scholarly journals Local adaptation and spatiotemporal patterns of genetic diversity revealed by repeated sampling of Caenorhabditis elegans across the Hawaiian Islands

2021 ◽  
Author(s):  
Timothy A. Crombie ◽  
Paul Battlay ◽  
Robyn E. Tanny ◽  
Kathryn S. Evans ◽  
Claire M. Buchanan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Caenorhabditis Elegans ◽  
Local Adaptation ◽  
Balancing Selection ◽  
Sampling Site ◽  
Hawaiian Islands ◽  
Pathogen Resistance ◽  
Pacific Rim ◽  
High Genetic Diversity ◽  
C Elegans

AbstractThe nematode Caenorhabditis elegans is among the most widely studied organisms, but relatively little is known about its natural ecology. Wild C. elegans have been isolated from both temperate and tropical climates, where they feed on bacteria associated with decomposing plant material. Genetic diversity is low across much of the globe but high in the Hawaiian Islands and across the Pacific Rim. The high genetic diversity found there suggests that: (1) the origin of the species lies in Hawaii or the surrounding Pacific Rim; and (2) the ancestral niche of the species is likely similar to the Hawaiian niche. A recent study of the Hawaiian niche found that genetically distinct groups appeared to correlate with elevation and temperature, but the study had a limited sample size. To better characterize the niche and genetic diversity of C. elegans on the Hawaiian Islands and to explore how genetic diversity might be influenced by local adaptation, we repeatedly sampled nematodes over a three-year period, measured various environmental parameters at each sampling site, and whole-genome sequenced the C. elegans isolates that we identified. We found that the typical Hawaiian C. elegans niche is moderately moist native forests at high elevations (500 to 1500 meters) where temperatures are cool (15 to 20°C). We measured levels of genetic diversity and differentiation among Hawaiian strains and found evidence of seven genetically distinct groups distributed across the islands. Then, we scanned these genomes for signatures of local adaptation and identified 18 distinct regions that overlap with hyperdivergent regions, which are likely maintained by balancing selection and enriched for genes related to environmental sensing, xenobiotic detoxification, and pathogen resistance. These results provide strong evidence of local adaptation among Hawaiian C. elegans and a possible genetic basis for this adaptation.

scholarly journals Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Tim A Crombie ◽  
Stefan Zdraljevic ◽  
Daniel E Cook ◽  
Robyn E Tanny ◽  
Shannon C Brady ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Caenorhabditis Elegans ◽  
Nematode Species ◽  
Specific Substrate ◽  
High Genetic Diversity ◽  
C Elegans ◽  
Worldwide Population ◽  
Shared Ancestry ◽  
Wild Strains ◽  
Caenorhabditis Species

Hawaiian isolates of the nematode species Caenorhabditis elegans have long been known to harbor genetic diversity greater than the rest of the worldwide population, but this observation was supported by only a small number of wild strains. To better characterize the niche and genetic diversity of Hawaiian C. elegans and other Caenorhabditis species, we sampled different substrates and niches across the Hawaiian islands. We identified hundreds of new Caenorhabditis strains from known species and a new species, Caenorhabditis oiwi. Hawaiian C. elegans are found in cooler climates at high elevations but are not associated with any specific substrate, as compared to other Caenorhabditis species. Surprisingly, admixture analysis revealed evidence of shared ancestry between some Hawaiian and non-Hawaiian C. elegans strains. We suggest that the deep diversity we observed in Hawaii might represent patterns of ancestral genetic diversity in the C. elegans species before human influence.

scholarly journals Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations

2019 ◽  
Author(s):  
Timothy A. Crombie ◽  
Stefan Zdraljevic ◽  
Daniel E. Cook ◽  
Robyn E. Tanny ◽  
Shannon C. Brady ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Caenorhabditis Elegans ◽  
Model Organism ◽  
Population Admixture ◽  
Selective Sweeps ◽  
High Genetic Diversity ◽  
C Elegans ◽  
Low Genetic Diversity ◽  
High Elevations ◽  
Global Population

