scholarly journals Global patterns and rates of habitat transitions across the eukaryotic tree of life

2021 ◽  
Author(s):  
Mahwash Jamy ◽  
Charlie Biwer ◽  
Daniel Vaulot ◽  
Aleix Obiol ◽  
Hongmei Jing ◽  
...  
Keyword(s):  
Ecological Niches ◽  
Eukaryotic Evolution ◽  
Short Read ◽  
Evolution Of Life ◽  
Long Read ◽  
Saline Habitats ◽  
Global Patterns ◽  
Almost All ◽  
New Habitats

The successful colonisation of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and terrestrial (including both freshwater and soil) communities. Although microbes represent by far the vast majority of eukaryote diversity, the role of the salt barrier in shaping the diversity across the eukaryotic tree is poorly known. Traditional views suggest rare and ancient marine-terrestrial transitions, but this view is being challenged by the discovery of several recently transitioned lineages. Here, we investigate habitat evolution across the tree of eukaryotes using a unique set of taxon-rich environmental phylogenies inferred from a combination of long-read and short-read metabarcoding data spanning the ribosomal DNA operon. Our results show that overall marine and terrestrial microbial communities are phylogenetically distinct, but transitions have occurred in both directions in almost all major eukaryotic lineages, with at least 350 transition events detected. Some groups have experienced relatively high rates of transitions, most notably fungi for which crossing the salt barrier has most likely been an important aspect of their successful diversification. At the deepest phylogenetic levels, ancestral habitat reconstruction analyses suggest that eukaryotes may have first evolved in non-saline habitats, and that the two largest known eukaryotic assemblages (TSAR and Amorphea) arose in different habitats. Overall, our findings indicate that crossing the salt barrier has played an important role in eukaryotic evolution by providing new ecological niches to fill.

scholarly journals The Role of Reticulate Evolution in Creating Innovation and Complexity

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Kristen S. Swithers ◽  
Shannon M. Soucy ◽  
J. Peter Gogarten
Keyword(s):  
Metabolic Pathways ◽  
Driving Forces ◽  
Reticulate Evolution ◽  
Neutral Evolution ◽  
Ecological Niches ◽  
Eukaryotic Evolution ◽  
New Host ◽  
Whole Genome Duplications ◽  
Genome Duplications

Reticulate evolution encompasses processes that conflict with traditional Tree of Life efforts. These processes, horizontal gene transfer (HGT), gene and whole-genome duplications through allopolyploidization, are some of the main driving forces for generating innovation and complexity. HGT has a profound impact on prokaryotic and eukaryotic evolution. HGTs can lead to the invention of new metabolic pathways and the expansion and enhancement of previously existing pathways. It allows for organismal adaptation into new ecological niches and new host ranges. Although many HGTs appear to be selected for because they provide some benefit to their recipient lineage, other HGTs may be maintained by chance through random genetic drift. Moreover, some HGTs that may initially seem parasitic in nature can cause complexity to arise through pathways of neutral evolution. Another mechanism for generating innovation and complexity, occurring more frequently in eukaryotes than in prokaryotes, is gene and genome duplications, which often occur through allopolyploidizations. We discuss how these different evolutionary processes contribute to generating innovation and complexity.

scholarly journals Local adaptation and archaic introgression shape global diversity at human structural variant loci

2021 ◽  
Author(s):  
Stephanie M. Yan ◽  
Rachel M. Sherman ◽  
Dylan J. Taylor ◽  
Divya R. Nair ◽  
Andrew N. Bortvin ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Human Populations ◽  
Sequencing Data ◽  
High Coverage ◽  
Short Read ◽  
Asian Populations ◽  
Long Read ◽  
Archaic Introgression ◽  
Immune Related Genes

