that describe a DNA sequencing technology which has revolutionized genomic research. Using NGS, an entire human genome can be sequenced within a single day. Conclusion: Analysis of NGS data unravels important clues in the quest for the treatment of various lifethreatening diseases and other related scientific problems related to human welfare.

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Dynamic Planning of Bicycle Stations in Dockless Public Bicycle-sharing System Using Gated Graph Neural Network

ACM Transactions on Intelligent Systems and Technology ◽

10.1145/3446342 ◽

2021 ◽

Vol 12 (2) ◽

pp. 1-22

Author(s):

Jianguo Chen ◽

Kenli Li ◽

Keqin Li ◽

Philip S. Yu ◽

Zeng Zeng

Keyword(s):

Large Scale ◽

Sequence Data ◽

Location Prediction ◽

City Management ◽

Dynamic Planning ◽

Graph Sequence ◽

Graph Modeling ◽

The Government ◽

Location Clustering ◽

Station Location

Benefiting from convenient cycling and flexible parking locations, the Dockless Public Bicycle-sharing (DL-PBS) network becomes increasingly popular in many countries. However, redundant and low-utility stations waste public urban space and maintenance costs of DL-PBS vendors. In this article, we propose a Bicycle Station Dynamic Planning (BSDP) system to dynamically provide the optimal bicycle station layout for the DL-PBS network. The BSDP system contains four modules: bicycle drop-off location clustering, bicycle-station graph modeling, bicycle-station location prediction, and bicycle-station layout recommendation. In the bicycle drop-off location clustering module, candidate bicycle stations are clustered from each spatio-temporal subset of the large-scale cycling trajectory records. In the bicycle-station graph modeling module, a weighted digraph model is built based on the clustering results and inferior stations with low station revenue and utility are filtered. Then, graph models across time periods are combined to create a graph sequence model. In the bicycle-station location prediction module, the GGNN model is used to train the graph sequence data and dynamically predict bicycle stations in the next period. In the bicycle-station layout recommendation module, the predicted bicycle stations are fine-tuned according to the government urban management plan, which ensures that the recommended station layout is conducive to city management, vendor revenue, and user convenience. Experiments on actual DL-PBS networks verify the effectiveness, accuracy, and feasibility of the proposed BSDP system.

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The Evolution of Life Modes in Stictidaceae, with Three Novel Taxa

Journal of Fungi ◽

10.3390/jof7020105 ◽

2021 ◽

Vol 7 (2) ◽

pp. 105

Author(s):

Vinodhini Thiyagaraja ◽

Robert Lücking ◽

Damien Ertz ◽

Samantha C. Karunarathna ◽

Dhanushka N. Wanasinghe ◽

...

Keyword(s):

New Species ◽

Large Scale ◽

Sequence Data ◽

Large Subunit ◽

Monte Carlo Sampling ◽

Small Subunit ◽

Sensu Stricto ◽

Internal Transcribed Spacers ◽

Character State ◽

Phenotypic Data

Ostropales sensu lato is a large group comprising both lichenized and non-lichenized fungi, with several lineages expressing optional lichenization where individuals of the same fungal species exhibit either saprotrophic or lichenized lifestyles depending on the substrate (bark or wood). Greatly variable phenotypic characteristics and large-scale phylogenies have led to frequent changes in the taxonomic circumscription of this order. Ostropales sensu lato is currently split into Graphidales, Gyalectales, Odontotrematales, Ostropales sensu stricto, and Thelenellales. Ostropales sensu stricto is now confined to the family Stictidaceae, which includes a large number of species that are poorly known, since they usually have small fruiting bodies that are rarely collected, and thus, their taxonomy remains partly unresolved. Here, we introduce a new genus Ostropomyces to accommodate a novel lineage related to Ostropa, which is composed of two new species, as well as a new species of Sphaeropezia, S. shangrilaensis. Maximum likelihood and Bayesian inference analyses of mitochondrial small subunit spacers (mtSSU), large subunit nuclear rDNA (LSU), and internal transcribed spacers (ITS) sequence data, together with phenotypic data documented by detailed morphological and anatomical analyses, support the taxonomic affinity of the new taxa in Stictidaceae. Ancestral character state analysis did not resolve the ancestral nutritional status of Stictidaceae with confidence using Bayes traits, but a saprotrophic ancestor was indicated as most likely in a Bayesian binary Markov Chain Monte Carlo sampling (MCMC) approach. Frequent switching in nutritional modes between lineages suggests that lifestyle transition played an important role in the evolution of this family.

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Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations

Genome Biology and Evolution ◽

10.1093/gbe/evab014 ◽

2021 ◽

Author(s):

Pamela Wiener ◽

Christelle Robert ◽

Abulgasim Ahbara ◽

Mazdak Salavati ◽

Ayele Abebe ◽

...

Keyword(s):

High Altitude ◽

Environmental Variables ◽

Large Scale ◽

Sequence Data ◽

Strong Association ◽

Environmental Adaptation ◽

Whole Genome Sequence ◽

Single Nucleotide Variants ◽

High Altitude Adaptation ◽

Altitude Adaptation

Abstract Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures, are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.

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