| 1. |
- Felsberg, Michael, et al.
(författare)
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The Thermal Infrared Visual Object Tracking VOT-TIR2015 Challenge Results
- 2015
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Ingår i: Proceedings of the IEEE International Conference on Computer Vision. - : Institute of Electrical and Electronics Engineers (IEEE). - 9781467383905 ; , s. 639-651
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Konferensbidrag (refereegranskat)abstract
- The Thermal Infrared Visual Object Tracking challenge 2015, VOTTIR2015, aims at comparing short-term single-object visual trackers that work on thermal infrared (TIR) sequences and do not apply prelearned models of object appearance. VOT-TIR2015 is the first benchmark on short-term tracking in TIR sequences. Results of 24 trackers are presented. For each participating tracker, a short description is provided in the appendix. The VOT-TIR2015 challenge is based on the VOT2013 challenge, but introduces the following novelties: (i) the newly collected LTIR (Linköping TIR) dataset is used, (ii) the VOT2013 attributes are adapted to TIR data, (iii) the evaluation is performed using insights gained during VOT2013 and VOT2014 and is similar to VOT2015.
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| 2. |
- Song, Kai, 1988-, et al.
(författare)
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Conservation genomics in the boreal forest : Population structure and local adaptation in the sibling species Chinese Grouse and Hazel Grouse
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The climate of the world’s arctic regions, including the poles and the Tibetan plateau region, act as a bellwether for global change. On the Tibetan plateau, there are numerous species well adapted to cold environments. The Chinese Grouse and Hazel Grouse are sibling species distributed in the Eurasian subarctic forests of the Tibetan plateau respectively. Conservation genomics are transforming our understanding of organismal responses in a changing Arctic boreal forest. In this study, we used 29 individuals from the sister species Chinese Grouse and Hazel Grouse from the boreal forest in Eurasia. Our results provide insights into the genetic diversity and differentiation in to different geographic populations of the two species. Full genome sequencing of samples covering the distribution area of grouse species throughout the Eurasian boreal forest has enabled us to provide the first analysis of the population structure and introgression. Through selective sweep analysis, we detected that the Chinese Grouse inhabiting the QTP high altitude environment show evidence of having evolved adaptations to hypobaric hypoxia and high ultraviolet radiation.
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| 3. |
- Song, Kai, 1988-, et al.
(författare)
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Demographic history and divergence of sibling grouse species inferred from whole genome sequencing reveal past effects of climate change
- 2021
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Ingår i: BMC Ecology and Evolution. - : BioMed Central (BMC). - 2730-7182. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- Background The boreal forest is one of the largest biomes on earth, supporting thousands of species. The global climate fluctuations in the Quaternary, especially the ice ages, had a significant influence on the distribution of boreal forest, as well as the divergence and evolution of species inhabiting this biome. To understand the possible effects of on-going and future climate change it would be useful to reconstruct past population size changes and relate such to climatic events in the past. We sequenced the genomes of 32 individuals from two forest inhabiting bird species, Hazel Grouse (Tetrastes bonasia) and Chinese Grouse (T. sewerzowi) and three representatives of two outgroup species from Europe and China. Results We estimated the divergence time of Chinese Grouse and Hazel Grouse to 1.76 (0.46-3.37) MYA. The demographic history of different populations in these two sibling species was reconstructed, and showed that peaks and bottlenecks of effective population size occurred at different times for the two species. The northern Qilian population of Chinese Grouse became separated from the rest of the species residing in the south approximately 250,000 years ago and have since then showed consistently lower effective population size than the southern population. The Chinese Hazel Grouse population had a higher effective population size at the peak of the Last Glacial Period (approx. 300,000 years ago) than the European population. Both species have decreased recently and now have low effective population sizes. Conclusions Combined with the uplift history and reconstructed climate change during the Quaternary, our results support that cold-adapted grouse species diverged in response to changes in the distribution of palaeo-boreal forest and the formation of the Loess Plateau. The combined effects of climate change and an increased human pressure impose major threats to the survival and conservation of both species.
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| 4. |
- Song, Kai, 1988-, et al.
