| 1. |
- Jamy, Mahwash, et al.
(författare)
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Long-read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity
- 2020
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 20:2, s. 429-443
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Tidskriftsartikel (refereegranskat)abstract
- High-throughput DNA metabarcoding of amplicon sizes below 500 bp has revolutionized the analysis of environmental microbial diversity. However, these short regions contain limited phylogenetic signal, which makes it impractical to use environmental DNA in full phylogenetic inferences. This lesser phylogenetic resolution of short amplicons may be overcome by new long-read sequencing technologies. To test this idea, we amplified soil DNA and used PacBio Circular Consensus Sequencing (CCS) to obtain an 4500-bp region spanning most of the eukaryotic small subunit (18S) and large subunit (28S) ribosomal DNA genes. We first treated the CCS reads with a novel curation workflow, generating 650 high-quality operational taxonomic units (OTUs) containing the physically linked 18S and 28S regions. To assign taxonomy to these OTUs, we developed a phylogeny-aware approach based on the 18S region that showed greater accuracy and sensitivity than similarity-based methods. The taxonomically annotated OTUs were then combined with available 18S and 28S reference sequences to infer a well-resolved phylogeny spanning all major groups of eukaryotes, allowing us to accurately derive the evolutionary origin of environmental diversity. A total of 1,019 sequences were included, of which a majority (58%) corresponded to the new long environmental OTUs. The long reads also allowed us to directly investigate the relationships among environmental sequences themselves, which represents a key advantage over the placement of short reads on a reference phylogeny. Together, our results show that long amplicons can be treated in a full phylogenetic framework to provide greater taxonomic resolution and a robust evolutionary perspective to environmental DNA.
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| 2. |
- Jarvis, Erich D., et al.
(författare)
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Phylogenomic analyses data of the avian phylogenomics project
- 2015
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Ingår i: GigaScience. - : Oxford University Press (OUP). - 2047-217X. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- Background: Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses. Findings: Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides, amino acids, indels, and transposable elements, as well as tree files containing gene trees and species trees. Inferring an accurate phylogeny required generating: 1) A well annotated data set across species based on genome synteny; 2) Alignments with unaligned or incorrectly overaligned sequences filtered out; and 3) Diverse data sets, including genes and their inferred trees, indels, and transposable elements. Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based ExaML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence. Conclusions: The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.
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| 3. |
- 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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| 4. |
- Koptekin, Dilek, et al.
(författare)
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Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean
- 2023
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Ingår i: Current Biology. - : Cell Press. - 0960-9822 .- 1879-0445. ; 33:1, s. 41-57
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Tidskriftsartikel (refereegranskat)abstract
- We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of com-plex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holo-cene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holo-cene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term "the expanding mobility model."Interestingly, this increase in in-ter-regional divergence can be captured by outgroup-f3-based genetic distances, but not by the commonly used FST statistic, due to the sensitivity of FST, but not outgroup-f3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.
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| 5. |
- Stamatakis, George, et al.
(författare)
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Autonomous Maintenance in IoT Networks via AoI-driven Deep Reinforcement Learning
- 2021
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Ingår i: IEEE CONFERENCE ON COMPUTER COMMUNICATIONS WORKSHOPS (IEEE INFOCOM WKSHPS 2021). - : IEEE. - 9781665404433 - 9781665447140
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Konferensbidrag (refereegranskat)abstract
- Internet of Things (IoT) with its growing number of deployed devices and applications raises significant challenges for network maintenance procedures. In this work, we formulate a problem of autonomous maintenance in IoT networks as a Partially Observable Markov Decision Process. Subsequently, we utilize Deep Reinforcement Learning algorithms (DRL) to train agents that decide if a maintenance procedure is in order or not and, in the former case, the proper type of maintenance needed. To avoid wasting the scarce resources of IoT networks we utilize the Age of Information (AoI) metric as a reward signal for the training of the smart agents. AoI captures the freshness of the sensory data which are transmitted by the IoT sensors as part of their normal service provision. Numerical results indicate that AoI integrates enough information about the past and present states of the system to be successfully used in the training of smart agents for the autonomous maintenance of the network.
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| 6. |
- Stamatakis, George J., et al.
(författare)
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Semantics-Aware Active Fault Detection in IoT
- 2022
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Ingår i: 2022 20TH INTERNATIONAL SYMPOSIUM ON MODELING AND OPTIMIZATION IN MOBILE, AD HOC, AND WIRELESS NETWORKS (WIOPT 2022). - : IEEE. - 9783903176492 - 9781665460767 ; , s. 161-168
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Konferensbidrag (refereegranskat)abstract
- In this work we address a problem of active fault detection in an IoT scenario, whereby a monitor probes a remote device in order to detect faults and acquire fresh information. However, probing can have a significant impact on the IoT networks energy and communication resources. To address this problem we utilize Age of Information as a measure of the freshness of information at the monitor and adopt a semanticsaware communication approach between the monitor and the remote device. In semantics-aware communications, the processes of generating and transmitting information are treated jointly in order to consider the importance of information and the purpose of communication. We formulate the problem as a Partially Observable Markov Decision Process and propose a computationally efficient stochastic approximation algorithm to approximate the optimal policy. Finally, we present numerical results that exhibit the advantage of our approach compared to a conventional delay-based probing policy.
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| 7. |
- Stamatakis, George, et al.
(författare)
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Semantics-Aware Active Fault Detection in Status Updating Systems
- 2024
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Ingår i: IEEE Open Journal of the Communications Society. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 2644-125X. ; 5, s. 1182-1196
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Tidskriftsartikel (refereegranskat)abstract
- With its growing number of deployed devices and applications, the Internet of Things (IoT) raises significant challenges for network maintenance procedures. In this work, we address a problem of active fault detection in an IoT scenario, whereby a monitor can probe a remote device to acquire fresh information and facilitate fault detection. However, probing could significantly impact the system's energy and communication resources. To this end, we utilize the Age of Information to measure the freshness of information at the monitor and adopt a semantics-aware communication approach between the monitor and the remote device. In semantics-aware communications, the processes of generating and transmitting information are treated jointly to consider the importance of information and the purpose of communication. We formulate the problem as a Partially Observable Markov Decision Process and show analytically that the optimal policy is of a threshold type. Finally, we use a computationally efficient stochastic approximation algorithm to approximate the optimal policy and present numerical results that exhibit the advantage of our approach compared to a conventional delay-based probing policy.
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