scholarly journals Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen

2019 ◽  
Author(s):  
Brian Arnold ◽  
Mashaal Sohail ◽  
Crista Wadsworth ◽  
Jukka Corander ◽  
William P. Hanage ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Positive Selection ◽  
Bacterial Pathogen ◽  
Directional Selection ◽  
Haplotype Structure ◽  
Fine Scale ◽  
Evolutionary Processes ◽  
Ecological Processes ◽  
Important Challenge ◽  
Repulsion Linkage

ABSTRACTIdentifying the forces that create and shape ecologically meaningful variation in bacteria remains an important challenge. For recombining bacteria, the sign and strength of linkage provide a unique lens into ongoing selection. We show derived alleles less than 300bp apart in Neisseria gonorrhoeae exhibit more coupling linkage than repulsion linkage, a pattern that cannot be explained by limited recombination or neutrality as these couplings are significantly stronger for nonsynonymous alleles compared to synonymous alleles. While linkage is shaped by many evolutionary processes, extensive simulations show only two distinct forms of positive selection can drive an excess of coupling linkage between neighboring nonsynonymous alleles: directional selection on introgressed alleles or selection that maintains distinct haplotypes in the presence of recombination. Our results establish a framework for identifying patterns of selection in fine-scale haplotype structure that indicate specific ecological processes in species that recombine with distantly related lineages or possess coexisting adaptive haplotypes.

scholarly journals Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen

2019 ◽  
Vol 37 (2) ◽  
pp. 417-428 ◽  
Author(s):  
Brian Arnold ◽  
Mashaal Sohail ◽  
Crista Wadsworth ◽  
Jukka Corander ◽  
William P Hanage ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Positive Selection ◽  
Balancing Selection ◽  
General Pattern ◽  
Bacterial Pathogen ◽  
Intermediate Frequency ◽  
Haplotype Structure ◽  
Fine Scale ◽  
Ecological Processes ◽  
Important Challenge

Abstract Identifying genetic variation in bacteria that has been shaped by ecological differences remains an important challenge. For recombining bacteria, the sign and strength of linkage provide a unique lens into ongoing selection. We show that derived alleles <300 bp apart in Neisseria gonorrhoeae exhibit more coupling linkage than repulsion linkage, a pattern that cannot be explained by limited recombination or neutrality as these couplings are significantly stronger for nonsynonymous alleles than synonymous alleles. This general pattern is driven by a small fraction of highly diverse genes, many of which exhibit evidence of interspecies horizontal gene transfer and an excess of intermediate frequency alleles. Extensive simulations show that two distinct forms of positive selection can create these patterns of genetic variation: directional selection on horizontally transferred alleles or balancing selection that maintains distinct haplotypes in the presence of recombination. Our results establish a framework for identifying patterns of selection in fine-scale haplotype structure that indicate specific ecological processes in species that recombine with distantly related lineages or possess coexisting adaptive haplotypes.

scholarly journals Selection for recombination in a polygenic model – the mechanism

1988 ◽  
Vol 51 (1) ◽  
pp. 59-63 ◽  
Author(s):  
J. Maynard Smith
Keyword(s):  
Linkage Disequilibrium ◽  
Recombination Rate ◽  
Phenotypic Variability ◽  
Directional Selection ◽  
Polygenic Model ◽  
Infinite Population ◽  
Selection For ◽  
Repulsion Linkage

SummaryA polygenic model has been simulated in order to reveal the process whereby selection in an infinite population can lead to an increase in the frequency of alleles causing higher rates of recombination (CH alleles). Directional selection generates repulsion linkage disequilibrium (+ − + −), which is less strong in CH gametes (gametes carrying CH alleles). In consequence, CH gametes contribute greater phenotypic variability, and therefore respond more to directional selection: that is, they accumulate more selectively favoured alleles. CH alleles then increase in frequency by hitch-hiking. In contrast, normalizing selection, or frequent changes in the direction of selection, favour alleles for a low recombination rate.

scholarly journals rehh2.0: a reimplementation of the R packagerehhto detect positive selection from haplotype structure

2016 ◽  
Vol 17 (1) ◽  
pp. 78-90 ◽  
Author(s):  
Mathieu Gautier ◽  
Alexander Klassmann ◽  
Renaud Vitalis
Keyword(s):  
Positive Selection ◽  
Haplotype Structure

Detecting recent positive selection in the human genome from haplotype structure

Nature ◽  
2002 ◽  
Vol 419 (6909) ◽  
pp. 832-837 ◽  
Author(s):  
Pardis C. Sabeti ◽  
David E. Reich ◽  
John M. Higgins ◽  
Haninah Z. P. Levine ◽  
Daniel J. Richter ◽  
...  
Keyword(s):  
Positive Selection ◽  
Human Genome ◽  
Haplotype Structure ◽  
Recent Positive Selection

scholarly journals Fine scale population structure linked to neutral divergence in the common sole (Solea solea), a marine fish with high dispersal capacity