AbstractRecent efforts to understand the natural niche of the keystone model organism Caenorhabditis elegans have suggested that this species is cosmopolitan and associated with rotting vegetation and fruits. However, most of the strains isolated from nature have low genetic diversity likely because recent chromosome-scale selective sweeps contain alleles that increase fitness in human-associated habitats. Strains from the Hawaii Islands are highly divergent from non-Hawaiian strains. This result suggests that Hawaiian strains might contain ancestral genetic diversity that was purged from most non-Hawaiian strains by the selective sweeps. To characterize the genetic diversity and niche of Hawaiian C. elegans, we sampled across the Hawaiian Islands and isolated 100 new C. elegans strains. We found that C. elegans strains are not associated with any one substrate but are found in cooler climates at high elevations. These Hawaiian strains are highly diverged compared to the rest of the global population. Admixture analysis identified 11 global populations, four of which are from Hawaii. Surprisingly, one of the Hawaiian populations shares recent ancestry with non-Hawaiian populations, including portions of globally swept haplotypes. This discovery provides the first evidence of gene flow between Hawaiian and non-Hawaiian populations. Most importantly, the high levels of diversity observed in Hawaiian strains might represent the complex patterns of ancestral genetic diversity in the C. elegans species before human influence.

scholarly journals Genomics of sorghum local adaptation to a parasitic plant

2020 ◽  
Vol 117 (8) ◽  
pp. 4243-4251 ◽  
Author(s):  
Emily S. Bellis ◽  
Elizabeth A. Kelly ◽  
Claire M. Lorts ◽  
Huirong Gao ◽  
Victoria L. DeLeo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Local Adaptation ◽  
Species Interactions ◽  
Balancing Selection ◽  
Control Plant ◽  
Farming Systems ◽  
Striga Hermonthica ◽  
Loss Of Function ◽  
Trade Offs ◽  
Genome Wide

Host–parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple crop Sorghum bicolor (L.) Moench and its association with the parasitic weed Striga hermonthica (Delile) Benth., a major constraint to food security in Africa. We hypothesize that geographic selection mosaics across gradients of parasite occurrence maintain genetic diversity in sorghum landrace resistance. Suggesting a role in local adaptation to parasite pressure, multiple independent loss-of-function alleles at sorghum LOW GERMINATION STIMULANT 1 (LGS1) are broadly distributed among African landraces and geographically associated with S. hermonthica occurrence. However, low frequency of these alleles within S. hermonthica-prone regions and their absence elsewhere implicate potential trade-offs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and below-ground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with trade-offs, we find signatures of balancing selection surrounding LGS1 and other candidates from analysis of genome-wide associations with parasite distribution. Experiments with CRISPR–Cas9-edited sorghum further indicate that the benefit of LGS1-mediated resistance strongly depends on parasite genotype and abiotic environment and comes at the cost of reduced photosystem gene expression. Our study demonstrates long-term maintenance of diversity in host resistance genes across smallholder agroecosystems, providing a valuable comparison to both industrial farming systems and natural communities.

scholarly journals A Stenotrophomonas maltophilia Strain Evades a Major Caenorhabditis elegans Defense Pathway

2015 ◽  
Vol 84 (2) ◽  
pp. 524-536 ◽  
Author(s):  
Corin V. White ◽  
Brian J. Darby ◽  
Robert J. Breeden ◽  
Michael A. Herman
Keyword(s):  
Caenorhabditis Elegans ◽  
Stenotrophomonas Maltophilia ◽  
Pathogenic Bacteria ◽  
Pathogen Resistance ◽  
Nosocomial Pathogen ◽  
Content Type ◽  
C Elegans ◽  
Novel Host ◽  
Bacterial Accumulation ◽  
Intestinal Distension

