| 1. |
|
|
| 2. |
-
- 2019
-
Tidskriftsartikel (refereegranskat)
|
|
| 3. |
- Jiang, Zhiyong, et al.
(författare)
-
Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae)
- 2024
-
Ingår i: BMC Biology. - : BioMed Central (BMC). - 1741-7007. ; 22:1
-
Tidskriftsartikel (refereegranskat)abstract
- BackgroundResolving the phylogeny of rapidly radiating lineages presents a challenge when building the Tree of Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that rapidly diversified at the Pliocene-Pleistocene boundary.ResultsHere we investigate the phylogenetic relationships of all species of Prunellidae using a chromosome-level de novo assembly of Prunella strophiata and 36 high-coverage resequenced genomes. We use homologous alignments of thousands of exonic and intronic loci to build the coalescent and concatenated phylogenies and recover four different species trees. Topology tests show a large degree of gene tree-species tree discordance but only 40-54% of intronic gene trees and 36-75% of exonic genic trees can be explained by incomplete lineage sorting and gene tree estimation errors. Estimated branch lengths for three successive internal branches in the inferred species trees suggest the existence of an empirical anomaly zone. The most common topology recovered for species in this anomaly zone was not similar to any coalescent or concatenated inference phylogenies, suggesting presence of anomalous gene trees. However, this interpretation is complicated by the presence of gene flow because extensive introgression was detected among these species. When exploring tree topology distributions, introgression, and regional variation in recombination rate, we find that many autosomal regions contain signatures of introgression and thus may mislead phylogenetic inference. Conversely, the phylogenetic signal is concentrated to regions with low-recombination rate, such as the Z chromosome, which are also more resistant to interspecific introgression.ConclusionsCollectively, our results suggest that phylogenomic inference should consider the underlying genomic architecture to maximize the consistency of phylogenomic signal.
|
|
| 4. |
- Klionsky, Daniel J., et al.
(författare)
-
Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
-
Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
|
|
| 5. |
- Song, Hong-Wei, et al.
(författare)
-
Thermal fatigue on pistons induced by shaped high power laser : Part II: Design of spatial intensity distribution via numerical simulation
- 2008
-
Ingår i: International Journal of Heat and Mass Transfer. - : Elsevier BV. - 0017-9310 .- 1879-2189. ; 51:3-4, s. 768-778
-
Tidskriftsartikel (refereegranskat)abstract
- In the laser induced thermal fatigue simulation test on pistons, the high power laser was transformed from the incident Gaussian beam into a concentric multi-circular pattern with specific intensity ratio. The spatial intensity distribution of the shaped beam, which determines the temperature field in the piston, must be designed before a diffractive optical element (DOE) can be manufactured. In this paper, a reverse method based on finite element model (FEM) was proposed to design the intensity distribution in order to simulate the thermal loadings on pistons. Temperature fields were obtained by solving a transient three-dimensional heat conduction equation with convective boundary conditions at the surfaces of the piston workpiece. The numerical model then was validated by approaching the computational results to the experimental data. During the process, some important parameters including laser absorptivity, convective heat transfer coefficient, thermal conductivity and Biot number were also validated. Then, optimization procedure was processed to find favorable spatial intensity distribution for the shaped beam, with the aid of the validated FEM. The analysis shows that the reverse method incorporated with numerical simulation can reduce design cycle and design expense efficiently. This method can serve as a kind of virtual experimental vehicle as well, which makes the thermal fatigue simulation test more controllable and predictable.
|
|
| 6. |
- Aamodt, K., et al.
