| 1. |
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| 2. |
- Jiang, Zhiyong, et al.
(författare)
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Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae)
- 2024
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Ingår i: BMC Biology. - : BioMed Central (BMC). - 1741-7007. ; 22:1
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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.
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| 3. |
- Cao, Qi, et al.
(författare)
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Jointly estimating the most likely driving paths and destination locations with incomplete vehicular trajectory data
- 2023
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Ingår i: Transportation Research, Part C: Emerging Technologies. - 0968-090X. ; 155
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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.
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| 4. |
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| 5. |
- Chen, Yilin, et al.
(författare)
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The combination of genomic offset and niche modelling provides insights into climate change-driven vulnerability
- 2022
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
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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.
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| 6. |
- Faber, Zachary J, et al.
(författare)
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The genomic landscape of core-binding factor acute myeloid leukemias
- 2016
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 48, s. 1551-1556
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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.
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| 7. |
- Ji, Yanzhu, et al.
(författare)
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Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds
- 2022
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 8:35
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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.
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| 8. |
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| 9. |
- Qu, Gang, et al.
(författare)
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Enhancing the Performance of the p-n Heterostructure Electrolyte for Solid Oxide Fuel Cells via A-Site-Deficiency Engineering
- 2023
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Ingår i: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 15:42, s. 49154-49169
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Tidskriftsartikel (refereegranskat)abstract
- Semiconductor ionic electrolytes are attracting growing interest for developing low-temperature solid oxide fuel cells (LT-SOFCs). Our recent study has proposed a p-n heterostructure electrolyte based on perovskite oxide BaCo0.4Fe0.4Zr0.1Y0.1O3-δ (BCFZY) and ZnO, achieving promising fuel cell performance. Herein, to further improve the performance of the heterostructure electrolyte, an A-site-deficiency strategy is used to solely modify BCFZY for regulating the ionic conduction and catalytic activity of the heterostructure. Two new electrolytes, B0.9CFZY-ZnO and B0.8CFZY-ZnO, were developed and systematically studied. The results show that the two samples gain improved ionic conductivity and auxiliary catalytic activity after A-site deficiency as a result of the increment of the surface and interface oxygen vacancies. The single cells with B0.9CFZY-ZnO and B0.8CFZY-ZnO exhibit enhanced peak power outputs at 450-550 °C compared to the cell based on B1.0CFZY-ZnO (typically, 745 and 795 vs 542 mW cm-2 at 550 °C). Particular attention is paid to the impact of A-site deficiency on the interface energy band alignment between BxCFZY and ZnO, which suggests that the p-n heterojunction effect of BxCFZY-ZnO for charge carrier regulation can be tuned by A-site deficiency to enable high proton transport while avoiding fuel cell current leakage. This study thus confirms the feasibility of A-site-deficiency engineering to optimize the performance of the heterostructure electrolyte for developing LT-SOFCs.
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| 10. |
- Qu, Qingming, et al.
(författare)
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What is a pore-canal system?
- 2011
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Ingår i: Program and Abstracts. - Philadelphia : Society of Vertebrate Paleontology. ; , s. 177-177
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 11. |
- Qu, Yanhua, 1974-, et al.
(författare)
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Genetic responses to seasonalvariation in altitudinal stress: whole-genome resequencing ofgreat tit in eastern Himalayas
- 2015
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 5
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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.
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| 12. |
- Qu, Yanhua, 1974-, et al.
(författare)
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Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau.
- 2013
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4, s. 2071-
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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.
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| 13. |
- Qu, Yanhua, 1974-, et al.
(författare)
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Long-term isolation and stability explain high genetic diversity in the Eastern Himalaya.
- 2014
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 23:3, s. 705-20
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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.
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| 14. |
- Qu, Yanhua, 1974-, et al.
(författare)
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The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau
- 2021
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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
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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.
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| 15. |
- Qu, Yanhua, 1974-, et al.
