An OWL representation of parts of the Geographic Metadata model described in ISO 19115:2003 with Corrigendum 2006 - LI Package @en

The forces driving the accumulation and removal of non-coding DNA and ultimately the evolution of genome size in complex organisms are intimately linked to genome structure and organisation. Our analysis provides a novel method for capturing the regional variation of lineage-specific DNA gain and loss events in their respective genomic contexts. To further understand this connection we used comparative genomics to identify genome-wide individual DNA gain and loss events in the human and mouse genomes. Focusing on the distribution of DNA gains and losses, relationships to important structural features and potential impact on biological processes, we found that in autosomes, DNA gains and losses both followed separate lineage-specific accumulation patterns. However, in both species chromosome X was particularly enriched for DNA gain, consistent with its high L1 retrotransposon content required for X inactivation. We found that DNA loss was associated with gene-rich open chromatin regions and DNA gain events with gene-poor closed chromatin regions. Additionally, we found that DNA loss events tended to be smaller than DNA gain events suggesting that they were able to accumulate in gene-rich open chromatin regions due to their reduced capacity to interrupt gene regulatory architecture. GO term enrichment showed that mouse loss hotspots were strongly enriched for terms related to developmental processes. However, these genes were also located in regions with a high density of conserved elements, suggesting that despite high levels of DNA loss, gene regulatory architecture remained conserved. This is consistent with a model in which DNA gain and loss results in turnover or “churning” in regulatory element dense regions of open chromatin, where interruption of regulatory elements is selected against.

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Abstract
One of the most powerful drivers of speciation in plants is pollinator-mediated disruptive selection, which leads to the divergence of floral traits adapted to the morphology and behavior of different pollinators. Despite the widespread importance of this speciation mechanism, its genetic basis has been explored in only a few groups. Here, we characterize the genetic basis of pollinator-mediated divergence of two species in genus Ipomopsis, I. guttata and I. tenuifolia, using quantitative trait locus (QTL) analyses of floral traits and other variable phenotypes. We detected 1-6 QTLs per trait, with each QTL generally explaining small to modest amounts of the phenotypic variance of a backcross hybrid population. In contrast, flowering time and anthocyanin abundance (a metric of colour variation) were controlled by a few QTLs of relatively large effect. QTLs were strongly clustered within linkage groups, with 26 of 37 QTLs localized to six marker-interval "hotspots," all of which harbored pleiotropic QTLs. In contrast to other studies that have examined the genetic basis of pollinator shifts, our results indicate that, in general, mutations of small to modest effect on phenotype were involved. Thus, the evolutionary transition between the distinct pollination modes of I. guttata and I. tenuifolia likely proceeded incrementally, rather than saltationally.

Additional file 3:. Table S2: Differential expression tests between IDH-A and IDH-O cells by cell type, computed via limma.

Abstract
We present an approach for quantitative trait locus (QTL) mapping, termed "lineage-specific QTL mapping", for inferring allelic changes of QTL evolution along branches in a phylogeny. We describe and analyze the simplest case: by adding a third taxon into the normal procedure of QTL mapping between pairs of taxa, such inferences can be made along lineages to a presumed common ancestor. While comparisons of QTL maps among species can identify homology of QTLs by apparent co-location, lineage specific mapping of QTL can classify homology into (1) orthology (shared origin of QTL) versus (2) paralogy (independent origin of QTL within resolution of map distance). In this light, we present a graphical method that identifies six modes of QTL evolution in a three taxon comparison. We then apply our model to map lineage-specific QTLs for inbreeding among three taxa of yellow monkeyflower: Mimulus guttatus and two inbreeders M. platycalyx and M. micranthus, but critically assuming outcrossing was the ancestral state. The two most common modes of homology across traits were orthologous (shared ancestry of mutation for QTL alleles). The outbreeder M. guttatus had the fewest lineage- specific QTL, in accordance with the presumed ancestry of outbreeding. Extensions of lineage-specific QTL mapping to other types of data and crosses, and to inference of ancestral QTL state, are discussed.

Ordnance Survey (OS) make an open dataset of rivers available as OS Open Rivers vector polylines under an Open Government Licence, derived from the detailed OS MasterMap Water Layer. Although widely used by the practitioner and the academic community it is not fully topologically connected, limiting its suitability for several uses and research applications such as linear referencing and reach analysis, hydro-ecological analysis, water quality monitoring, restoration and remediation prioritisation, connectivity planning and integration in decision support tools. The entire river network for Great Britain was corrected for topological errors and attributed with additional data. The network consisted of 183,349 polylines representing 147,387 kilometres.To ensure the network was a topologically correct river network, canals and channels that broke the dendritic connectivity of the river network were removed. The network was further simplified by removing loops. Small unconnected sections that were within the great catchment they sat within were also deleted out.With the topological errors removed, the network was passed through the river network processing tool RivEX to create added-value attribution. Encoding the network with these pre-computed values allows for rapidly analyse of the network alongside site data (points snapped to the network).Further details on edits made to the network and the attribute fields added are recorded in the lineage and fields section of the metadata.For further info see https://openrivers.net/

