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194 results for “host adaptation”
Explosive networking: the role of adaptive host radiations and ecological opportunity in a species-rich host-parasite assembly
<p>Dataset for Cruz-Laufer et al. (2021) Explosive networking: the role of adaptive host radiations and ecological opportunity in a species-rich host-parasite assembly.</p> <p><strong>Abstract: </strong>Many species-rich ecological communities emerge from adaptive radiation events. The effects of this explosive speciation on community assembly remain poorly understood. Here, we explore the well-documented radiations of African cichlid fishes and their interactions with the flatworm gill parasites <em>Cichlidogyrus </em>spp., including 10529 reported infections and 477 different host-parasite combinations collected through a survey of peer-reviewed literature. We assess how evolutionary, ecological, and morphological parameters determine host-parasite meta-communities affected by adaptive radiation events through network metrics, host repertoire measures, and network link prediction. The hosts’ evolutionary history mostly determined host repertoires of the parasites. Ecological and evolutionary parameters determined host-parasite interactions. Generally, ecological opportunity and fitting have shaped cichlid-<em>Cichlidogyrus</em> meta-communities suggesting an invasive potential for hosts used in aquaculture. Meta-communities affected by adaptive radiations are increasingly specialised with higher environmental stability. These trends should be verified across other systems to infer generalities in the evolution of species-rich host-parasite networks.</p>
Host-adaptation in Legionellales is 1.9 Gya, coincident with eukaryogenesis
<p>This dataset contains genomes, proteomes and protein alignments mentioned in Hugoson et al (2021). It has been used to analyze the evolution of host-adaptation in the order Legionellales.</p> <p>The data is organized by dataset type, and then by dataset.</p> <p>The four datasets used here are</p> <ul> <li><strong>Gamma105</strong>, comprising 105 <em>Gammaproteobacteria</em> and 5 outgroups;</li> <li><strong>Legio93</strong>, comprising 93 <em>Legionellales</em> and 20 outgroups;</li> <li><strong>Bacteria134</strong>, built on Gamma105, adding 27 genomes from Betts et al. (2018)</li> <li><strong>Bacteria93</strong>, built by removing <em>Legionella</em>, <em>Francisella</em>, <em>Fangia</em> and <em>Piscirickettsia</em> genera from Bacteria134</li> </ul> <p><strong>1_genomes</strong><br> Genomes as downloaded or assembled</p> <ul> <li>1_1_Gamma105</li> <li>1_2_Legio93</li> </ul> <p><strong>2_proteomes</strong><br> Proteomes, as annotated by prokka</p> <ul> <li>2_1_Gamma105</li> <li>2_2_Legio93</li> <li>2_3_Bacteria134</li> </ul> <p><strong>3_alignments</strong></p> <p>In the first three and the fifth folders, the following files are found. All sequence and alignment files are in fasta format:</p> <ul> <li>*_concatenated.fasta: concatenated alignment, trimmed.</li> <li>*.map: map of the files, tab-separated. The first row is a title row. The three first columns give the organism, the marker and the id (as found in the fasta file) for the protein.</li> <li>*_unaligned: non-aligned sequences for each marker.</li> <li>*_aligned: aligned sequences, for each marker. The prefix gives the software used for the alignment.</li> <li>*_trimmed: aligned, trimmed sequences for each marker. The prefix gives the software used to trim the alignment.</li> </ul> <p> </p> <ul> <li><strong>3_1_Gamma105</strong>: Based on the Bact109 set of markers.</li> <li><strong>3_2_Legio93</strong>: Based on the Bact109 set of markers.</li> <li><strong>3_3_Bacteria134</strong>: Based on Gamma105 set and Bact109 set of markers.</li> <li><strong>3_4_Bacteria93</strong>: Based on Bacteria134 (removed fast-evolving genomes).</li> <li><strong>3_5_TB4SS_auto</strong>: Alignment of 12 genes of the T4BSS, automatically detected in all genomes. </li> <li><strong>3_6_TB4SS_manual</strong>: Alignment of 25 genes of the T4BSS, manually curated by collinearity analysis.</li> </ul> <p> </p>
Fig. 2 in Host-adapted Cryptosporidium and Enterocytozoon bieneusi genotypes in straw-colored fruit bats in Nigeria
Fig. 2. Genotyping of Cryptosporidium spp. in strawcolored fruit bats by small subunit rRNA-based PCRRFLP. Upper panel: SspI RFLP patterns; lower panel: VspI RFLP patterns; M: 100-bp molecular markers; H: C. hominis positive control; P: C. parvum positive control; B1: Cryptosporidium bat genotype XIV; B2: Cryptosporidium bat genotype XV.