(författare)
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The influence of geological events on the endemism of East Asian birds studied through comparative phylogeography
- 2015
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 42:1, s. 179-192
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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.
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| 16. |
- Savas, Suleyman, et al.
(författare)
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Generating hardware and software for RISC-V cores generated with Rocket Chip generator
- 2021
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Ingår i: Proceedings - 34th IEEE International System-on-Chip Conference, SOCC 2021. - 2164-1676 .- 2164-1706. - 9781665429313 ; 2021-September, s. 89-94
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Konferensbidrag (refereegranskat)abstract
- This paper presents the hardware/software generation backend of a code generation framework. The backend aims at synthesizing complete systems based on RISC-V cores with accelerators from a single-language description. The framework takes the dataflow description of an algorithm as input and generates a combination of hardware (in Chisel) and software (in C) that interacts with the hardware. The hardware can be integrated with RISC-V cores created by the Rocket Chip generator and the software can be executed on these cores.The generated hardware requires similar amount of resources as the hand-written hardware while achieving equal or higher clock rates. As expected, the accelerators perform the calculations faster than the general purpose processor, 5 to 33x in our experiments. When these accelerators are integrated with the Rocket cores, they increase the performance by 25% and 260% in the two use-cases we investigate.
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| 17. |
- She, Huishang, et al.
(författare)
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Quantifying adaptive divergence of the snowfinches in a common landscape
- 2022
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Ingår i: Diversity & distributions. - : Wiley. - 1366-9516 .- 1472-4642. ; 28, s. 2579-2592
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Tidskriftsartikel (refereegranskat)abstract
- AimSpecies living in a shared environment face similar selective pressures and often evolve adaptive divergence to avoid competition. Quantifying phenotypic divergence and its genetic parallelism among sympatric species is important for understanding of ecologically moderated biodiversity. Here, we integrate ecologic, phenotypic and genomic datasets to study to what extent three sympatrically snowfinches (Montifringilla adamsi, Pyrgilauda ruficollis and Onychostruthus taczanowskii) differ in their adaptations in order to co-exist in a shared environment.LocationQinghai–Tibetan Plateau.MethodsWe used principal component analysis to summarize and compare environmental and phenotypic divergence. We compared phenotypes relevant to body and beak sizes (n = 68) because they are indicators of niche and food segregation, thus critical for establishing co-existence of sympatric birds. We used comparative genomics (n = 33) to identify genetic loci that are highly divergent between species as well as loci unique for each of species. Using vector analyses, we integrated correlation and permutation to quantify parallelism between phenotypic and genetic divergences.ResultsWe found that body and beak sizes are significantly different among three snowfinches. The phenotypic differentiations are greater in species that share similar ecological conditions than in those that do not. We showed that genes related to developmental process are over-represented within highly divergent genomic regions and unique genetic loci of each species. We found that the extent of phenotypic divergence between snowfinch pairs is more strongly correlated with the magnitude of divergence in developmental genes than in the whole genome.Main conclusionsAdaptive divergence of sympatric snowfinches is highly constrained on developmental genes. As this genetic divergence is strongly correlated with divergence of the traits related to segregation in niche and food resources, this correlation reflects either causal effects or indirect consequences of ecological mediated changes. Our study provides novel insights into the mechanisms underlying evolutionary versatility and ecological success among sympatric species.
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| 18. |
- Song, Gang, et al.