The dataset was derived by the Bioregional Assessment Programme from one or more source datasets. Any source datasets are identified in the Lineage field in this metadata statement. The processes undertaken to produce this derived dataset are described in the History field in this metadata statement. This is a shape file showing the progressive extent of proposed Carmichael Coal Mine (open cut only). Footprint area maps were obtained from the SEIS report of Carmichael Coal Mine and rail Project.

Abstract

Dinoflagellates possess many unique cellular characteristics with unresolved evolutionary histories including nuclei with greatly expanded genomes and chromatin packaged using histone-like proteins and dinoflagellate-viral nucleoproteins instead of histones, highly reduced mitochondrial genomes with extensive RNA editing, a mix of photosynthetic and cryptic secondary plastids, and tertiary plastids. Resolving the evolutionary origin of these traits requires understanding their ancestral states and early intermediates. Several deep-branching dinoflagellate lineages are good candidates for such reconstruction, however they tend to be delicate and environmentally sparse, so such analyses are not always simple. Here, we employ transcriptome sequencing from manually-isolated and microscopically documented cells to resolve the placement of two cells of one such genus, Abedinium, collected by ROV in deep waters off the coast of Monterey Bay. One cell corresponds to the only described species, A. dasypus, while the second cell is distinct and formally described as Abedinium folium, sp. nov. Abedinium has classically been assigned to the deep-branching dinoflagellates subgroup Noctilucea, which is weakly supported by phylogenetic analyses of the single characterized gene from any member of the genus, small subunit ribosomal RNA (SSU rRNA). However, a phylogenetic analysis based on 221 proteins from the transcriptome places Abedinium in a distinct lineage, separate from and basal to the Noctilucea and the rest of the core dinoflagellates. The transcriptome also contains evidence of a cryptic plastid functioning in the biosynthesis of isoprenoids, iron-sulfur clusters, and heme, a mitochondrial genome with all three expected protein-coding genes (cob, cox1, and cox3), and the presence of some but not all dinoflagellate-specific chromatin packaging proteins.

COCO mAP@0.5 calculations for lineage classification of the domains.

AbstractDioecy, the sexual system in which male and female organs are found in separate individuals, allows greater specialization for sex-specific functions and can be advantageous under various ecological and environmental conditions. However, dioecy is rare among flowering plants. Previous studies identified contradictory trends regarding the relative diversification rates of dioecious lineages vs their nondioecious counterparts, depending on the methods and data used. We gathered detailed species-level data for dozens of genera that contain both dioecious and nondioecious species. We then applied a probabilistic approach that accounts for differential speciation, extinction, and transition rates between states to examine whether there is an association between dioecy and lineage diversification. We found a bimodal distribution, whereby dioecious lineages exhibited higher diversification in certain genera but lower diversification in others. Additional analyses did not uncover an ecological or life history trait that could explain a context-dependent effect of dioecy on diversification. Furthermore, in-depth simulations of neutral characters demonstrated that such bimodality is also found when simulating neutral characters across the observed trees. Our analyses suggest that – at least for these genera with the currently available data – dioecy neither consistently places a strong brake on diversification nor is a strong driver. Usage notesPhylogenetic trees and sexual system classificationsProvided are: (1) Trees - a directory with phylogenetic trees for all genera in the study. (2) Sexual_systems - a directory with sexual system assignments for all species. (3) sexual.system.classifications.csv - a file with the classifications of sexual system (per species) into "broad" and "strict" definitions.Data_from_Sabath_at_al_2015.zip

Trimmed_SE_TrinityFasta file with the Trinity assembly for Sinningia eumorphaTrimmed_SM_TrinityFasta file with Trinity assembly for Sinningia magnificanewBLASTX_allgenesSESMBlastX for all genes assembled for S. eumorpha (SE_) and S. magnifica (SM_)newBLASTP_allgenes_SESMBlastP for all genes assembled for S. eumorpha (SE_) and S. magnifica (SM_)ORF_SESM_CDSFasta file with the predicted ORF (Open Reading Frame) in S. eumorpha and S. magnificaOrthGroups_SE_SMOrthoMLC ortholog groups between S. eumorpha and S. magnifica. Input file the predicted ORF.ORF_SE_SM_CDS.fastaPredicted SSR makers (Single Sequence Repeat) in S. eumorpha and S. magnifica. Input file the predicted ORF.

