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Sökning: WFRF:(Liu Shanlin)

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1.
  • Liu, Shanlin, et al. (författare)
  • Ancient and modem genomes unravel the evolutionary history of the rhinoceros family
  • 2021
  • Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 184:19, s. 4874-4885.e16
  • Tidskriftsartikel (refereegranskat)abstract
    • Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (similar to 16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.
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3.
  • von Seth, Johanna, et al. (författare)
  • Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations
  • 2021
  • Ingår i: Nature Communications. - 2041-1723 .- 2041-1723. ; 12:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Highly endangered species like the Sumatran rhinoceros are at risk from inbreeding. Five historical and 16 modern genomes from across the species range show mutational load, but little evidence for local adaptation, suggesting that future inbreeding depression could be mitigated by assisted gene flow among populations. Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations.
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4.
  • Cappellini, Enrico, et al. (författare)
  • Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny
  • 2019
  • Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 574:7776, s. 103-
  • Tidskriftsartikel (refereegranskat)abstract
    • The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa(1). However, the irreversible post-mortem degradation(2) of ancient DNA has so far limited its recovery-outside permafrost areasto specimens that are not older than approximately 0.5 million years (Myr)(3). By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I-4. and suggested the presence of protein residues in fossils of the Cretaceous period(5)-although with limited phylogenetic use(6). In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch(7-9), using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)(10). Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the Glade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck's rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel-which is the hardest tissue in vertebrates(11), and is highly abundant in the fossil record-can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.
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5.
  • Derst, Christian, et al. (författare)
  • Evolution of neuropeptides in non-pterygote hexapods
  • 2016
  • Ingår i: BMC Evolutionary Biology. - 1471-2148 .- 1471-2148. ; 16
  • Tidskriftsartikel (refereegranskat)abstract
    • BackgroundNeuropeptides are key players in information transfer and act as important regulators of development, growth, metabolism, and reproduction within multi-cellular animal organisms (Metazoa). These short protein-like substances show a high degree of structural variability and are recognized as the most diverse group of messenger molecules. We used transcriptome sequences from the 1KITE (1K Insect Transcriptome Evolution) project to search for neuropeptide coding sequences in 24 species from the non-pterygote hexapod lineages Protura (coneheads), Collembola (springtails), Diplura (two-pronged bristletails), Archaeognatha (jumping bristletails), and Zygentoma (silverfish and firebrats), which are often referred to as “basal” hexapods. Phylogenetically, Protura, Collembola, Diplura, and Archaeognatha are currently placed between Remipedia and Pterygota (winged insects); Zygentoma is the sistergroup of Pterygota. The Remipedia are assumed to be among the closest relatives of all hexapods and belong to the crustaceans.ResultsWe identified neuropeptide precursor sequences within whole-body transcriptome data from these five hexapod groups and complemented this dataset with homologous sequences from three crustaceans (including Daphnia pulex), three myriapods, and the fruit fly Drosophila melanogaster. Our results indicate that the reported loss of several neuropeptide genes in a number of winged insects, particularly holometabolous insects, is a trend that has occurred within Pterygota. The neuropeptide precursor sequences of the non-pterygote hexapods show numerous amino acid substitutions, gene duplications, variants following alternative splicing, and numbers of paracopies. Nevertheless, most of these features fall within the range of variation known from pterygote insects. However, the capa/pyrokinin genes of non-pterygote hexapods provide an interesting example of rapid evolution, including duplication of a neuropeptide gene encoding different ligands.ConclusionsOur findings delineate a basic pattern of neuropeptide sequences that existed before lineage-specific developments occurred during the evolution of pterygote insects.
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6.
  • Nolen, Zachary J., et al. (författare)
  • Historical isolation facilitates species radiation by sexual selection : Insights from Chorthippus grasshoppers
  • 2020
  • Ingår i: Molecular Ecology. - : WILEY. - 0962-1083 .- 1365-294X. ; 29:24, s. 4985-5002
  • Tidskriftsartikel (refereegranskat)abstract
    • Theoretical and empirical studies have shown that species radiations are facilitated when a trait under divergent natural selection is also involved in sexual selection. It is yet unclear how quick and effective radiations are where assortative mating is unrelated to the ecological environment and primarily results from sexual selection. We address this question using sympatric grasshopper species of the genus Chorthippus, which have evolved strong behavioural isolation while lacking noticeable ecomorphological divergence. Mitochondrial genomes suggest that the radiation is relatively recent, dating to the mid-Pleistocene, which leads to extensive incomplete lineage sorting throughout the mitochondrial and nuclear genomes. Nuclear data shows that hybrids are absent in sympatric localities but that all species have experienced gene flow, confirming that reproductive isolation is strong but remains incomplete. Demographic modelling is most consistent with a long period of geographic isolation, followed by secondary contact and extensive introgression. Such initial periods of geographic isolation might facilitate the association between male signaling and female preference, permitting the coexistence of sympatric species that are genetically, morphologically, and ecologically similar, but otherwise behave mostly as good biological species.
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7.