AbstractLarge genomic insertions, deletions, and inversions are a potent source of functional and fitness-altering variation, but are challenging to resolve with short-read DNA sequencing alone. While recent long-read sequencing technologies have greatly expanded the catalog of structural variants (SVs), their costs have so far precluded their application at population scales. Given these limitations, the role of SVs in human adaptation remains poorly characterized. Here, we used a graph-based approach to genotype 107,866 long-read-discovered SVs in short-read sequencing data from diverse human populations. We then applied an admixture-aware method to scan these SVs for patterns of population-specific frequency differentiation—a signature of local adaptation. We identified 220 SVs exhibiting extreme frequency differentiation, including several SVs that were among the lead variants at their corresponding loci. The top two signatures traced to separate insertion and deletion polymorphisms at the immunoglobulin heavy chain locus, together tagging a 325 Kbp haplotype that swept to high frequency and was subsequently fragmented by recombination. Alleles defining this haplotype are nearly fixed (60-95%) in certain Southeast Asian populations, but are rare or absent from other global populations composing the 1000 Genomes Project. Further investigation revealed that the haplotype closely matches with sequences observed in two of three high-coverage Neanderthal genomes, providing strong evidence of a Neanderthal-introgressed origin. This extraordinary episode of positive selection, which we infer to have occurred between 1700 and 8400 years ago, corroborates the role of immune-related genes as prominent targets of adaptive archaic introgression. Our study demonstrates how combining recent advances in genome sequencing, genotyping algorithms, and population genetic methods can reveal signatures of key evolutionary events that remained hidden within poorly resolved regions of the genome.

scholarly journals Local adaptation and archaic introgression shape global diversity at human structural variant loci

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Stephanie M Yan ◽  
Rachel M Sherman ◽  
Dylan J Taylor ◽  
Divya R Nair ◽  
Andrew N Bortvin ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Functional Variation ◽  
Short Read ◽  
Adaptive Introgression ◽  
Asian Populations ◽  
Human Genomes ◽  
Long Read ◽  
Technical Advances ◽  
Immune Related Genes

Large genomic insertions and deletions are a potent source of functional variation, but are challenging to resolve with short-read sequencing, limiting knowledge of the role of such structural variants (SVs) in human evolution. Here, we used a graph-based method to genotype long-read-discovered SVs in short-read data from diverse human genomes. We then applied an admixture-aware method to identify 220 SVs exhibiting extreme patterns of frequency differentiation—a signature of local adaptation. The top two variants traced to the immunoglobulin heavy chain locus, tagging a haplotype that swept to near fixation in certain Southeast Asian populations, but is rare in other global populations. Further investigation revealed evidence that the haplotype traces to gene flow from Neanderthals, corroborating the role of immune-related genes as prominent targets of adaptive introgression. Our study demonstrates how recent technical advances can help resolve signatures of key evolutionary events that remained obscured within technically challenging regions of the genome.

Michael Kelly, Hilary Footitt, Myriam Salama-Carr (eds.): The Palgrave Handbook of Languages and Conflict

2020 ◽  
Vol 55 (2) ◽  
Author(s):  
Ľubomír Zvada
Keyword(s):  
International Relations ◽  
Foreign Languages ◽  
Military Operations ◽  
Sources Of Information ◽  
War And Peace ◽  
Interdisciplinary Field ◽  
Speakers Of Other Languages ◽  
War And Conflict ◽  
Almost All

This Handbook maps the contours of an exciting and burgeoning interdisciplinary field concerned with the role of language and languages in situations of conflict. It explores conceptual approaches, sources of information that are available, and the institutions and actors that mediate language encounters. It examines case studies of the role that languages have played in specific conflicts, from colonial times through to the Middle East and Africa today. The contributors provide vibrant evidence to challenge the monolingual assumptions that have affected traditional views of war and conflict. They show that languages are woven into every aspect of the making of war and peace, and demonstrate how language shapes public policy and military strategy, setting frameworks and expectations. The Handbook's 22 chapters powerfully illustrate how the encounter between languages is integral to almost all conflicts, to every phase of military operations and to the lived experiences of those on the ground, who meet, work and fight with speakers of other languages. This comprehensive work will appeal to scholars from across the disciplines of linguistics, translation studies, history, and international relations; and provide fresh insights for a broad range of practitioners interested in understanding the role and implications of foreign languages in war.