Supplementary material accompanying manuscript "Lepidopteran scale cells derive from sensory organ precursors through a canonical lineage". Authors: Ling S. Loh, Kyle A. DeMarr, Martina Tsimba, Christa Heryanto, Alejandro Berrio, Nipam H. Patel, Arnaud Martin, W. Owen McMillan, Gregory A. Wray, Joseph J. Hanly

Abstract

The Galapagos Archipelago is recognized as a natural laboratory for studying evolutionary processes. San Cristóbal was one of the first islands colonized by tortoises, which radiated from there across the archipelago to inhabit 10 islands. Here, we sequenced the mitochondrial control region from six historical giant tortoises from San Cristóbal (five long deceased individuals found in a cave and one found alive during an expedition in 1906) and discovered that the five from the cave are from a clade that is distinct among known Galapagos giant tortoises but closely related to the species from Española and Pinta Islands. The haplotype individual collected alive in 1906 is in the same clade as the haplotype in the contemporary population. To search for traces of a second lineage in the contemporary population on San Cristóbal, we closely examined the population by sequencing the mitochondrial control region for 129 individuals and genotyping 70 of these for both 21 microsatellite loci and >12 000 genome-wide single nucleotide polymorphisms [SNPs]. The dataset archived here consists of a VCF file of the SNPs genotyped through ddRAD and a structure file of the 21 microsatellites with the genotypes for the same 64 individuals in each. Only a single mitochondrial haplotype was found, with no evidence to suggest substructure based on the nuclear markers.

This dataset includes selected rivers in the United States preserved for possessing outstandingly, remarkable scenic, recreational, geologic, fish and wildlife, historic, cultural, or other similar values. Rivers, or sections of rivers, so designated are preserved in their free-flowing condition and are not dammed or otherwise improved.This dataset and its attribution establishes a lineage of the river segments for future reference, as their boundaries may change over time. Their attributes serve to store feature level metadata information for the lines, as well as document the origin and characteristics of each line segment. Lines shall be segmented when any of the attributes change (e.g. when the classification changes) or to capture changes in Outstandingly Remarkable Value (ORV). Every river segment must have at least one record in the related table, nlcs_wsr_orv_tbl. Please see the Entity and Attribute section of this metadata for information regarding the ORV table (nlcs_wsr_orv_tbl) and its relationship to this feature class (nlcs_wsr_ln).The footprints depicted in this NLCS dataset are based on the results of the river suitability determination within the Record of Decision (ROD) (May 29, 1996) and the follow-up BLM Arizona Statewide Wild and Scenic Rivers Study/Report (February, 1997). Thirteen of the twenty river areas reviewed for eligibility were considered suitable for classification/designation. River areas deemed "unsuitable" were not recommended for designation were released from wild and scenic river consideration. Additional supplemental information (plans, assessments, and amendments) are described in sections 1 and 3 of the ROD.On October 2, 1968, President Johnson signed the Wild and Scenic Rivers Act, sponsored by Senator Frank Church. The act currently protects more than two hundred rivers in thirty-five states and Puerto Rico. The Act’s legacy is one of protecting the special character of certain rivers, while recognizing the potential for use and development. In June 2000, the Bureau of Land Management (BLM) responded to growing public concern over the loss of open space by establishing the National Landscape Conservation System (NLCS). The NLCS stores some of the BLM’s premier designation areas in the hopes of increasing public awareness of the scientific, cultural, educational, ecological, and other values of these areas.

In sickle cell disease (SCD), the β6Glu→Val substitution in the β-globin chain leads to sickle hemoglobin (HbS) polymerization and red blood cell (RBC) sickling. Transplantation of autologous, genetically modified hematopoietic stem and progenitor cells (HSPCs) represents a promising therapeutic option for patients lacking a compatible donor. We previously designed a new lentiviral vector (DREPAGLOBE LV) expressing a potent anti-sickling βAS3 globin and demonstrated its safety and efficacy in SCD patient cells (PMID: 1508458). In vitro and in vivo preclinical studies demonstrated the safety and efficacy of a gene therapy (GT) protocol based on the efficient transduction of plerixafor-mobilized SCD HSPCs by the DREPAGLOBE LV. We therefore initiated a Phase I/II open label clinical trial for severe SCD patients. Here, for the 4 treated patients, we report the follow-up of 8 to 33 months. No drug-related adverse events or signs of clonal hematopoiesis were observed. Despite the similar VCN in the drug product, gene marking in peripheral blood mononuclear cells (PBMCs) was variable and as a consequence the correction of the clinical phenotype. These results pinpoint the difficulty to estimate the gene marking, self-renewal and engraftment potential of hematopoietic stem cells (HSCs) in the grafts. Therefore, we performed a transcriptomic analysis at single cell level for studying the pathophysiological mechanisms underlying SCD HSCs dysfunction. This analysis unraveled in the most immature HSCs in the two patients with partial loss of corrected cells, an exacerbated inflammatory signature through IL1-signaling pathways or TNFα and interferon. This was accompanied respectively by a lineage bias of HSCs. Overall, these clinical data indicate a variable efficacy of the DREPAGLOBE GT treatment, which likely depends on the number of infused HSCs and the intrinsic inflammatory alterations of genetically modified HSCs in SCD patients reducing their engraftment capability. Transcriptomic analysis of HSPCs and evaluation of the bone marrow niche in SCD patients will aid in defining critical parameters for achieving successful outcomes in future GT clinical trials for SCD.