Fig. 4 in Host-adapted Cryptosporidium and Enterocytozoon bieneusi genotypes in straw-colored fruit bats in Nigeria
Fig. 4. Phylogeny of Enterocytozoon bieneusi genotypes in bats based on Bayesian inference analysis of sequences of the internal transcribed spacer of the rRNA gene. The posterior probability values are indicated on the branches. Red ones are E. bieneusi genotypes identified in straw-colored fruit bats in the present study. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Data for: Biomechanical adaptations enable phoretic mite species to occupy distinct spatial niches on host burying beetles
<p>Niche theory predicts that ecologically similar species coexist by minimising interspecific competition through niche partitioning. Therefore understanding the mechanisms of niche partitioning is essential for predicting interactions and coexistence between competing organisms. Here we study two phoretic mite species, <em>Poecilochirus carabi, </em>and <em>Macrocheles nataliae</em> that coexist on the same host-burying beetle <em>Nicrophorus vespilloides </em>and use it to 'hitchhike' between reproductive sites. Field observations revealed clear spatial partitioning between species in distinct host body parts. <em>P. carabi</em> preferred the ventral side of the thorax, whereas <em>M. nataliae </em>were exclusively found ventrally at the hairy base of the abdomen. Experimental manipulations of mite density showed that each species preferred these body parts, largely regardless of the density of the other mite species on the host beetle. Force measurements indicated that this spatial distribution is mediated by biomechanical adaptations, because each mite species required more force to be removed from their preferred location on the beetle. While <em>P. carabi</em> attached with large adhesive pads to the smooth thorax cuticle, <em>M. nataliae</em> gripped abdominal setae with their chelicerae. Our results show that specialist biomechanical adaptations for attachment can mediate spatial niche partitioning among species sharing the same host.</p>
Data from: Adaptive division of growth and development between hosts in helminths with two-host life cycles
<p>Parasitic worms (helminths) with complex life cycles divide growth and development between successive hosts. Using data from 597 species of acanthocephalans, cestodes, and nematodes with two-host life cycles, we found that helminths with larger intermediate hosts were more likely to infect larger, endothermic definitive hosts, although some evolutionarily shifts in definitive host mass occurred without changes in intermediate host mass. Life-history theory predicts parasites to shift growth to hosts in which they can grow rapidly and/or safely. Accordingly, helminth species grew relatively less as larvae and more as adults if they infected smaller intermediate hosts and/or larger, endothermic definitive hosts. Growing larger than expected in one host, relative to host mass/endothermy, was not associated with growing less in the other host, implying a lack of cross-host tradeoffs. Rather, some helminth orders had both large larvae and large adults. Within these taxa, though, size at maturity in the definitive host was unaffected by changes to larval growth, as predicted by optimality models. Parasite life-history strategies were mostly (though not entirely) consistent with theoretical expectations, suggesting that helminths adaptively divide growth and development between the multiple hosts in their complex life cycles.</p>
Data from: A host-adapted auxotrophic gut symbiont induces mucosal immunodeficiency
<p>The microbiome holds great promise as a source of novel therapeutic targets for many diseases. Mining for causative microorganisms that impact processes underlying disease states should utilize Koch's postulates. Here we show a functional screen for the bacterial microbiota of intestinal immunoglobulin A (IgA)-deficient mice; we identified a novel Gram-negative bacterium, proposed to be named as <em>Tomasiella immunophila</em> that induces and degrades IgA in mouse intestine. <em>T. immunophila</em> is auxotrophic for the bacterial cell wall amino sugar N-acetylmuramic acid (MurNAc). <em>T. immunophila</em> secretes IgA-degrading enzymes into outer membrane vesicles that preferentially degrade rodent antibodies with kappa but not lambda light chains. We propose this study uncovers a new paradigm for the role of symbionts in immunodeficiency that can ultimately be applied to human disease.</p>