ON EVALUATION OF THE ROLE OF THERMAL AND WIND FACTORS FOR A PHYSICAL MODEL OF THE WORLD OCEAN GENERAL CIRCULATION SYSTEM

2019 ◽  
Vol 47 (3) ◽  
pp. 80-91
Author(s):  
V. G. Neiman
Keyword(s):  
Physical Model ◽  
Ocean Circulation ◽  
General Circulation ◽  
World Ocean ◽  
Circulation System ◽  
The Public ◽  
The World ◽  
Almost All ◽  
Conceptual Foundations

The main content of the work consists of certain systematization and addition of longexisting, but eventually deformed and partly lost qualitative ideas about the role of thermal and wind factors that determine the physical mechanism of the World Ocean’s General Circulation System (OGCS). It is noted that the conceptual foundations of the theory of the OGCS in one form or another are contained in the works of many well-known hydrophysicists of the last century, but the aggregate, logically coherent description of the key factors determining the physical model of the OGCS in the public literature is not so easy to find. An attempt is made to clarify and concretize some general ideas about the two key blocks that form the basis of an adequate physical model of the system of oceanic water masses motion in a climatic scale. Attention is drawn to the fact that when analyzing the OGCS it is necessary to take into account not only immediate but also indirect effects of thermal and wind factors on the ocean surface. In conclusion, it is noted that, in the end, by the uneven flow of heat to the surface of the ocean can be explained the nature of both external and almost all internal factors, in one way or another contributing to the excitation of the general, or climatic, ocean circulation.

Methyl mercury in the dutch rhine delta

1994 ◽  
Vol 30 (10) ◽  
pp. 213-219 ◽  
Author(s):  
Hendrik Pieters ◽  
Victor Geuke
Keyword(s):  
Suspended Matter ◽  
Methyl Mercury ◽  
Mercury Contamination ◽  
Benthic Organisms ◽  
Considerable Decrease ◽  
Continuous Sedimentation ◽  
Highly Correlated ◽  
High Level ◽  
Almost All

Samples of yellow eel from various locations in the Dutch Rhine area have been analyzed for trend monitoring of mercury since 1977. In the western Rhine delta mercury levels in eels have hardly changed since the seventies, whereas in the eastern part of the Dutch Rhine area a considerable decrease of mercury concentrations in eel has occurred. Because of continuous sedimentation of contaminated suspended matter transported from upstream regions, accumulation rates and concentrations of mercury in eel in the western Rhine delta remained at a relatively high level. Analyses of methyl mercury in biota have been performed to elucidate the role of methyl mercury in the mercury contamination of the Dutch Rhine ecosystem. Low percentages of methyl mercury were observed in zooplankton (3 to 35%). In benthic organisms (mussels) percentages of methyl mercury ranged from 30 to 57%, while in fish species and liver of aquatic top predator birds almost all the mercury was present in the form of methyl mercury (> 80%). During the period 1970-1990 mercury concentrations of suspended matter in the eastern Rhine delta have drastically decreased. These concentrations seemed to be highly correlated with mercury concentrations of eel (R = 0.84). The consequences of this relation are discussed.

scholarly journals Crayfish hemocytes develop along the granular cell lineage

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Fang Li ◽  
Zaichao Zheng ◽  
Hongyu Li ◽  
Rongrong Fu ◽  
Limei Xu ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Cell Lineage ◽  
Granular Cell ◽  
Marker Genes ◽  
Hematopoietic Tissue ◽  
Differentiated Cells ◽  
Stage Of Development ◽  
Almost All ◽  
Relationship Of

AbstractDespite the central role of hemocytes in crustacean immunity, the process of hemocyte differentiation and maturation remains unclear. In some decapods, it has been proposed that the two main types of hemocytes, granular cells (GCs) and semigranular cells (SGCs), differentiate along separate lineages. However, our current findings challenge this model. By tracking newly produced hemocytes and transplanted cells, we demonstrate that almost all the circulating hemocytes of crayfish belong to the GC lineage. SGCs and GCs may represent hemocytes of different developmental stages rather than two types of fully differentiated cells. Hemocyte precursors produced by progenitor cells differentiate in the hematopoietic tissue (HPT) for 3 ~ 4 days. Immature hemocytes are released from HPT in the form of SGCs and take 1 ~ 3 months to mature in the circulation. GCs represent the terminal stage of development. They can survive for as long as 2 months. The changes in the expression pattern of marker genes during GC differentiation support our conclusions. Further analysis of hemocyte phagocytosis indicates the existence of functionally different subpopulations. These findings may reshape our understanding of crustacean hematopoiesis and may lead to reconsideration of the roles and relationship of circulating hemocytes.