(författare)
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A zoogeographical boundary between the Palaearctic and Sino-Japanese realms documented by consistent north/south phylogeographical divergences in three woodland birds in eastern China
- 2016
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 43:11, s. 2099-2112
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Tidskriftsartikel (refereegranskat)abstract
- AimThe location of zoogeographical boundaries in eastern China has long been the subject of debate. To identify any north/south genetic divergence between the Palaearctic and Sino-Japanese realms proposed by previous studies, we conducted a comparative phylogeographical study involving three passerine species with wide latitudinal distributions in eastern China.LocationEastern China.MethodsTwo mitochondrial genes and three nuclear introns were amplified and sequenced. Population structures were analysed using intra-specific phylogeny, tcs networks, AMOVA and structure inferences. We tested for evidence of genetic barriers based on pairwise differences. Lineage divergences, demographic dynamics and gene flow between lineages were estimated using Bayesian methods.ResultsA congruent north/south phylogeographical divergence was identified for three species. A geographical barrier was inferred at c. 40° N in eastern China. The population sizes of the northern and southern lineages have both been stable through the late Pleistocene, while multiple divergences were inferred during the early and middle Pleistocene.Main conclusionsOur results suggest a general phylogeographical break in north-eastern China, coinciding with the Palaearctic/Sino-Japanese boundary. Physical blocking of the Yan Mountains and fragmentation of suitable habitat during glacial stages between the north and south probably acted together to provide long-lasting barrier effects. Our comparative phylogeographical approach demonstrates that the Palaearctic/Sino-Japanese boundary may represent a gene-flow barrier even within widespread species.
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| 19. |
- Song, Gang, et al.
(författare)
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Complete taxon sampling of the avian genus Pica (magpies) reveals ancient relictual populations and synchronous Late-Pleistocene demographic expansion across the Northern Hemisphere
- 2018
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Ingår i: Journal of Avian Biology. - : WILEY. - 0908-8857 .- 1600-048X. ; 49:2
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Tidskriftsartikel (refereegranskat)abstract
- Previous studies have suggested that bird populations in east Asia were less affected by Pleistocene climatic fluctuations than those in Europe and North America. However, this is mainly based on comparisons among species. It would be more relevant to analyse geographical populations of widespread species or species complexes. We analyzed two mitochondrial genes and two nuclear introns for all taxa of Pica to investigate 1) which Earth history factors have shaped the lineage divergence, and 2) whether different geographical populations were differently affected by the Pleistocene climatic changes. Our mitochondrial tree recovered three widespread lineages, 1) in east Asia, 2) across north Eurasia, and 3) in North America, respectively, with three isolated lineages in northwest Africa, Arabia and the Qinghai‐Tibet Plateau, respectively. Divergences among lineages took place 1.4–3.1 million yr ago. The northwest African population was sister to the others, which formed two main clades. In one of these, Arabia was sister to Qinghai‐Tibet, and these formed the sister clade to the east Asia clade. The other main clade comprised the North American and north Eurasian clades. There was no or very slight structure within these six geographical clades, including a lack of differentiation between the two North American species black‐billed magpie P. hudsonia and yellow‐billed magpie P. nutalli. Demographic expansion was recorded in the three most widespread lineages after 0.06 Ma. Asymmetric gene flow was recorded in the north Eurasian clade from southwestern Europe eastward, whereas the east Asian clade was rooted in south central China. Our results indicate that the fragmentation of the six clades of Pica was related to climatic cooling and aridification during periods of the Pliocene–Pleistocene. Populations on both sides of the Eurasian continent were similarly influenced by the Pleistocene climate changes and expanded concomitantly with the expansion of steppes. Based on results we also propose a revised taxonomy recognising seven species of Pica.
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| 20. |
- Song, Gang, et al.