(författare)
-
Alignment of the ALICE Inner Tracking System with cosmic-ray tracks
- 2010
-
Ingår i: Journal of Instrumentation. - 1748-0221. ; 5
-
Konferensbidrag (refereegranskat)abstract
- ALICE (A Large Ion Collider Experiment) is the LHC (Large Hadron Collider) experiment devoted to investigating the strongly interacting matter created in nucleus-nucleus collisions at the LHC energies. The ALICE ITS, Inner Tracking System, consists of six cylindrical layers of silicon detectors with three different technologies; in the outward direction: two layers of pixel detectors, two layers each of drift, and strip detectors. The number of parameters to be determined in the spatial alignment of the 2198 sensor modules of the ITS is about 13,000. The target alignment precision is well below 10 mu m in some cases (pixels). The sources of alignment information include survey measurements, and the reconstructed tracks from cosmic rays and from proton-proton collisions. The main track-based alignment method uses the Millepede global approach. An iterative local method was developed and used as well. We present the results obtained for the ITS alignment using about 10(5) charged tracks from cosmic rays that have been collected during summer 2008, with the ALICE solenoidal magnet switched off.
|
|
| 7. |
- Andersson, Anna, et al.
(författare)
-
The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias.
- 2015
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:4, s. 192-330
-
Tidskriftsartikel (refereegranskat)abstract
- Infant acute lymphoblastic leukemia (ALL) with MLL rearrangements (MLL-R) represents a distinct leukemia with a poor prognosis. To define its mutational landscape, we performed whole-genome, exome, RNA and targeted DNA sequencing on 65 infants (47 MLL-R and 18 non-MLL-R cases) and 20 older children (MLL-R cases) with leukemia. Our data show that infant MLL-R ALL has one of the lowest frequencies of somatic mutations of any sequenced cancer, with the predominant leukemic clone carrying a mean of 1.3 non-silent mutations. Despite this paucity of mutations, we detected activating mutations in kinase-PI3K-RAS signaling pathway components in 47% of cases. Surprisingly, these mutations were often subclonal and were frequently lost at relapse. In contrast to infant cases, MLL-R leukemia in older children had more somatic mutations (mean of 6.5 mutations/case versus 1.3 mutations/case, P = 7.15 × 10(-5)) and had frequent mutations (45%) in epigenetic regulators, a category of genes that, with the exception of MLL, was rarely mutated in infant MLL-R ALL.
|
|
| 8. |
- Bhat, Goutam, et al.
(författare)
-
NTIRE 2022 Burst Super-Resolution Challenge
- 2022
-
Ingår i: 2022 IEEE/CVF CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION WORKSHOPS (CVPRW 2022). - : IEEE. - 9781665487399 - 9781665487405 ; , s. 1040-1060
-
Konferensbidrag (refereegranskat)abstract
- Burst super-resolution has received increased attention in recent years due to its applications in mobile photography. By merging information from multiple shifted images of a scene, burst super-resolution aims to recover details which otherwise cannot be obtained using a simple input image. This paper reviews the NTIRE 2022 challenge on burst super-resolution. In the challenge, the participants were tasked with generating a clean RGB image with 4x higher resolution, given a RAW noisy burst as input. That is, the methods need to perform joint denoising, demosaicking, and super-resolution. The challenge consisted of 2 tracks. Track 1 employed synthetic data, where pixel-accurate high-resolution ground truths are available. Track 2 on the other hand used real-world bursts captured from a handheld camera, along with approximately aligned reference images captured using a DSLR. 14 teams participated in the final testing phase. The top performing methods establish a new state-of-the-art on the burst super-resolution task.
|
|
| 9. |
- Cao, Qi, et al.