Stenotrophomonas maltophiliais a ubiquitous bacterium and an emerging nosocomial pathogen. This bacterium is resistant to many antibiotics, associated with a number of infections, and a significant health risk, especially for immunocompromised patients. Given thatCaenorhabditis elegansshares many conserved genetic pathways and pathway components with higher organisms, the study of its interaction with bacterial pathogens has biomedical implications.S. maltophiliahas been isolated in association with nematodes from grassland soils, and it is likely thatC. elegansencounters this bacterium in nature. We found that a localS. maltophiliaisolate, JCMS, is more virulent than the otherS. maltophiliaisolates (R551-3 and K279a) tested. JCMS virulence correlates with intestinal distension and bacterial accumulation and requires the bacteria to be alive. Many of the conserved innate immune pathways that serve to protectC. elegansfrom various pathogenic bacteria also play a role in combatingS. maltophiliaJCMS. However,S. maltophiliaJCMS is virulent to normally pathogen-resistant DAF-2/16 insulin-like signaling pathway mutants. Furthermore, several insulin-like signaling effector genes were not significantly differentially expressed betweenS. maltophiliaJCMS and avirulent bacteria (Escherichia coliOP50). Taken together, these findings suggest thatS. maltophiliaJCMS evades the pathogen resistance conferred by the loss of DAF-2/16 pathway components. In summary, we have discovered a novel host-pathogen interaction betweenC. elegansandS. maltophiliaand established a new animal model with which to study the mode of action of this emerging nosocomial pathogen.

scholarly journals Balancing selection of the Intracellular Pathogen Response in natural Caenorhabditis elegans populations

2019 ◽  
Author(s):  
Lisa van Sluijs ◽  
Kobus J. Bosman ◽  
Frederik Pankok ◽  
Tatiana Blokhina ◽  
Joost A. G. Riksen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Caenorhabditis Elegans ◽  
Balancing Selection ◽  
Model Organism ◽  
Evolutionary Strategies ◽  
Intracellular Pathogen ◽  
C Elegans ◽  
Pathogen Response ◽  
Orsay Virus ◽  
Selection Of

AbstractBackgroundGenetic variation in host populations may lead to differential viral susceptibilities. Here, we investigate the role of natural genetic variation present for an antiviral pathway, the Intracellular Pathogen Response (IPR), underlying susceptibility to Orsay virus in the model organism Caenorhabditis elegans. The IPR involves transcriptional activity of 80 genes including the pals-genes. The pals-genes form an expanded gene family which hints they could be shaped by an evolutionary selective pressure. Here we examine the genetic variation in the pals-family for traces of selection and explore the molecular and phenotypic effects of having distinct pals-gene alleles.ResultsGenetic analysis of 330 world-wide C. elegans strains reveals that genetic diversity within the IPR-related pals-genes can be categorized in a few haplotypes worldwide. Importantly, two key-IPR regulators, pals-22 and pals-25, are in a genomic region carrying signatures of balancing selection. Therefore, distinct pals-22/pals-25 alleles have been maintained in C. elegans populations over time, which suggests different evolutionary strategies exist in IPR regulation. We investigated the IPR by infecting two C. elegans strains that represent distinct pals-22/pals-25 haplotypes, N2 and CB4856, with Orsay virus to determine their susceptibility and transcriptional response to infection. Our data suggests that regulatory genetic variation underlies constant high activity of IPR genes in CB4856 which could determine the host transcriptional defense. We found that CB4856 shows initially lower viral susceptibility than N2. High basal IPR expression levels might help counteract viral infection directly, whereas N2-like strains that need to activate the IPR genes first may have a slower response. Nevertheless, most wild strains harbor N2-like alleles for the pals-genes.ConclusionsOur work provides evidence for balancing genetic selection of immunity genes in C. elegans and illustrated how this may shape the transcriptional defense against pathogens. The transcriptional and genetic data presented in this study therefore provide a novel perspective on the functional diversity that can develop within a main antiviral response in natural host populations.

scholarly journals Genetic diversity in two leading Plasmodium vivax malaria vaccine candidates AMA1 and MSP119 at three sites in India