Summary from GEO:

"Lineage tracing provides unprecedented insights into the fate of individual cells and their progeny in complex organisms. While effective genetic approaches have been developed in vitro and in animal models, these cannot be used to interrogate human physiology in vivo. Instead, naturally occurring somatic mutations have been utilized to infer clonality and lineal relationships between cells in human tissues, but current approaches are limited by high error rates and scale, and provide little information about the state or function of the cells. Here, we show how somatic mutations in mitochondrial DNA (mtDNA) can be tracked by current single cell RNA-Seq (scRNA-Seq) or single cell ATAC-Seq (scATAC-Seq) for simultaneous analysis of single cell lineage and state. We leverage somatic mtDNA mutations as natural genetic barcodes and demonstrate their use as clonal markers to infer lineal relationships. We trace the lineage of human cells by somatic mtDNA mutations in a native context both in vitro and in vivo, and relate it to expression profiles and chromatin accessibility. Our approach should allow lineage tracing at a 100- to 1,000-fold greater scale than with single cell whole genome sequencing, while providing information on cell state, opening the way to chart detailed cell lineage and fate maps in human health and disease.

A variety of experimental designs using cells derived from both in vitro and in vivo to determine the efficacy of using mtDNA mutations in human clonal tracing."

Overall design from GEO:

"TF1 (sub-)clones were clonally derived by single cell sorting in an iterative manner and expanded before processing each clone with bulk ATAC-seq. Sample names reflect the clonal lineage order."

Species are seen as the fundamental unit of biotic diversity, and thus their delimitation is crucial for defining measures for diversity assessments and studying evolution. Differences between species have traditionally been associated with variation in morphology. And yet, the discovery of cryptic diversity suggests that the evolution of distinct lineages does not necessarily involve trait differences. Here, we analyze 1,684,987 variant sites and over 4000 genes for more than 400 samples to show how a tropical montane plant lineage (Geonoma undata species complex) is composed of numerous unrecognized genetic groups that are not morphologically distinct. We find that 11 to 14 clades do not correspond to the three currently recognized species. Most clades are genetically independent and geographic distance and topography are the most important factors determining this genetic divergence. This lineage does not match the model of an adaptive radiation, but instead, constitutes the first example of a hyper-cryptic plant radiation in tropical mountains.

No description was included in this Dataset collected from the OSF

Proteins from thermophiles are generally more thermostable than their mesophilic homologs, but little is known about the evolutionary process driving these differences. Here we attempt to understand how the diverse thermostabilities of bacterial ribonuclease H1 (RNH) proteins evolved. RNH proteins from Thermus thermophilus (ttRNH) and Escherichia coli (ecRNH) share similar structures but differ in melting temperature (Tm) by 20°C. ttRNH's greater stability is caused in part by the presence of residual structure in the unfolded state, which results in a low heat capacity of unfolding (ΔCp) relative to ecRNH. We first characterized RNH proteins from a variety of extant bacteria and found that Tm correlates with the species' growth temperatures, consistent with environmental selection for stability. We then used ancestral sequence reconstruction to statistically infer evolutionary intermediates along lineages leading to ecRNH and ttRNH from their common ancestor, which existed approximately 3 billion years ago. Finally, we synthesized and experimentally characterized these intermediates. The shared ancestor has a melting temperature between those of ttRNH and ecRNH; the Tms of intermediate ancestors along the ttRNH lineage increased gradually over time, while the ecRNH lineage exhibited an abrupt drop in Tm followed by relatively little change. To determine whether the underlying mechanisms for thermostability correlate with the changes in Tm, we measured the thermodynamic basis for stabilization—ΔCp and other thermodynamic parameters—for each of the ancestors. We observed that, while the Tm changes smoothly, the mechanistic basis for stability fluctuates over evolutionary time. Thus, even while overall stability appears to be strongly driven by selection, the proteins explored a wide variety of mechanisms of stabilization, a phenomenon we call “thermodynamic system drift.” This suggests that even on lineages with strong selection to increase stability, proteins have wide latitude to explore sequence space, generating biophysical diversity and potentially opening new evolutionary pathways.