(författare)
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Demographics and divergence of the sibling species Chinese Grouse and Hazel Grouse inferred from whole genome sequencing
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The boreal forest is one of the largest biomes on earth, supporting thousands of species. The global climate fluctuations in the Quaternary, especially the ice ages, had a significant influence on the distribution of boreal forest, as well as the divergence and evolution of species inhabiting this biome. To provide insights into the role of recent ice ages in species divergence and population history in southern Eurasian boreal forests, we sequenced the genomes of 32 individuals from the sister species Hazel Grouse (Tetrastes bonasia) and Chinese Grouse (T. sewerzowi) and three representatives of outgroup species from Europe and China. Our results show very different population demographic histories between the sibling species. Using PSMC we show that the peak and bottleneck of effective population size (Ne) occurred at different times; the Hazel Grouse had a peak in the Mid-Pleistocene and a bottleneck during the Last Glacial Period, in contrast to the Chinese Grouse, which peaked with a larger population size after the Hazel Grouse. In addition, the northern population of Chinese Grouse inhabiting the Qilian Mountains became separated from the main population residing in the south and since then consistently showed lower effective population size than the southern population. The Hazel Grouse population in northern China had a higher effective population size at the peak of the Last Glacial Period compared to the European population, which appeared to have gone through a severe bottleneck. As revealed by MSMC modelling, both species have recently decreased and now have low effective population sizes. The results of this study, suggest that differences in the demographic processes that shaped the evolutionary history and distribution for both species, will contribute to the understanding of the biological processes affecting the fauna in boreal forests in Eurasia.
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| 5. |
- Song, Kai, 1988-
(författare)
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Divergence, selection, demographic history and conservation genomics of sibling bird species in boreal forest in Northern Eurasia and the Qinghai-Tibetan Plateau
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- I used two pairs of sibling boreal forest bird species to study divergence, selection, demographics, and conservation in northern Eurasia and the Qinghai-Tibetan Plateau at the microsatellite level (chapter 1) and whole genome level (chapters 2, 3, 4 and 5). In chapter 1, which is the first study to describe genetic diversity of the Sichuan Jay, I used microsatellite markers to estimate genetic differentiation in Sichuan Jay and Siberian Jay populations. The results showed similar levels of genetic variability, strong population structure, and high genetic differentiation between the two species and among different populations. In chapter 2, I used demographic analyses, and found that the Chinese Grouse has experienced substantial changes in population size from the beginning of the last interglacial, with a peak just before the last glacial maximum. The results inferred from the whole genome sequencing and species distribution models support a history of population size fluctuations. In chapter 3 to 5, I used population genomic methods to explore genomic variation, demographic divergence, local adaptation, and inbreeding from 29 whole genome re-sequenced individuals of Chinese Grouse and Hazel Grouse. I found strong evidence for population structure, changing demographic histories, and varying inbreeding levels and genetic load within both species. In Chinese Grouse, an isolated population in the northern part of the species range showed the lowest genetic diversity, high pairwise FST, high LD decay, higher inbreeding and genetic load compared to two other populations. In Hazel Grouse, there were strong population differences and inbreeding levels among the three populations, especially among the Swedish and German populations. The Swedish population likely lost genetic diversity during the re-colonization of the boreal forests in Scandinavia after the last glaciation. Analyses of genetic load showed that purifying selection of mildly deleterious mutations has been more efficient in Hazel Grouse, a species with a larger population size and range compared to Chinese Grouse. However, when I compared the genetic load as the ratio between highly deleterious loss-of-function mutations and synonymous mutations for Chinese Grouse and Hazel Grouse, purifying selection did not seem to have a large effect. My findings show that small, isolated and fragmented populations of forests birds loose genetic variation and may thereby become vulnerable to future challenges and also that populations may track past habitat changes and adapt to local conditions.
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| 6. |
- Song, Kai, 1988-, et al.