(författare)
-
Jointly estimating the most likely driving paths and destination locations with incomplete vehicular trajectory data
- 2023
-
Ingår i: Transportation Research, Part C: Emerging Technologies. - 0968-090X. ; 155
-
Tidskriftsartikel (refereegranskat)abstract
- With an ever-increasing deployment density of probe and fixed sensors, massive vehicular trajectory data is available and show a promising foundation to improve the observability of dynamic traffic demand pattern. However, due to technical and privacy issues, the raw trajectories are not always complete and the paths and destinations between discontinuous trajectory nodes are usually missing. This paper proposes a probabilistic method to jointly reconstruct the missing driving path and destination location of vehicles with incomplete trajectory data. One problem-specific HMM-structured model incorporating spatial and temporal analysis (ST-HMM) is constructed to define the matching probability between observed data and possible movement. Two algorithms, namely candidate set generation and best-match search algorithms, are developed to seek the most possible one as matching result. It can implement end-to-end processing from incomplete trajectory data to complete and connective paths and destinations for the target vehicle. The proposed method is tested based on field-test data and city-wide road network. Compared with two benchmark methods, the proposed method improved the matching accuracy in terms of both path identification and destination inference. Additionally, sensitivity analyses on the size of training dataset and candidate set were performed. We believe that experiment results of these sensitivity analyses can help to provide guidance on data sensing and candidate generation.
|
|
| 10. |
- Chen, Guanying, et al.
(författare)
-
(alpha-NaYbF4:Tm3+)/CaF2 Core/Shell Nanoparticles with Efficient Near-Infrared to Near-Infrared Upconversion for High-Contrast Deep Tissue Bioimaging
- 2012
-
Ingår i: ACS Nano. - : American Chemical Society (ACS). - 1936-0851 .- 1936-086X. ; 6:9, s. 8280-8287
-
Tidskriftsartikel (refereegranskat)abstract
- We describe the development of novel and biocompatible core/shell (alpha-NaYbF4:Tm3+)/CaF2 nanoparticles that exhibit highly efficient NIRin-NIROut upconversion (UC) for high contrast and deep bioimaging. When excited at similar to 980 nm, these nanoparticles emit photoluminescence (PL) peaked at similar to 800 nm. The quantum yield of this UC PL under low power density excitation (similar to 0.3 W/cm(2)) is 0.6 +/- 0.1%. This high UC PL efficiency is realized by suppressing surface quenching effects via heteroepitaxial growth of a biocompatible CaF2 shell, which results in a 35-fold increase in the intensity of UC PL from the core. Small-animal whole-body UC PL imaging with exceptional contrast (signal-to-background ratio of 310) is shown using BALB/c mice intravenously injected with aqueously dispersed nanoparticles (700 pmol/kg). High-contrast UC PL imaging of deep tissues is also demonstrated, using a nanoparticle-loaded synthetic fibrous mesh wrapped around rat femoral bone and a cuvette with nanoparticle aqueous dispersion covered with a 3.2 cm thick animal tissue (pork).
|
|
| 11. |
|
|
| 12. |
- Chen, Yilin, et al.
(författare)
-
The combination of genomic offset and niche modelling provides insights into climate change-driven vulnerability
- 2022
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
-
Tidskriftsartikel (refereegranskat)abstract
- Global warming is increasingly exacerbating biodiversity loss. Populations locally adapted to spatially heterogeneous environments may respond differentially to climate change, but this intraspecific variation has only recently been considered when modelling vulnerability under climate change. Here, we incorporate intraspecific variation in genomic offset and ecological niche modelling to estimate climate change-driven vulnerability in two bird species in the Sino-Himalayan Mountains. We found that the cold-tolerant populations show higher genomic offset but risk less challenge for niche suitability decline under future climate than the warm-tolerant populations. Based on a genome-niche index estimated by combining genomic offset and niche suitability change, we identified the populations with the least genome-niche interruption as potential donors for evolutionary rescue, i.e., the populations tolerant to climate change. We evaluated potential rescue routes via a landscape genetic analysis. Overall, we demonstrate that the integration of genomic offset, niche suitability modelling, and landscape connectivity can improve climate change-driven vulnerability assessments and facilitate effective conservation management.
|
|
| 13. |
- Dong, Gang, et al.
(författare)
-
Mobility analysis and kinematic synthesis of a novel 4-DoF parallel manipulator
- 2016
-
Ingår i: Robotica (Cambridge. Print). - 0263-5747 .- 1469-8668.