  • Pei, Jun, et al. (författare)
  • Minimizing the makespan for a serial-batching scheduling problem with arbitrary machine breakdown and dynamic job arrival
  • 2016
  • Ingår i: Advanced Manufacturing Technology. - 0885-5684. ; 86:9-12, s. 3315-3331
  • Tidskriftsartikel (refereegranskat)abstract
    • Many dynamic events exist in real manufacturing systems, such as arbitrary machine breakdowns and dynamic job arrivals, which makes the scheduling problem even more complicated. In this paper, we address a serial-batching scheduling problem with the above dynamic events. Jobs need to be processed on the serial-batching machines of two manufacturers and then transported by vehicles to a customer for further processing. The objective of the scheduling problem is to minimize the makespan, and the problem is proved to be strongly NP-hard. Some structural properties and a lower bound of the problem are also proved or derived. On the basis of job arrival times, we divide the problem into two phases and propose different rules regarding these two phases. Based on these properties and rules, a heuristic algorithm is developed to solve the problem and its worst case performance is analyzed. The heuristic algorithm is tested on a large set of randomly generated problem instances, and the relative gaps between the found lower bound and the solutions of the proposed heuristic algorithm are reported. The experimental results illustrate the high efficiency and effectiveness of the proposed heuristic algorithm compared with other four classic approaches.
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8.
  • Pei, Jun, et al. (författare)
  • Scheduling jobs on a single serial-batching machine with dynamic job arrivals and multiple job types
  • 2016
  • Ingår i: Annals of Mathematics and Artificial Intelligence. - 1012-2443 .- 1573-7470. ; 76:1-2, s. 215-228
  • Tidskriftsartikel (refereegranskat)abstract
    • This paper investigates a scheduling model with certain co-existing features of serial-batching, dynamic job arrival, multi-types of job, and setup time. In this proposed model, the jobs of all types are first partitioned into serial batches, which are then processed on a single serial-batching machine with an independent constant setup time for each new batch. In order to solve this scheduling problem, we divide it into two phases based on job arrival times, and we also derive and prove certain constructive properties for these two phases. Relying on these properties, we develop a two-phase hybrid algorithm (TPHA). In addition, a valid lower bound of the problem is also derived. This is used to validate the quality of the proposed algorithm. Computational experiments, both with small- and large-scale problems, are performed in order to evaluate the performance of TPHA. The computational results indicate that TPHA outperforms seven other heuristic algorithms. For all test problems of different job sizes, the average gap percentage between the makespan, obtained using TPHA, and the lower bound does not exceed 5.41 %.
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9.
  • Pei, Jun, et al. (författare)
  • Serial-batching scheduling with time-dependent setup time and effects of deterioration and learning on a single-machine
  • 2017
  • Ingår i: Journal of Global Optimization. - : Springer. - 0925-5001 .- 1573-2916. ; 67:1-2, s. 251-262
  • Tidskriftsartikel (refereegranskat)abstract
    • This paper deals with serial-batching scheduling problems with the effects of deterioration and learning, where time-dependent setup time is also considered. In the proposed scheduling models, all jobs are first partitioned into serial batches, and then all batches are processed on a single serial-batching machine. The actual job processing time is a function of its starting time and position. In addition, a setup time is required when a new batch is processed, and the setup time of the batches is time-dependent, i.e., it is a linear function of its starting time. Structural properties are derived for the problems of minimizing the makespan, the number of tardy jobs, and the maximum earliness. Then, three optimization algorithms are developed to solve them, respectively
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10.
  • Pereira, Ricardo J., et al. (författare)
  • Mind the numt : Finding informative mitochondrial markers in a giant grasshopper genome
  • 2021
  • Ingår i: Journal of Zoological Systematics and Evolutionary Research. - : WILEY. - 0947-5745 .- 1439-0469. ; 59:3, s. 635-645
  • Tidskriftsartikel (refereegranskat)abstract
    • The barcoding of the mitochondrial COX1 gene has been instrumental in cataloguing the tree of life, and in providing insights in the phylogeographic history of species. Yet, this strategy has encountered difficulties in major clades characterized by large genomes, which contain a high frequency of nuclear pseudogenes originating from the mitochondrial genome (numts). Here, we use the meadow grasshopper (Chorthippus parallelus), which possesses a giant genome of similar to 13 Gb, to identify mitochondrial genes that are underrepresented as numts, and test their use as informative phylogeographic markers. We recover the same full mitochondrial sequence using both whole genome and transcriptome sequencing, including functional protein-coding genes and tRNAs. We show that a region of the mitogenome containing the COX1 gene, typically used in DNA barcoding, has disproportionally higher diversity and coverage than the rest of the mitogenome, consistent with multiple insertions of that region into the nuclear genome. By designing new markers in regions of less elevated diversity and coverage, we identify two mitochondrial genes that are less likely to be duplicated as numts. We show that, while these markers show high levels of incomplete lineage sorting between subspecies, as expected for mitochondrial genes, genetic variation reflects their phylogeographic history accurately. These findings allow us to identify useful mitochondrial markers for future studies in C. parallelus, an important biological system for evolutionary biology. More generally, this study exemplifies how non-PCR-based methods using next-generation sequencing can be used to avoid numts in species characterized by large genomes, which have remained challenging to study in taxonomy and evolution.
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