| 1. |
- Zhang, Guojie, et al.
(författare)
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Comparative genomics reveals insights into avian genome evolution and adaptation
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1311-1320
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Tidskriftsartikel (refereegranskat)abstract
- Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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| 2. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 3. |
- Blunden, Jessica, et al.
(författare)
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State of the climate in 2013
- 2014
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Ingår i: Bulletin of the American Meteorological Society. - 0003-0007. ; 95
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Tidskriftsartikel (refereegranskat)abstract
- © 2014, American Meteorological Society. All rights reserved. In 2013, the vast majority of the monitored climate variables reported here maintained trends established in recent decades. ENSO was in a neutral state during the entire year, remaining mostly on the cool side of neutral with modest impacts on regional weather patterns around the world. This follows several years dominated by the effects of either La Niña or El Niño events. According to several independent analyses, 2013 was again among the 10 warmest years on record at the global scale, both at the Earth’s surface and through the troposphere. Some regions in the Southern Hemisphere had record or near-record high temperatures for the year. Australia observed its hottest year on record, while Argentina and New Zealand reported their second and third hottest years, respectively. In Antarctica, Amundsen-Scott South Pole Station reported its highest annual temperature since records began in 1957. At the opposite pole, the Arctic observed its seventh warmest year since records began in the early 20th century. At 20-m depth, record high temperatures were measured at some permafrost stations on the North Slope of Alaska and in the Brooks Range. In the Northern Hemisphere extratropics, anomalous meridional atmospheric circulation occurred throughout much of the year, leading to marked regional extremes of both temperature and precipitation. Cold temperature anomalies during winter across Eurasia were followed by warm spring temperature anomalies, which were linked to a new record low Eurasian snow cover extent in May. Minimum sea ice extent in the Arctic was the sixth lowest since satellite observations began in 1979. Including 2013, all seven lowest extents on record have occurred in the past seven years. Antarctica, on the other hand, had above-average sea ice extent throughout 2013, with 116 days of new daily high extent records, including a new daily maximum sea ice area of 19.57 million km2 reached on 1 October. ENSO-neutral conditions in the eastern central Pacific Ocean and a negative Pacific decadal oscillation pattern in the North Pacific had the largest impacts on the global sea surface temperature in 2013. The North Pacific reached a historic high temperature in 2013 and on balance the globally-averaged sea surface temperature was among the 10 highest on record. Overall, the salt content in nearsurface ocean waters increased while in intermediate waters it decreased. Global mean sea level continued to rise during 2013, on pace with a trend of 3.2 mm yr-1 over the past two decades. A portion of this trend (0.5 mm yr-1) has been attributed to natural variability associated with the Pacific decadal oscillation as well as to ongoing contributions from the melting of glaciers and ice sheets and ocean warming. Global tropical cyclone frequency during 2013 was slightly above average with a total of 94 storms, although the North Atlantic Basin had its quietest hurricane season since 1994. In the Western North Pacific Basin, Super Typhoon Haiyan, the deadliest tropical cyclone of 2013, had 1-minute sustained winds estimated to be 170 kt (87.5 m s-1) on 7 November, the highest wind speed ever assigned to a tropical cyclone. High storm surge was also associated with Haiyan as it made landfall over the central Philippines, an area where sea level is currently at historic highs, increasing by 200 mm since 1970. In the atmosphere, carbon dioxide, methane, and nitrous oxide all continued to increase in 2013. As in previous years, each of these major greenhouse gases once again reached historic high concentrations. In the Arctic, carbon dioxide and methane increased at the same rate as the global increase. These increases are likely due to export from lower latitudes rather than a consequence of increases in Arctic sources, such as thawing permafrost. At Mauna Loa, Hawaii, for the first time since measurements began in 1958, the daily average mixing ratio of carbon dioxide exceeded 400 ppm on 9 May. The state of these variables, along with dozens of others, and the 2013 climate conditions of regions around the world are discussed in further detail in this 24th edition of the State of the Climate series.
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| 4. |
- Jarvis, Erich D., et al.
(författare)
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Whole-genome analyses resolve early branches in the tree of life of modern birds
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331
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Tidskriftsartikel (refereegranskat)abstract
- To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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| 5. |
- Li, Cai, et al.
(författare)
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Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment
- 2014
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Ingår i: GigaScience. - 2047-217X. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Background: Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adelie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri]. Results: Phylogenetic dating suggests that early penguins arose similar to 60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from similar to 1 million years ago to similar to 100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology. Conclusions: Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.
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| 6. |
- Liu, Shiping, et al.
(författare)
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Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears
- 2014
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Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 157:4, s. 785-794
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Tidskriftsartikel (refereegranskat)abstract
- Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyper-lipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear using population genomic modeling and show that the species diverged only 479-343 thousand years BP. We find that genes on the polar bear lineage have been under stronger positive selection than in brown bears; nine of the top 16 genes under strong positive selection are associated with cardiomyopathy and vascular disease, implying important reorganization of the cardiovascular system. One of the genes showing the strongest evidence of selection, APOB, encodes the primary lipoprotein component of low-density lipoprotein (LDL); functional mutations in APOB may explain how polar bears are able to cope with life-long elevated LDL levels that are associated with high risk of heart disease in humans.
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| 7. |
- Orlando, Ludovic, et al.