(författare)
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Genetic differentiation in Sichuan jay (Perisoreus internigrans) and itssibling species Siberian jay (P. infaustus)
- 2020
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Ingår i: Conservation Genetics. - : Springer Nature. - 1566-0621 .- 1572-9737. ; 21:2, s. 319-327
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Tidskriftsartikel (refereegranskat)abstract
- The Pleistocene ice age and recent forest fragmentation have both played a significant role in shaping the population geneticvariation of boreal coniferous species in the Qinghai-Tibet Plateau (QTP) and Eurasian coniferous forests. The Sichuan jay isone of the least know endemic bird species in QTP coniferous forests in western China while its sibling species, the SiberianJay, is widespread within the coniferous forests in northern Eurasia. Here we used 11 microsatellite markers to assay geneticdiversity across 58 Sichuan jay samples from China and 205 Siberian jay samples from Sweden and Russia. Results showedthree distinct genetic clusters from the Sichuan jay sampling. Furthermore, the pair-wise FST values indicated high geneticdifferentiation not only among the two species but also between Swedish and Russian Siberian jay populations. What ismore, a pattern of isolation by distance was found among the analyzed populations. Our study suggests that targeted
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| 7. |
- Song, Kai, 1988-, et al.
(författare)
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Genomic analysis of demographic history and ecological niche modeling in the endangered Chinese Grouse Tetrastes sewerzowi
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Background: The Quaternary is characterized by marked climatic oscillations between glacial and interglacial periods that had worldwide consequences in forming the contemporary diversity of many populations, species and communities. The origin and evolution of biodiversity in mountainous areas are highly dependent on historical orogenesis and associated climatic changes. The Chinese grouse Tetrastes sewerzowi is a forest-dwelling species endemic to the mountains to the east of the Qinghai–Tibet Plateau, which has been listed as Near Threatened with a decreasing trend by the IUCN because of ongoing deforestation and fragmentation of coniferous forests. Understanding demographic history is important in placing current population status into a broader ecological and evolutionary context.Results: Analysis of the Chinese Grouse genome reveals fluctuation in effective population size throughout the Pleistocene. Populations decreased during early to middle Pleistocene but showed an expansion during late Pleistocene then followed a sharp decline during the last glacial maximum (LGM). Ecological niche modeling indicated that suitable habitat shift between high altitude regions to low altitude regions were due to a changing climate. The result parallels patterns of population size change in Chinese Grouse estimated from PSMC modelling, which suggested an expansion in population size from the last interglacial period and then a peak and a bottleneck occurring at the LGM. Furthermore, the present-day distribution of Chinese Grouse is greatly reduced and will become highly fragmented if boreal forest cover restricts the ecological niche.Conclusions: The Chinese Grouse have experienced substantial population size changes from the beginning to the LIG and reached a peak before the LGM. A sharp decrease and bottleneck happened during the LGM, when the conifer forests were subjected to extensive loss. The results inferred from the whole genome sequencing and species distribution models both support the historical population fluctuation. The distribution of the Chinese Grouse was strongly dependent on the boreal forest cover. To protect the fragmented boreal forest is an essential action to protect the Chinese Grouse.
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| 8. |
- Song, Kai, 1988-, et al.
(författare)
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Genomic analysis of demographic history and ecological niche modeling in the endangered Chinese GrouseTetrastes sewerzowi
- 2020
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Ingår i: BMC Genomics. - : BMC. - 1471-2164. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- Background The Quaternary had worldwide consequences in forming the contemporary diversity of many populations, species and communities, which is characterized by marked climatic oscillations between glacial and interglacial periods. The origin and evolution of biodiversity in mountainous areas are highly dependent on historical orogenesis and associated climatic changes. The Chinese grouseTetrastes sewerzowiis a forest-dwelling species endemic to the mountains to the east of the Qinghai-TibetPlateau, which has been listed as Near Threatened with a decreasing trend by the IUCN because of ongoing deforestation and fragmentation of coniferous forests. It is important to place current population status into a broader ecological and evolutionary context to understand their demographic history. Results Analyses of the Chinese Grouse genome revealed fluctuations throughout the Pleistocene in effective population size. Populations decreased during early to middle Pleistocene but showed an expansion during late Pleistocene which was then followed by a sharp decline during the last glacial maximum (LGM). Ecological niche modeling indicated that a suitable habitat shift between high altitude regions to low altitude regions was due to a changing climate. This result parallels patterns of population size change in Chinese Grouse estimated from PSMC modelling, which suggested an expansion in population size from the last interglacial period (LIG) and then a peak and a bottleneck occurring at the last glacial maximum (LGM). Furthermore, the present-day distribution of Chinese Grouse is greatly reduced and fragmented. It will likely become even more fragmented in the future since coniferous forest cover is threatened in the region of their distribution and the availability of such habitat restricts their ecological niche. Conclusions The Chinese Grouse have experienced substantial population size changes from the beginning to the LIG and reached a peak before the LGM. A sharp decrease and bottleneck occurred during the LGM, when the coniferous forests were subjected to extensive loss. The results inferred from the whole genome sequencing and species distribution models both support historical population fluctuations. The distribution of the Chinese Grouse is strongly dependent on the coniferous forest cover. To protect the fragmented coniferous forests is an essential action to protect the Chinese Grouse.