-
Tidskriftsartikel (refereegranskat)abstract
- This paper proposes a novel parallel manipulator with 1 translational and 3 rotational degrees of freedom, which may be designed as the docking equipment for large-scale component assemblage in the aircraft industry. First, the mobility and kinematic analysis of the novel manipulator is performed using the screw theory and the closed-loop vector method. To evaluate the kinematic performance of the manipulator, its workspace is calculated, and the dimensional homogeneous Jacobian matrix of this manipulator is deduced. Mainly based on a nonlinear programming approach, the kinematic dimensional synthesis is performed to optimise the dimensional parameters of this novel parallel manipulator in a prescribed workspace. The results of this paper may lay a solid foundation for the prototype design and manufacture of the novel parallel manipulator.
|
|
| 14. |
- Faber, Zachary J, et al.
(författare)
-
The genomic landscape of core-binding factor acute myeloid leukemias
- 2016
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 48, s. 1551-1556
-
Tidskriftsartikel (refereegranskat)abstract
- Acute myeloid leukemia (AML) comprises a heterogeneous group of leukemias frequently defined by recurrent cytogenetic abnormalities, including rearrangements involving the core-binding factor (CBF) transcriptional complex. To better understand the genomic landscape of CBF-AMLs, we analyzed both pediatric (n = 87) and adult (n = 78) samples, including cases with RUNX1-RUNX1T1 (n = 85) or CBFB-MYH11 (n = 80) rearrangements, by whole-genome or whole-exome sequencing. In addition to known mutations in the Ras pathway, we identified recurrent stabilizing mutations in CCND2, suggesting a previously unappreciated cooperating pathway in CBF-AML. Outside of signaling alterations, RUNX1-RUNX1T1 and CBFB-MYH11 AMLs demonstrated remarkably different spectra of cooperating mutations, as RUNX1-RUNX1T1 cases harbored recurrent mutations in DHX15 and ZBTB7A, as well as an enrichment of mutations in epigenetic regulators, including ASXL2 and the cohesin complex. This detailed analysis provides insights into the pathogenesis and development of CBF-AML, while highlighting dramatic differences in the landscapes of cooperating mutations for these related AML subtypes.
|
|
| 15. |
- Feng, Shaohong, et al.
(författare)
-
Dense sampling of bird diversity increases power of comparative genomics
- 2020
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
-
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.
|
|
| 16. |
- Holmfeldt, Linda, et al.
(författare)
-
The genomic landscape of hypodiploid acute lymphoblastic leukemia
- 2013
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:3, s. 242-252
-
Tidskriftsartikel (refereegranskat)abstract
- The genetic basis of hypodiploid acute lymphoblastic leukemia (ALL), a subtype of ALL characterized by aneuploidy and poor outcome, is unknown. Genomic profiling of 124 hypodiploid ALL cases, including whole-genome and exome sequencing of 40 cases, identified two subtypes that differ in the severity of aneuploidy, transcriptional profiles and submicroscopic genetic alterations. Near-haploid ALL with 24-31 chromosomes harbor alterations targeting receptor tyrosine kinase signaling and Ras signaling (71%) and the lymphoid transcription factor gene IKZF3 (encoding AIOLOS; 13%). In contrast, low-hypodiploid ALL with 32-39 chromosomes are characterized by alterations in TP53 (91.2%) that are commonly present in nontumor cells, IKZF2 (encoding HELIOS; 53%) and RB1 (41%). Both near-haploid and low-hypodiploid leukemic cells show activation of Ras-signaling and phosphoinositide 3-kinase (PI3K)-signaling pathways and are sensitive to PI3K inhibitors, indicating that these drugs should be explored as a new therapeutic strategy for this aggressive form of leukemia.
|
|
| 17. |
- Hu, Chun, et al.