2021 ◽  
Vol 15 (8) ◽  
pp. e0009652
Author(s):  
Sonal Kale ◽  
Veena Pande ◽  
Om P. Singh ◽  
Jane M. Carlton ◽  
Prashant K. Mallick
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
South America ◽  
Plasmodium Vivax ◽  
Nucleotide Diversity ◽  
Vaccine Development ◽  
Balancing Selection ◽  
Global Scale ◽  
High Genetic Diversity ◽  
Global Population

Plasmodium vivax, a major contributor to the malaria burden in India, has the broadest geographic distribution and shows higher genetic diversity than P. falciparum. Here, we investigated the genetic diversity of two leading P. vivax vaccine candidate antigens, at three geographically diverse malaria-endemic regions in India. Pvama1 and Pvmsp119 partial coding sequences were generated from one hundred P. vivax isolates in India (Chennai n = 28, Nadiad n = 50 and Rourkela n = 22) and ~1100 published sequences from Asia, South America, North America, and Oceania regions included. These data were used to assess the genetic diversity and potential for vaccine candidacy of both antigens on a global scale. A total of 44 single nucleotide polymorphism (SNPs) were identified among 100 Indian Pvama1 sequences, including 10 synonymous and 34 nonsynonymous mutations. Nucleotide diversity was higher in Rourkela and Nadiad as compared to Chennai. Nucleotide diversity measures showed a strong balancing selection in Indian and global population for domain I of Pvama1, which suggests that it is a dominant target of the protective immune response. In contrast, the Pvmsp119 region showed highly conserved sequences in India and across the Oceania, South America, North America and Asia, demonstrating low genetic diversity in the global population when compared to Pvama1. Results suggest the possibility of including Pvmsp119 in a multivalent vaccine formulation against P. vivax infections. However, the high genetic diversity seen in Pvama1 would be more challenging for vaccine development.

scholarly journals An evolutionary medicine perspective on Neandertal extinction

2016 ◽  
Author(s):  
Alexis P. Sullivan ◽  
Marc de Manuel ◽  
Tomas Marques-Bonet ◽  
George H. Perry
Keyword(s):  
Genetic Diversity ◽  
Balancing Selection ◽  
Pathogen Resistance ◽  
Modern Human ◽  
Innate Immune ◽  
Evolutionary Medicine ◽  
Genetic Admixture ◽  
Human Populations ◽  
Modern Humans ◽  
Anatomically Modern Humans

AbstractThe Eurasian sympatry of Neandertals and anatomically modern humans – beginning at least 45,000 years ago and lasting for more than 5,000 years – has long sparked anthropological interest into the factors that potentially contributed to Neandertal extinction. Among many different hypotheses, the “differential pathogen resistance” extinction model posits that Neandertals were disproportionately affected by exposure to novel infectious diseases that were transmitted during the period of spatiotemporal sympatry with modern humans. Comparisons of new archaic hominin paleogenome sequences with modern human genomes have confirmed a history of genetic admixture – and thus direct contact – between humans and Neandertals. Analyses of these data have also shown that Neandertal nuclear genome genetic diversity was likely considerably lower than that of the Eurasian anatomically modern humans with whom they came into contact, perhaps leaving Neandertal innate immune systems relatively more susceptible to novel pathogens. In this study, we compared levels of genetic diversity in genes for which genetic variation is hypothesized to benefit pathogen defense among Neandertals and African, European, and Asian modern humans, using available exome sequencing data (six chromosomes per population). We observed that Neandertals had only 31-39% as many nonsynonymous (amino acid changing) polymorphisms across 73 innate immune system genes compared to modern human populations. We also found that Neandertal genetic diversity was relatively low in an unbiased set of balancing selection candidate genes for primates – genes with the highest 1% genetic diversity genome-wide in non-human apes. In contrast, Neandertals had similar to higher levels of genetic diversity than humans in 13 major histocompatibility complex (MHC) genes. Thus, while Neandertals may have been relatively more susceptible to some novel pathogens and differential pathogen resistance could be considered as one potential contributing factor in their extinction, this model does have limitations.

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