arXiv subjects

Daniel H. Huson

Publications and source records attributed to Daniel H. Huson.

7 recordsLinked to original sources

arXiv2026

Intermediate stages in the origin of metabolism at a phosphorylating hydrothermal vent

The origin of life required the emergence of metabolism, an autocatalytic network of enzymatic reactions that synthesize amino acids, nucleotides and cofactors. At the origin of metabolism there were no enzymes--how did it start? Empirical studies addressing early metabolic evolution are lacking. Harnessing protein structures for metabolic enzymes, we identify intermediate states in primordial metabolic assembly. We show that enzymatic metabolism in the universal common ancestor was incomplete, undergoing final assembly independently in the lineages leading to Bacteria and Archaea. Native transition metals--Fe0, Co0, Ni0, Pd0--served as the catalytic forerunners of both enzymes and cofactors at metabolic origin while phosphite supplied energy, as it phosphorylates AMP to ADP and serine to phosphoserine using native metal catalysts in water. Phosphite and native metals occur in serpentinizing hydrothermal systems, identifying an energy-supplying, catalytic site of metabolic origin. Cofactors liberated nascent metabolism from native metal catalysts, engendering its autocatalytic state.

q-bio.PE↗

arXiv2024

Transformations to simplify phylogenetic networks

The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or lateral gene transfer events between lineages, and so the history of life is more accurately described by a rooted phylogenetic network. Nevertheless, phylogenetic networks may be complex and difficult to interpret, so biologists sometimes prefer a tree that summarises the central tree-like trend of evolution. In this paper, we formally investigate methods for transforming an arbitrary phylogenetic network into a tree (on the same set of leaves) and ask which ones (if any) satisfy a simple consistency condition. This consistency condition states that if we add additional species into a phylogenetic network (without otherwise changing this original network) then transforming this enlarged network into a rooted phylogenetic tree induces the same tree on the original set of species as transforming the original network. We show that the LSA (lowest stable ancestor) tree method satisfies this consistency property, whereas several other commonly used methods (and a new one we introduce) do not. We also briefly consider transformations that convert arbitrary phylogenetic networks to another simpler class, namely normal networks.

q-bio.PE↗

arXiv2021

Normalising phylogenetic networks

Rooted phylogenetic networks provide a way to describe species' relationships when evolution departs from the simple model of a tree. However, networks inferred from genomic data can be highly tangled, making it difficult to discern the main reticulation signals present. In this paper, we describe a natural way to transform any rooted phylogenetic network into a simpler canonical network, which has desirable mathematical and computational properties, and is based only on the 'visible' nodes in the original network. The method has been implemented and we demonstrate its application to some examples.

q-bio.PE↗

arXiv2020

Tegula -- exploring a galaxy of two-dimensional periodic tilings

Periodic tilings play a role in the decorative arts, in construction and in crystal structures. Combinatorial tiling theory allows the systematic generation, visualization and exploration of such tilings of the plane, sphere and hyperbolic plane, using advanced algorithms and software.Here we present a "galaxy" of tilings that consists of the set of all 2.4 billion different types of periodic tilings that have Dress complexity up to 24. We make these available in a database and provide a new program called Tegula that can be used to search and visualize such tilings. Availability: All tilings and software and are open source and available here: https://ab.inf.uni-tuebingen.de/software/tegula.

math.CO↗

arXiv2015

MetaScope - Fast and accurate identification of microbes in metagenomic sequencing data

MetaScope is a fast and accurate tool for analyzing (host-associated) metagenome datasets. Sequence alignment of reads against the host genome (if requested) and against microbial Genbank is performed using a new DNA aligner called SASS. The output of SASS is processed so as to assign all microbial reads to taxa and genes, using a new weighted version of the LCA algorithm. MetaScope is the winner of the 2013 DTRA software challenge entitled "Identify Organisms from a Stream of DNA Sequences".

q-bio.GN↗

arXiv2012

Identifying a species tree subject to random lateral gene transfer

A major problem for inferring species trees from gene trees is that evolutionary processes can sometimes favour gene tree topologies that conflict with an underlying species tree. In the case of incomplete lineage sorting, this phenomenon has recently been well-studied, and some elegant solutions for species tree reconstruction have been proposed. One particularly simple and statistically consistent estimator of the species tree under incomplete lineage sorting is to combine three-taxon analyses, which are phylogenetically robust to incomplete lineage sorting. In this paper, we consider whether such an approach will also work under lateral gene transfer (LGT). By providing an exact analysis of some cases of this model, we show that there is a zone of inconsistency for triplet-based species tree reconstruction under LGT. However, a triplet-based approach will consistently reconstruct a species tree under models of LGT, provided that the expected number of LGT transfers is not too high. Our analysis involves a novel connection between the LGT problem and random walks on cyclic graphs. We have implemented a procedure for reconstructing trees subject to LGT or lineage sorting in settings where taxon coverage may be patchy and illustrate its use on two sample data sets.

q-bio.PE↗

arXiv1999

On Three-Dimensional Space Groups

An entirely new and independent enumeration of the crystallographic space groups is given, based on obtaining the groups as fibrations over the plane crystallographic groups, when this is possible. For the 35 ``irreducible'' groups for which it is not, an independent method is used that has the advantage of elucidating their subgroup relationships. Each space group is given a short ``fibrifold name'' which, much like the orbifold names for two-dimensional groups, while being only specified up to isotopy, contains enough information to allow the construction of the group from the name.

math.MG↗