(författare)
-
Intestinal metabolite compound K of panaxoside inhibits the growth of gastric carcinoma by augmenting apoptosis via Bid-mediated mitochondrial pathway
- 2012
-
Ingår i: Journal of Cellular and Molecular Medicine (Print). - : Wiley-Blackwell. - 1582-1838 .- 1582-4934. ; 16:1, s. 96-106
-
Tidskriftsartikel (refereegranskat)abstract
- Compound K (20-O-beta-D-glucopyranosyl-20(S)-protopanaxadiol, CK), an intestinal bacterial metabolite of panaxoside, has been shown to inhibit tumour growth in a variety of tumours. However, the mechanisms involved are largely unknown. We use human gastric carcinoma cell lines BGC823, SGC7901 and human gastric carcinoma xenograft in nude mice as models to study the mechanisms of CK in gastric cancers. We found that CK significantly inhibits the viabilities of BGC823 and SGC7901 cells in dose- and time-dependent manners. CK-induced BGC823 and SGC7901 cells apoptosis and cell cycle arrest in G2 phase by up-regulation of p21 and down-regulation of cdc2 and cyclin B1. Further studies show that CK induces apoptosis in BGC823 and SGC7901 cells mainly through mitochondria-mediated internal pathway, and that CK induces the translocation of nuclear Bid to mitochondria. Finally, we found that CK effectively inhibited the tumour formation of SGC7901 cells in nude mice. Our studies show that CK can inhibit the viabilities and induce apoptosis of human gastric carcinoma cells via Bid-mediated mitochondrial pathway.
|
|
| 18. |
- Hu, Li-Peng, et al.
(författare)
-
Terbinafine prevents colorectal cancer growth by inducing dNTP starvation and reducing immune suppression
- 2022
-
Ingår i: Molecular Therapy. - : Elsevier BV. - 1525-0024 .- 1525-0016. ; 30:10, s. 3284-3299
-
Tidskriftsartikel (refereegranskat)abstract
- Existing evidence indicates that gut fungal dysbiosis might play a key role in the pathogenesis of colorectal cancer (CRC). We sought to explore whether reversing the fungal dysbiosis by terbinafine, an approved antifungal drug, might inhibit the development of CRC. A population-based study from Sweden identified a total of 185 patients who received terbinafine after their CRC diagnosis and found that they had a decreased risk of death (hazard ratio=0.50) and metastasis (hazard ratio=0.44) compared with patients without terbinafine administration. In multiple mouse models of CRC, administration of terbinafine decreased the fungal load, the fungus-induced myeloid-derived suppressor cell (MDSC) expansion, and the tumor burden. Fecal microbiota transplantation from mice without terbinafine treatment reversed MDSC infiltration and partially restored tumor proliferation. Mechanistically, terbinafine directly impaired tumor cell proliferation by reducing the ratio of nicotinamide adenine dinucleotide phosphate (NADP+) to reduced form of nicotinamide adenine dinucleotide phosphate (NADPH), suppressing the activity of glucose-6-phosphate dehydrogenase (G6PD), resulting in nucleotide synthesis disruption, deoxyribonucleotide (dNTP) starvation and cell cycle arrest. Collectively, terbinafine can inhibit CRC by reversing fungal dysbiosis, suppressing tumor cell proliferation, inhibiting fungus-induced MDSC infiltration, and restoring antitumor immune response.
|
|
| 19. |
- Ji, Yanzhu, et al.
(författare)
-
Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds
- 2022
-
Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 8:35
-
Tidskriftsartikel (refereegranskat)abstract
- The rate of mutation accumulation in germline cells can be affected by cell replication and/or DNA damage, which are further related to life history traits such as generation time and body mass. Leveraging the existing datasets of 233 neoavian bird species, here, we investigated whether generation time and body mass contribute to the interspecific variation of orthologous microsatellite length, transposable element (TE) length, and deletion length and how these genomic attributes affect genome sizes. In nonpasserines, we found that generation time is correlated to both orthologous microsatellite length and TE length, and body mass is negatively correlated to DNA deletions. These patterns are less pronounced in passerines. In all species, we found that DNA deletions relate to genome size similarly as TE length, suggesting a role of body mass dynamics in genome evolution. Our results indicate that generation time and body mass shape the evolution of genomic attributes in neoavian birds.
|
|
| 20. |
|
|
| 21. |
- Qu, Yanhua, 1974-, et al.