2019 ◽  
Author(s):  
Alan Le Moan ◽  
Belén Jiménez-Mena ◽  
Dorte Bekkevold ◽  
Jakob Hemmer-Hansen
Keyword(s):  
Baltic Sea ◽  
Transition Zone ◽  
Structured Populations ◽  
Fine Scale ◽  
The Baltic Sea ◽  
Evolutionary Processes ◽  
Solea Solea ◽  
The Common ◽  
The Baltic ◽  
Common Sole

AbstractThe Baltic Sea provides a classical example of how an environmental gradient is associated with the distribution of marine species. Here, numerous genetic studies have revealed clear patterns of population structuring linked to the physical features of the gradient itself. Nevertheless, it remains difficult to distinguish clearly between the different micro-evolutionary processes that shape these structured populationsin situ. The common sole (Solea solea) is a benthic flatfish that rarely occurs within the Baltic Sea, but that exhibits a clear genetic break between populations from the North Sea – Baltic Sea transition zone and the remainder of the Atlantic Ocean. Here, we aim to evaluate the extent to which natural selection is involved in the observed patterns of divergence of sole populations occurring in the transition zone by comparing them with population structures of other flatfish species that have successfully colonized the Baltic Sea. By using several thousand of ddRAD-derived SNPs, we identified a fine-scale pattern of isolation-by-distance (IBD) of sole populations in the region. However, despite strong biological similarities among the flatfishes compared here, the sole IBD was, by far, the lowest detected across the transition zone. While selection was inferred to strongly influence all other flatfishes evolutionary histories, the analytical inference on the sole demographic history suggests that this fine-scale IBD is mainly maintained by neutral processes due to low effective population size of sole in the transition zone and asymmetrical gene flow. Our work contributes to a growing body of evidence suggesting that the strength of the different micro-evolutionary processes is species-specific, even when species occur in the same environment.

scholarly journals Medium Plant Cover has the Highest Heterogeneity of Fine-Scale Spatial Vegetation Patterns in Humid grasslands

2021 ◽  
Author(s):  
Qin Yang ◽  
Hua Cheng ◽  
Hongmei Pu ◽  
Xuechun Zhao ◽  
Rui Dong ◽  
...  
Keyword(s):  
Large Scale ◽  
Patch Size ◽  
Management Practices ◽  
Plant Cover ◽  
Rapid Expansion ◽  
Edge Density ◽  
Vegetation Patterns ◽  
Fine Scale ◽  
Ecological Processes ◽  
Patch Density

Abstract Context Fine-scale spatial vegetation patterns are ubiquitous and can have profound impacts on large scale ecological processes including surface runoff, soil erosion, and livestock forage efficiency. However, we have limited knowledge of the fine-scale spatial vegetation patterns in humid grasslands.Objectives The objectives were to characterize the spatial vegetation patterns at centimeter scale in humid grasslands, quantify the vegetation patterns variation under different image pixel sizes and plant covers, and explore the potential ecological implications of the spatial vegetation patterns.Methods Seventy plots with plant covers ranging from 30.8–99.3% were selected from seven humid grasslands in southwest China and their spatial vegetation patterns quantified at image pixel sizes of 0.04, 0.25, 1, and 4 cm.Results With increasing pixel size, plant patch density and total edge density decreased, plant patch size increased, and the plant patch shape became more regular. At a plant cover level below 50%, increasing plant cover will result in increasing patch density and patch size, leading to greater spatial heterogeneity. At plant cover levels above 50%, increasing plant cover will cause the rapid expansion of patch size, along with a lower patch density, forming a more homogeneous landscape dominated by plant patches. The small stems, branches, and leaves of grasses fragmented non-plant patches into smaller patches with increasing plant cover; this fragmentation resembles road-induced landscape fragmentation processes.Conclusions Medium plant cover has the highest heterogeneity of spatial vegetation pattern at the fine scale, which may have significant implications on ecological processes and related management practices.

scholarly journals Identifying branch-specific positive selection throughout the regulatory genome using an appropriate neutral proxy

2019 ◽  
Author(s):  
Alejandro Berrio ◽  
Ralph Haygood ◽  
Gregory A Wray
Keyword(s):  
Positive Selection ◽  
Regulatory Elements ◽  
Directional Selection ◽  
Neutral Evolution ◽  
Sequence Length ◽  
Open Chromatin ◽  
Sequence Alignments ◽  
Noncoding Dna ◽  
Region Length ◽  
The Impact

