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"Schmidt, A."
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Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies
Background
Recent developments in third-gen long read sequencing and diploid-aware assemblers have resulted in the rapid release of numerous reference-quality assemblies for diploid genomes. However, assembly of highly heterozygous genomes is still problematic when regional heterogeneity is so high that haplotype homology is not recognised during assembly. This results in regional duplication rather than consolidation into allelic variants and can cause issues with downstream analysis, for example variant discovery, or haplotype reconstruction using the diploid assembly with unpaired allelic contigs.
Results
A new pipeline—Purge Haplotigs—was developed specifically for third-gen sequencing-based assemblies to automate the reassignment of allelic contigs, and to assist in the manual curation of genome assemblies. The pipeline uses a draft haplotype-fused assembly or a diploid assembly, read alignments, and repeat annotations to identify allelic variants in the primary assembly. The pipeline was tested on a simulated dataset and on four recent diploid (phased) de novo assemblies from third-generation long-read sequencing, and compared with a similar tool. After processing with Purge Haplotigs, haploid assemblies were less duplicated with minimal impact on genome completeness, and diploid assemblies had more pairings of allelic contigs.
Conclusions
Purge Haplotigs improves the haploid and diploid representations of third-gen sequencing based genome assemblies by identifying and reassigning allelic contigs. The implementation is fast and scales well with large genomes, and it is less likely to over-purge repetitive or paralogous elements compared to alignment-only based methods. The software is available at
https://bitbucket.org/mroachawri/purge_haplotigs
under a permissive MIT licence.
Journal Article
A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA
Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago
1
had climates resembling those forecasted under future warming
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. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11–19 °C above contemporary values
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,
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. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare
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. Here we report an ancient environmental DNA
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(eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.
Analysis of two-million-year-old ancient environmental DNA from the Kap København Formation in North Greenland shows there was an open boreal forest with diverse plant and animal species, of which several taxa have not previously been detected at the site, representing an ecosystem that has no present-day analogue.
Journal Article
Cultural and contextual perspectives on developmental risk and well-being
\"Developmental risk refers to conditions, characteristics, experiences, or situations with potentially deleterious effects that lead to outcomes later in life that do not meet societal expectations. While risk is typically framed as the statistical probability of a problematic outcome in relation to the general population, the converse notion of well-being is considered in relation to the level of functioning at a given developmental stage. The contributors to this volume provide insight into developmental well-being by examining the ways that culture and context affect outcomes associated with various types of risk, such as those related to oppression, academic performance, family background, life history, physical health, and psychiatric conditions. Even though certain outcomes may seem inevitable in cases involving harmful environments, diseases, and disorders, they are virtually all influenced by complex interactions among individuals, their families, communities, and societies\"-- Provided by publisher.
Book
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.
Journal Article
On the Implications of Ground‐Based High‐Definition Imaging of Io's Surface
The capability to observe temporal changes on Io's surface at optical wavelengths has recently been demonstrated by Conrad et al. (2024, https://doi.org/10.1029/2024GL108609) using new instrumentation at the Large Binocular Telescope. Monitoring of Io's surface morphology would be impactful since preexisting metrics of the degree, location and composition of Io's plume activities are severely limited. Relationships with external data sets appear especially fruitful. Comparisons with spatially resolved data on gas distributions and thermal hots spots would better characterize composition and chemistry in Io's volcanic plumes. Comparisons with measurements remote from Io are posed to advance our understanding of atmospheric escape and how eruptions connect to transient enhancements at disparate size and time scales in the extended neutral clouds and plasma torus. Plain Language Summary Recent innovations in telescope technology offer a new way to monitor volcanic eruptions on Jupiter's moon, Io. Several observatories can measure thermal radiation from Io's active volcanic sites, but this typically signifies lava on its surface, and until now there have been comparatively few ways for observers to identify active eruptions that loft gas and dust to high altitudes. When combined with other observations, this new insight is useful for understanding the nature of volcanically vented materials and how Io loses its atmosphere. Key Points Monitoring of Io's surface morphology presents a new path toward understanding processes in volcanic plumes and atmospheric escape
Journal Article
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%. IQ-TREE is freely available at http://www.cibiv.at/software/iqtree.
Journal Article