(författare)
-
Genetic responses to seasonalvariation in altitudinal stress: whole-genome resequencing ofgreat tit in eastern Himalayas
- 2015
-
Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 5
-
Tidskriftsartikel (refereegranskat)abstract
- Species that undertake altitudinal migrations are exposed to a considerable seasonal variationin oxygen levels and temperature. How they cope with this was studied in a population of greattit (Parus major) that breeds at high elevations and winters at lower elevations in the easternHimalayas. Comparison of population genomics of high altitudinal great tits and those living inlowlands revealed an accelerated genetic selection for carbohydrate energy metabolism (aminosugar, nucleotide sugar metabolism and insulin signaling pathways) and hypoxia response (PI3K-akt,mTOR and MAPK signaling pathways) in the high altitudinal population. The PI3K-akt, mTOR andMAPK pathways modulate the hypoxia-inducible factors, HIF-1α and VEGF protein expression thusindirectly regulate hypoxia induced angiogenesis, erythropoiesis and vasodilatation. The strategiesobserved in high altitudinal great tits differ from those described in a closely related species onthe Tibetan Plateau, the sedentary ground tit (Parus humilis). This species has enhanced selectionin lipid-specific metabolic pathways and hypoxia-inducible factor pathway (HIF-1). Comparativepopulation genomics also revealed selection for larger body size in high altitudinal great tits.
|
|
| 22. |
- Qu, Yanhua, 1974-, et al.
(författare)
-
Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau.
- 2013
-
Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4, s. 2071-
-
Tidskriftsartikel (refereegranskat)abstract
- The ground tit (Parus humilis) is endemic to the Tibetan plateau. It is a member of family Paridae but it was long thought to be related to the ground jays because of their morphological similarities. Here we present the ground tit's genome and re-sequence two tits and one ground jay, to clarify this controversially taxonomic status and uncover its genetic adaptations to the Tibetan plateau. Our results show that ground tit groups with two tits and it diverges from them between 7.7 and 9.9 Mya. Compared with other avian genomes, ground tit shows expansion in genes linked to energy metabolism and contractions in genes involved in immune and olfactory perception. We also found positively selected and rapidly evolving genes in hypoxia response and skeletal development. These results indicated that ground tit evolves basic strategies and 'tit-to-jay' change for coping with the life in an extreme environment.
|
|
| 23. |
- Qu, Yanhua, 1974-, et al.
(författare)
-
Long-term isolation and stability explain high genetic diversity in the Eastern Himalaya.
- 2014
-
Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 23:3, s. 705-20
-
Tidskriftsartikel (refereegranskat)abstract
- China's Southwest Mountainous Region in Eastern Himalaya is a ‘biodiversity hotspot’ of global interest for conservation. Yet little is known about what has driven this unique diversity. The dramatic topography of the Southwest Mountainous Region resulting from the tectonic uplift during the late Pliocene leads to dramatic ecological stratification, which creates physical barriers to migration and isolates organisms into different subregions and mountain systems. This agrees with the observation that the phylogeographical patterns found in four species of birds (Alcippe morrisonia, Stachyridopsis ruficeps, Parus monticolus and Aegithalos concinnus) distributed in this region are characterized by deep splits between lineages that coalesce between 0.8 and 2.1 Ma. Unlike other regions at this latitude, the Southwest Mountainous Region was largely unaffected by the Pleistocene glaciations. Genetically isolated populations of these birds could thus be maintained throughout the Pleistocene in these rather stable montane environments. In comparison, we found radically different phylogeographical patterns in populations of the same four species distributed in the adjacent lowland, the Central China region. This region has a distinctly different geological history with dramatic, climate-induced shifts in vegetation during the Pleistocene. Here, we found a considerably less geographical structure in the genetic variation and a much younger coalescence time (0.3-0.7 Ma). We also found evidence of genetic bottlenecks during the glacial periods and gene flow during the interglacial expansions. We conclude that the high genetic diversity in the Southwest Mountainous Region results from a long-term in situ diversification within these evolutionary isolated and environment stable montane habitats.
|
|
| 24. |
- Qu, Yanhua, 1974-, et al.
