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  • Money, Daniel, et al. (author)
  • GeLL : a generalized likelihood library for phylogenetic models
  • 2015
  • In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 31:14, s. 2391-2393
  • Journal article (peer-reviewed)abstract
    • Phylogenetic models are an important tool in molecular evolution allowing us to study the pattern and rate of sequence change. The recent influx of new sequence data in the biosciences means that to address evolutionary questions, we need a means for rapid and easy model development and implementation. Here we present GeLL, a Java library that lets users use text to quickly and efficiently define novel forms of discrete data and create new substitution models that describe how those data change on a phylogeny. GeLL allows users to define general substitution models and data structures in a way that is not possible in other existing libraries, including mixture models and non-reversible models. Classes are provided for calculating likelihoods, optimizing model parameters and branch lengths, ancestral reconstruction and sequence simulation.
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3.
  • Wang, Yucheng, et al. (author)
  • Late Quaternary Dynamics of Arctic Biota from Ancient Environmental Genomics
  • 2021
  • In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 600:7887, s. 86-92
  • Journal article (peer-reviewed)abstract
    • During the last glacial–interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1–8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key fndings include: (1) a relatively homogeneous steppe–tundra fora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher efective precipitation, as well as an increase in the proportion of wetland plants, show negative efects on animal diversity; (5) the persistence of the steppe–tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our fndings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics
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4.
  • Wang, Yucheng, et al. (author)
  • Reply to: When did mammoths go extinct?
  • 2022
  • In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 612:7938, s. 4-6
  • Journal article (peer-reviewed)
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