AbstractAdaptive changes in cis-regulatory elements are an essential component of evolution by natural selection. Identifying adaptive and functional noncoding DNA elements throughout the genome is therefore crucial for understanding the relationship between phenotype and genotype. Here, we introduce a method we called adaptyPhy, which adds significant improvements to our earlier method that tests for branch-specific directional selection in noncoding sequences. The motivation for these improvements is to provide a more sensitive and better targeted characterization of directional selection and neutral evolution across the genome. We use ENCODE annotations to identify appropriate proxy neutral sequences and demonstrate that the conservativeness of the test can be modulated during the filtration of reference alignments. We apply the method to noncoding Human Accelerated Elements as well as open chromatin elements previously identified in 125 human tissues and cell lines to demonstrate its utility. We also simulate sequence alignments under different classes of evolution in order to validate the ability of adaptiPhy to distinguish positive selection from relaxation of constraint and neutral evolution. Finally, we evaluate the impact of query region length, proxy neutral sequence length, and branch count on test sensitivity.

scholarly journals Neisseria gonorrhoeae subverts formin-dependent actin polymerization to colonize human macrophages

2021 ◽  
Vol 17 (12) ◽  
pp. e1010184
Author(s):  
Stanimir S. Ivanov ◽  
Reneau Castore ◽  
Maria Dolores Juarez Rodriguez ◽  
Magdalena Circu ◽  
Ana-Maria Dragoi
Keyword(s):  
Plasma Membrane ◽  
Neisseria Gonorrhoeae ◽  
Actin Polymerization ◽  
Bacterial Pathogens ◽  
Transmitted Disease ◽  
Bacterial Pathogen ◽  
Host Cells ◽  
Human Macrophages ◽  
Sexually Transmitted ◽  
Bacterial Replication

Dynamic reorganization of the actin cytoskeleton dictates plasma membrane morphogenesis and is frequently subverted by bacterial pathogens for entry and colonization of host cells. The human-adapted bacterial pathogen Neisseria gonorrhoeae can colonize and replicate when cultured with human macrophages, however the basic understanding of how this process occurs is incomplete. N. gonorrhoeae is the etiological agent of the sexually transmitted disease gonorrhea and tissue resident macrophages are present in the urogenital mucosa, which is colonized by the bacteria. We uncovered that when gonococci colonize macrophages, they can establish an intracellular or a cell surface-associated niche that support bacterial replication independently. Unlike other intracellular bacterial pathogens, which enter host cells as single bacterium, establish an intracellular niche and then replicate, gonococci invade human macrophages as a colony. Individual diplococci are rapidly phagocytosed by macrophages and transported to lysosomes for degradation. However, we found that surface-associated gonococcal colonies of various sizes can invade macrophages by triggering actin skeleton rearrangement resulting in plasma membrane invaginations that slowly engulf the colony. The resulting intracellular membrane-bound organelle supports robust bacterial replication. The gonococci-occupied vacuoles evaded fusion with the endosomal compartment and were enveloped by a network of actin filaments. We demonstrate that gonococcal colonies invade macrophages via a process mechanistically distinct from phagocytosis that is regulated by the actin nucleating factor FMNL3 and is independent of the Arp2/3 complex. Our work provides insights into the gonococci life-cycle in association with human macrophages and defines key host determinants for macrophage colonization.

scholarly journals Semen-Derived Enhancer of Viral Infection (SEVI) Binds Bacteria, Enhances Bacterial Phagocytosis by Macrophages, and Can Protect against Vaginal Infection by a Sexually Transmitted Bacterial Pathogen

2013 ◽  
Vol 57 (6) ◽  
pp. 2443-2450 ◽  
Author(s):  
David Easterhoff ◽  
Fernando Ontiveros ◽  
Lauren R. Brooks ◽  
Yoel Kim ◽  
Brittany Ross ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Neisseria Gonorrhoeae ◽  
Viral Infection ◽  
Bacterial Pathogen ◽  
Prostatic Acid Phosphatase ◽  
Necrosis Factor Alpha ◽  
Content Type ◽  
Sexually Transmitted ◽  
A Charge

ABSTRACTThe semen-derived enhancer of viral infection (SEVI) is a positively charged amyloid fibril that is derived from a self-assembling proteolytic cleavage fragment of prostatic acid phosphatase (PAP248-286). SEVI efficiently facilitates HIV-1 infectionin vitro, but its normal physiologic function remains unknown. In light of the fact that other amyloidogenic peptides have been shown to possess direct antibacterial activity, we investigated whether SEVI could inhibit bacterial growth. Neither SEVI fibrils nor the unassembled PAP248-286peptide had significant direct antibacterial activityin vitro. However, SEVI fibrils bound to both Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coliandNeisseria gonorrhoeae) bacteria, in a charge-dependent fashion. Furthermore, SEVI fibrils but not the monomeric PAP248-286peptide promoted bacterial aggregation and enhanced the phagocytosis of bacteria by primary human macrophages. SEVI also enhanced binding of bacteria to macrophages and the subsequent release of bacterially induced proinflammatory cytokines (tumor necrosis factor alpha [TNF-α], interleukin-6 [IL-6], and IL-1β). Finally, SEVI fibrils inhibited murine vaginal colonization withNeisseria gonorrhoeae. These findings demonstrate that SEVI has indirect antimicrobial activity and that this activity is dependent on both the cationic charge and the fibrillar nature of SEVI.

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