(författare)
-
The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau
- 2021
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 10.1073/pnas.2012398118:13, s. e2012398118-e2012398118
-
Tidskriftsartikel (refereegranskat)abstract
- Species in a shared environment tend to evolve similar adaptations under the influence of their phylogenetic context. Using snowfinches, a monophyletic group of passerine birds (Passeridae), we study the relative roles of ancestral and species-specific adaptations to an extreme high-elevation environment, the Qinghai–Tibet Plateau. Our ancestral trait reconstruction shows that the ancestral snowfinch occupied high elevations and had a larger body mass than most nonsnowfinches in Passeridae. Subsequently, this phenotypic adaptation diversified in the descendant species. By comparing high-quality genomes from representatives of the three phylogenetic lineages, we find that about 95% of genes under positive selection in the descendant species are different from those in the ancestor. Consistently, the biological functions enriched for these species differ from those of their ancestor to various degrees (semantic similarity values ranging from 0.27 to 0.5), suggesting that the three descendant species have evolved divergently from the initial adaptation in their common ancestor. Using a functional assay to a highly selective gene, DTL, we demonstrate that the nonsynonymous substitutions in the ancestor and descendant species have improved the repair capacity of ultraviolet-induced DNA damage. The repair kinetics of the DTL gene shows a twofold to fourfold variation across the ancestor and the descendants. Collectively, this study reveals an exceptional case of adaptive evolution to high-elevation environments, an evolutionary process with an initial adaptation in the common ancestor followed by adaptive diversification of the descendant species.
|
|
| 25. |
- Qu, Yanhua, 1974-, et al.
(författare)
-
The influence of geological events on the endemism of East Asian birds studied through comparative phylogeography
- 2015
-
Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 42:1, s. 179-192
-
Tidskriftsartikel (refereegranskat)abstract
- Aim: East Asia is known for its exceptionally high biological diversity and endemism. Various geological and climatic events during the Pliocene and Pleistocene have been invoked to explain this high endemism, and these processes have had different impacts on different organisms. Herein, we investigate the relative role of these historical processes in the genetic evidence for endemism of intraspecific lineages of two East Asian species: the grey-cheeked fulvetta (Alcippe morrisonia) and the red-headed tree babbler (Stachyridopsis ruficeps).Location: East Asia.Methods: We studied the genetic structure based on mitochondrial and nuclear DNA and evaluated the phylogeographical lineages using coalescent species tree approaches. The influences of different historical processes on diversification among phylogeographical lineages were analysed using coalescent models. We tested correlations between ecological divergence and phylogeographical splits.Results: The genetic structure analysis and species tree estimation revealed three deeply divergent lineages within both species. One lineage is endemic to the mountains of Southwest China and the other to Taiwan. Coalescent simulations suggested that lineage diversification mostly occurred during the late Pliocene. Within this time frame, uplift of the mountains of Southwest China and formation of the island of Taiwan are geological events consistent with the geographical isolation and ecological niche divergence of these phylogeographical lineages.Main conclusions: Our results suggest that the main driver of avian endemism in East Asia was the formation of new montane and island habitats following the uplift of the mountains of Southwest China and formation of the island of Taiwan in the Pliocene. However, the populations in the two regions were affected differently by the climatic oscillations during the Pleistocene. The mountains of Southwest China were climatically stable during glaciations,allowing populations to persist throughout the Pleistocene and maintain their genetic uniqueness. In contrast, glaciations resulted in lowered sea levels, allowing dispersal between the island of Taiwan and mainland China, thus obscuring the genetic endemism of the Taiwanese populations.
|
|