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| 9. |
- Song, Kai, 1988-, et al.
(författare)
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Improve the roles of nature reserves in conservation of endangered pheasant in a highly urbanized region
- 2020
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Nature reserves play an extraordinarily important role in conserving animal populations and their habitats. However, landscape change and unreasonable zoning designations often render these protected areas inadequate. Therefore, regular evaluation of the efficacy of protected lands is critical for maintaining and improving management strategies. Using species distribution models and GAP analysis, we assessed the changes in suitable habitat for the Brown Eared-pheasant (Crossoptilon mantchuricum) in two Chinese nature reserves between 1995 and 2013. Our results showed that the habitat suitability of Brown Eared-pheasant has changed dramatically during this period, and fragmentation analyses showed an increase in concentration area and decrease in patch area. In particular, our findings show that the national nature reserves need to adjust their ranges to ensure the conservation of this flagship species. Our study further provides a new viewpoint for evaluating the efficacy of protected lands, particularly in highly urbanized regions where conservation goals must be balanced with changing landscapes.
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| 10. |
- Song, Kai, 1988-, et al.
(författare)
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Inbreeding and genetic load in a pair of sibling grouse species : Tetrastes sewersowi and T. bonasia
- 2024
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Ingår i: Avian Research. - : Elsevier. - 2053-7166. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Genetic load and inbreeding are recognized as important factors to be considered in conservation programs. Elevated levels of both can increase the risk of population extinction by negatively impacting fitness-related characters in many species of plants and animals, including humans (inbreeding depression). Genomic techniques are increasingly used in measuring and understanding genetic load and inbreeding and their importance in evolution and conservation. We used whole genome resequencing data from two sibling grouse species in subarctic Eurasia to quantify both. We found a large range of inbreeding measured as FROH (fraction of runs of homozygosity) in individuals from different populations of Chinese Grouse (Tetrastes sewerzowi) and Hazel Grouse (T. bonasia). FROH estimated from genome-wide runs of homozygosity (ROH) ranged from 0.02 to 0.24 among Chinese Grouse populations and from 0.01 to 0.44 in Hazel Grouse. Individuals from a population of Chinese Grouse residing in the Qilian mountains and from the European populations of Hazel Grouse (including samples from Sweden, Germany and Northeast Poland) were the most inbred (FROH ranged from 0.10 to 0.23 and 0.11 to 0.44, respectively). These levels are comparable to other highly inbred populations of birds. Hazel Grouse from northern China and Chinese Grouse residing in the Qinghai-Tibetan Plateau showed relatively lower inbreeding levels. Comparisons of the ratio between deleterious missense mutations and synonymous mutations revealed higher levels in Chinese Grouse as compared to Hazel Grouse. These results are possibly explained by higher fixation rates, mutational melt down, in the range-restricted Chinese Grouse compared to the wide-ranging Hazel Grouse. However, when we compared the relatively more severe class of loss-of-function mutations, Hazel Grouse had slightly higher levels than Chinese Grouse, a result which may indicate that purifying selection (purging) has been more efficient in Chinese Grouse on this class of mutations.
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