scholarly journals Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Seth Commichaux ◽  
Kiran Javkar ◽  
Padmini Ramachandran ◽  
Niranjan Nagarajan ◽  
Denis Bertrand ◽  
...  
Keyword(s):  
Public Health ◽  
Public Health Response ◽  
High Quality ◽  
Short Read ◽  
Short Reads ◽  
The Core ◽  
Long Reads ◽  
Health Response ◽  
Long Read ◽  
Core Genes

Abstract Background Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks. Quasimetagenomics can substantially reduce the amount of culturing needed before a high quality genome can be recovered. Highly accurate short read data is analyzed for single nucleotide polymorphisms and multi-locus sequence types to differentiate strains but cannot span many genomic repeats, resulting in highly fragmented assemblies. Long reads can span repeats, resulting in much more contiguous assemblies, but have lower accuracy than short reads. Results We evaluated the accuracy of Listeria monocytogenes assemblies from enrichments (quasimetagenomes) of naturally-contaminated ice cream using long read (Oxford Nanopore) and short read (Illumina) sequencing data. Accuracy of ten assembly approaches, over a range of sequencing depths, was evaluated by comparing sequence similarity of genes in assemblies to a complete reference genome. Long read assemblies reconstructed a circularized genome as well as a 71 kbp plasmid after 24 h of enrichment; however, high error rates prevented high fidelity gene assembly, even at 150X depth of coverage. Short read assemblies accurately reconstructed the core genes after 28 h of enrichment but produced highly fragmented genomes. Hybrid approaches demonstrated promising results but had biases based upon the initial assembly strategy. Short read assemblies scaffolded with long reads accurately assembled the core genes after just 24 h of enrichment, but were highly fragmented. Long read assemblies polished with short reads reconstructed a circularized genome and plasmid and assembled all the genes after 24 h enrichment but with less fidelity for the core genes than the short read assemblies. Conclusion The integration of long and short read sequencing of quasimetagenomes expedited the reconstruction of a high quality pathogen genome compared to either platform alone. A new and more complete level of information about genome structure, gene order and mobile elements can be added to the public health response by incorporating long read analyses with the standard short read WGS outbreak response.

scholarly journals Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Sharon A. Huws ◽  
Joan E. Edwards ◽  
Wanchang Lin ◽  
Francesco Rubino ◽  
Mark Alston ◽  
...  
Keyword(s):  
Energy Harvesting ◽  
Perennial Ryegrass ◽  
Transcriptional Activity ◽  
Ecological Niches ◽  
Ecological Interactions ◽  
Carbohydrate Degradation ◽  
Host Nutrition ◽  
Role Based ◽  
Insight Into

Abstract Background Gut microbiomes, such as the rumen, greatly influence host nutrition due to their feed energy-harvesting capacity. We investigated temporal ecological interactions facilitating energy harvesting at the fresh perennial ryegrass (PRG)-biofilm interface in the rumen using an in sacco approach and prokaryotic metatranscriptomic profiling. Results Network analysis identified two distinct sub-microbiomes primarily representing primary (≤ 4 h) and secondary (≥ 4 h) colonisation phases and the most transcriptionally active bacterial families (i.e Fibrobacteriaceae, Selemondaceae and Methanobacteriaceae) did not interact with either sub-microbiome, indicating non-cooperative behaviour. Conversely, Prevotellaceae had most transcriptional activity within the primary sub-microbiome (focussed on protein metabolism) and Lachnospiraceae within the secondary sub-microbiome (focussed on carbohydrate degradation). Putative keystone taxa, with low transcriptional activity, were identified within both sub-microbiomes, highlighting the important synergistic role of minor bacterial families; however, we hypothesise that they may be ‘cheating’ in order to capitalise on the energy-harvesting capacity of other microbes. In terms of chemical cues underlying transition from primary to secondary colonisation phases, we suggest that AI-2-based quorum sensing plays a role, based on LuxS gene expression data, coupled with changes in PRG chemistry. Conclusions In summary, we show that fresh PRG-attached prokaryotes are resilient and adapt quickly to changing niches. This study provides the first major insight into the complex temporal ecological interactions occurring at the plant-biofilm interface within the rumen. The study also provides valuable insights into potential plant breeding strategies for development of the utopian plant, allowing optimal sustainable production of ruminants.

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