(författare)
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Great journey of Great Tits (Parus major group) : Origin, diversification and historical demographics of a broadly distributed bird lineage
- 2020
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Ingår i: Journal of Biogeography. - : WILEY. - 0305-0270 .- 1365-2699. ; 47:7, s. 1585-1598
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Tidskriftsartikel (refereegranskat)abstract
- Aim The Pleistocene glacial cycles play a prominent role in shaping phylogeographical patterns of organisms, while few studies have focused on the regional difference of glacial effects. By acquiring comprehensive knowledge of the origin, diversification and historical demography of an intensively studied passerine species complex, Great Tit, we aim to test the regional variation of the Late Pleistocene glaciation impacts on this widely distributed bird lineage. Location Eurasia and associated peninsulas and archipelagos. Taxa Parus major species complex. Methods Phylogeny, divergence times and demographic dynamics were estimated with Bayesian methods. Population structure, genetic diversity and correlation between genetic and physical distances were estimated based on mtDNA variation. Glacial-to-present distributional changes were assessed via ecological niche modelling (ENM). Results Five major clades (Central Asia, Eastern Asia, Eastern Himalaya, Northern and Western Eurasia and Southern Asia) were detected, with divergence times ranging 1.57-0.50 million years ago. Genetic diversity values and Bayesian skyline plots suggest that the three eastern clades had a deeper population history. A more complex geographic structure was observed in East Asia. Demographic expansion during the last glacial cycle was indicated for all five clades. ENM results showed broad conservatism of traits related to climate tolerances, and generally broader and more continuous distributional patterns under glacial conditions. Main Conclusions The Great Tit complex probably originated in Southeast Asia. Geographic barriers, such as the deserts of Central Asia and the Qinghai-Tibet Plateau appear to be related to the lineage divergence. Late Pleistocene climate cycles influenced both demographic dynamics and divergence, especially in terms of east-west differences in relation to geographic complexity.
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| 21. |
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| 22. |
- Zhang, Dezhi, et al.
(författare)
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Genomic differentiation and patterns of gene flow between two long-tailed tit species (Aegithalos)
- 2017
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Ingår i: Molecular Ecology. - : WILEY. - 0962-1083 .- 1365-294X. ; 26:23, s. 6654-6665
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Tidskriftsartikel (refereegranskat)abstract
- Patterns of heterogeneous genomic differentiation have been well documented between closely related species, with some highly differentiated genomic regions (genomic differentiation islands) spread throughout the genome. Differential levels of gene flow are proposed to account for this pattern, as genomic differentiation islands are suggested to be resistant to gene flow. Recent studies have also suggested that genomic differentiation islands could be explained by linked selection acting on genomic regions with low recombination rates. Here, we investigate genomic differentiation and gene-flow patterns for autosomes using RAD-seq data between two closely related species of long-tailed tits (Aegithalos bonvaloti and A.fuliginosus) in both allopatric and contact zone populations. The results confirm recent or ongoing gene flow between these two species. However, there is little evidence that the genomic regions that were found to be highly differentiated between the contact zone populations are resistant to gene flow, suggesting that differential levels of gene flow is not the cause of the heterogeneous genomic differentiation. Linked selection may be the cause of genomic differentiation islands between the allopatric populations with no or very limited gene flow, but this could not account for the heterogeneous genomic differentiation between the contact zone populations, which show evidence of recent or ongoing gene flow.
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| 23. |
- Zhang, Dezhi, et al.
(författare)
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"Ghost Introgression" As a Cause of Deep Mitochondrial Divergence in a Bird Species Complex
- 2019
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Ingår i: Molecular biology and evolution. - : OXFORD UNIV PRESS. - 0737-4038 .- 1537-1719. ; 36:11, s. 2375-2386
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Tidskriftsartikel (refereegranskat)abstract
- In the absence of nuclear-genomic differentiation between two populations, deep mitochondrial divergence (DMD) is a form of mito-nuclear discordance. Such instances of DMD are rare and might variably be explained by unusual cases of female-linked selection, by male-biased dispersal, by "speciation reversal" or by mitochondrial capture through genetic introgression. Here, we analyze DMD in an Asian Phylloscopus leaf warbler (Aves: Phylloscopidae) complex. Bioacoustic, morphological, and genomic data demonstrate close similarity between the taxa affinis and occisinensis, even though DMD previously led to their classification as two distinct species. Using population genomic and comparative genomic methods on 45 whole genomes, including historical reconstructions of effective population size, genomic peaks of differentiation and genomic linkage, we infer that the form affinis is likely the product of a westward expansion in which it replaced a now-extinct congener that was the donor of its mtDNA and small portions of its nuclear genome. This study provides strong evidence of "ghost introgression" as the cause of DMD, and we suggest that "ghost introgression" may be a widely overlooked phenomenon in nature.