(författare)
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Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
- 2013
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 499:7456, s. 74-
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Tidskriftsartikel (refereegranskat)abstract
- The rich fossil record of equids has made them a model for evolutionary processes(1). Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560-780 thousand years before present (kyr BP)(2,3). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski's horse (E. f. prze-walskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0-4.5 million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus(4,5). We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski's and domestic horse populations diverged 38-72 kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski's horse investigated. This supports the contention that Przewalski's horses represent the last surviving wild horse population(6). We find similar levels of genetic variation among Przewalski's and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski's horse. Such regions could correspond to loci selected early during domestication.
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| 8. |
- Amankwah, Solomon Obiri Yeboah, et al.
(författare)
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Landslide detection from bitemporal satellite imagery using attention-based deep neural networks
- 2022
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Ingår i: Landslides. - : Springer Science and Business Media LLC. - 1612-510X .- 1612-5118. ; 19:10, s. 2459-2471
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Tidskriftsartikel (refereegranskat)abstract
- Torrential rainfall predisposes hills to catastrophic landslides resulting in serious damage to life and property. Landslide inventory maps are therefore essential for rapid response and developing disaster mitigation strategies. Manual mapping techniques are laborious and time-consuming, and thus not ideal in rapid response situations. Automated landslide mapping from optical satellite imagery using deep neural networks (DNNs) is becoming popular. However, distinguishing landslides from other changed objects in optical imagery using backbone DNNs alone is difficult. Attention modules have been introduced recently into the architecture of DNNs to address this problem by improving the discriminative ability of DNNs and suppressing noisy backgrounds. This study compares two state-of-the-art attention-boosted deep Siamese neural networks in mapping rainfall-induced landslides in the mountainous Himalayan region of Nepal using Planetscope (PS) satellite imagery. Our findings confirm that attention networks improve the performance of DNNs as they can extract more discriminative features. The Siamese Nested U-Net (SNUNet) produced the best and most coherent landslide inventory map among the methods in the test area, achieving an F1-score of 0.73, which is comparable to other similar studies. Our findings demonstrate a prospect for application of the attention-based DNNs in rapid landslide mapping and disaster mitigation not only for rainfall-triggered landslides but also for earthquake-triggered landslides.
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| 9. |
- Chen, Zixuan, et al.
(författare)
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Basin-Scale Daily Drought Prediction Using Convolutional Neural Networks in Fenhe River Basin, China
- 2024
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Ingår i: Atmosphere. - 2073-4433. ; 15:2
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Tidskriftsartikel (refereegranskat)abstract
- Drought is a natural disaster that occurs globally and can damage the environment, disrupt agricultural production and cause large economic losses. The accurate prediction of drought can effectively reduce the impacts of droughts. Deep learning methods have shown promise in drought prediction, with convolutional neural networks (CNNs) being particularly effective in handling spatial information. In this study, we employed a deep learning approach to predict drought in the Fenhe River (FHR) basin, taking into account the meteorological conditions of surrounding regions. We used the daily SAPEI (Standardized Antecedent Precipitation Evapotranspiration Index) as the drought evaluation index. Our results demonstrate the effectiveness of the CNN model in predicting drought events 1~10 days in advance. We evaluated the predictions made by the model; the average Nash–Sutcliffe efficiency (NSE) between the predicted and true values for the next 10 days was 0.71. While the prediction accuracy slightly decreased with longer prediction lengths, the model remained stable and effective in predicting heavy drought events that are typically difficult to predict. Additionally, key meteorological variables for drought predictions were identified, and we found that training the CNN model with these key variables led to higher prediction accuracy than training it with all variables. This study approves an effective deep learning approach for daily drought prediction, particularly when considering the meteorological conditions of surrounding regions.
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| 10. |
- Dong, Zhen, et al.
(författare)
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Mapping inundation extents in Poyang Lake area using Sentinel-1 data and transformer-based change detection method
- 2023
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Ingår i: Journal of Hydrology. - : Elsevier BV. - 0022-1694. ; 620
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Tidskriftsartikel (refereegranskat)abstract
- Accurate and timely mapping of inundation extents during flood periods is essential for disaster evaluation and development of rescue strategies. With unique advantages over the optical sensors (e.g., little effect of clouds, and observations at day and night), Synthetic aperture radar (SAR) sensors provide an important data source for mapping inundation, particularly during flood periods. Freely available SAR images from Sentinel-1 have been increasingly used for many applications. This study applied an efficient transformer-based change detection method, bitemporal image transformer (BiT) with bitemporal Sentniel-1 images, to map inundation extents and evolution in Poyang Lake area in 2020. The transformer-based change detection method firstly adopted ResNet for high-level semantic features extraction, and applied a transformer mechanism to refine these features pixel-wise, followed by employing a FCN as the prediction head for generating the results of change detection. Besides, we constructed a water change detection dataset with spatial-and-temporal generalization from bitemporal Sentinel-1 images; this dataset consists of the seasonal variation water samples of Poyang Lake for years. We compared the results from the BiT method with other convolutional neural network (CNN) based methods (STANets and SNUNet). Mapped inundation extents were evaluated with the ground truth visually derived from high spatial resolution images. The evaluation showed the BiT method generated high accurate mapped inundation extents with the F1-score of 95.5%. The BiT model has proven its superior performance in detecting increased water. Based on the results of the BiT method, the variation of inundation extents in Poyang Lake during May-November 2020 was further analyzed. It was found that the water surface coverage of Poyang Lake is the smallest in late May; it gradually increased to the maximum on 14th July, and then began to stabilize and show a significant downward trend before November. The flood distribution map shows that cultivated land has been inundated with the largest area of approximately 600 km2.
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