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| 24. |
- Zhang, Dezhi, et al.
(författare)
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Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow
- 2021
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Ingår i: Systematic Biology. - : Oxford University Press. - 1063-5157 .- 1076-836X. ; 70:5, s. 961-975
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic trees based on genome-wide sequence data may not always represent the true evolutionary history for a variety of reasons. One process that can lead to incorrect reconstruction of species phylogenies is gene flow, especially if interspecific gene flow has affected large parts of the genome. We investigated phylogenetic relationships within a clade comprising eight species of passerine birds (Phylloscopidae, Phylloscopus, leafwarblers) using one de novo genome assembly and 78 resequenced genomes. Onthe basis of hypothesis-exclusion trials based on D-statistics, phylogenetic network analysis, and demographic inference analysis, we identified ancient gene flow affecting large parts of the genome between one species and the ancestral lineage of a sister species pair. This ancient gene flow consistently caused erroneous reconstruction of the phylogeny when using large amounts of genome-wide sequence data. In contrast, the true relationships were captured when smaller parts of the genome were analyzed, showing that the "winner-takes-all democratic majority tree" is not necessarily the true species tree. Under this condition, smaller amounts of data may sometimes avoid the effects of gene flow due to stochastic sampling, as hidden reticulation histories are more likely to emerge from the use of larger data sets, especially whole-genome data sets. In addition, we also found that genomic regions affected by ancient gene flow generally exhibited higher genomic differentiation but a lower recombination rate and nucleotide diversity. Our study highlights the importance of considering reticulation in phylogenetic reconstructions in the genomic era.
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| 25. |
- Zhang, Dezhi, et al.
(författare)
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Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae)
- 2023
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Ingår i: SYSTEMATIC BIOLOGY. - 1063-5157 .- 1076-836X.
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Tidskriftsartikel (refereegranskat)abstract
- Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of 4 Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of Emberiza godlewskii (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Analyses based on both the whole mitochondrial genome and similar to 39 kilobases from the non-recombining W chromosome reveal sister relationships between each the northern and southern populations of E. godlewskii with E. cioides and E. cia, respectively. In contrast, the monophyly of E. godlewskii is reflected by the phylogenetic signal of autosomal and Z chromosomal sequence data as well as demographic inference analyses, which-in combination-support the following tree topology: ([{E. godlewskii, E. cia}, E. cioides], E. jankowskii). Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to E. cioides or introgression from an unsampled mitochondrial + W chromosomal lineage of E. cioides into northern E. godlewskii may explain the phylogenetic conflict between the species tree estimated from genome-wide data versus mtDNA/W tree topologies. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.
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| 26. |
- Zhang, Ruiying, et al.
(författare)
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Comparative phylogeography of two widespread magpies : importance of habitat preference and breeding behavior on genetic structure in China.
- 2012
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 65:2, s. 562-72
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Tidskriftsartikel (refereegranskat)abstract
- Historical geological events and climatic changes are believed to have played important roles in shaping the current distribution of species. However, sympatric species may have responded in different ways to such climatic fluctuations. Here we compared genetic structures of two corvid species, the Azure-winged Magpie Cyanopica cyanus and the Eurasian Magpie Pica pica, both widespread but with different habitat dependence and some aspects of breeding behavior. Three mitochondrial genes and two nuclear introns were used to examine their co-distributed populations in East China and the Iberian Peninsula. Both species showed deep divergences between these two regions that were dated to the late Pliocene/early Pleistocene. In the East Chinese clade of C. cyanus, populations were subdivided between Northeast China and Central China, probably since the early to mid-Pleistocene, and the Central subclade showed a significant pattern of isolation by distance. In contrast, no genetic structure was found in the East China populations of P. pica. We suggest that the different patterns in the two species are at least partly explained by ecological differences between them, especially in habitat preference and perhaps also breeding behavior. These dissimilarities in life history traits might have affected the dispersal and survival abilities of these two species differently during environmental fluctuations.
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