Rapid and transient evolution of local adaptation to seasonal host fruits in an invasive pest fly
<p><span>Both local adaptation and adaptive phenotypic plasticity can influence the match between phenotypic traits and local environmental conditions. Theory predicts that environments stable for multiple generations promote local adaptation, while highly heterogeneous environments favor adaptive phenotypic plasticity. However, when environments have periods of stability mixed with heterogeneity, the relative importance of local adaptation and adaptive phenotypic plasticity is unclear. Here, we used <em>Drosophila suzukii</em> as a model system to evaluate the relative influence of genetic and plastic effects on the match of populations to environments with periods of stability from three to four generations. This invasive pest insect can develop within different fruits, and persists throughout the year in a given location on a succession of distinct host fruits, each one being available for only a few generations. Using reciprocal common environment experiments of natural <em>D. suzukii</em> populations collected from cherry, strawberry and blackberry, we found that both oviposition preference and offspring performance were higher on medium made with the fruit from which the population originated, than on media made with alternative fruits. This pattern, which remained after two generations in the laboratory, was analyzed using a statistical method we developed to quantify the contributions of local adaptation and adaptive plasticity in determining fitness. Altogether, we found that genetic effects (local adaptation) dominate over plastic effects (adaptive phenotypic plasticity). Our study demonstrates that spatially and temporally variable selection does not prevent the rapid evolution of local adaptation in natural populations. The speed and strength of adaptation may be facilitated by several mechanisms including a large effective population size and strong selective pressures imposed by host plants.</span></p>
MAG Collection - Rühlemann et al.: Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids
<p>This tar-Archives hold the complete collection of n=7,506 metagenome-assembled genomes presented in the preprint "Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids" by Rühlemann <em>et al., <a href="https://www.biorxiv.org/content/10.1101/2023.03.01.530589v1">bioRxiv</a>, </em>2023.</p> <p>Article Summary</p> <p>Characterizing trajectories of the composition and function of hominid gut microbiota across diverse environments and host species can help reveal specific properties of the human microbiota, with possible implications for host evolution and health. Using shotgun metagenomic sequencing, we investigated taxonomic and functional diversity in the gut microbiota of wild-living great apes, including two gorilla subspecies (<em>Gorilla gorilla gorilla, Gorilla beringei beringei</em>), three chimpanzee subspecies (<em>Pan troglodytes verus, P.t. troglodytes, P.t. schweinfurthii</em>), and bonobos (<em>Pan paniscus</em>), together with human samples from Africa and Europe. We identified microbial taxonomic and functional adaptations convergent with host phylogeny at both the community and microbial genomic levels. We could show that repeated horizontal gene transfer and gene loss are processes involved in these adaptations. We hypothesize, that these adaptation processes and changes in the microbiome predispose the host to chronic inflammatory disorders, such as type 2 diabetes via altered histidine metabolism and inflammatory bowel disease indicated by adaptation of microbes to aerobic conditions. Additionally, we find multiple lines of evidence suggesting a widespread loss of microbial diversity and evolutionary conserved clades in the human microbiota, especially in the European population. Lastly, we observed patterns consistent with codivergence of hosts and microbes, particularly for the bacterial family <em>Dialisteraceae</em>, though we find that overall, co-phylogeny patterns are frequently disrupted in humans.</p>
Data for: A mosquito parasite is locally adapted to its host but not temperature
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Rapid and transient evolution of local adaptation to seasonal host fruits in an invasive pest fly
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Data for: Biomechanical adaptations enable phoretic mite species to occupy distinct spatial niches on host burying beetles
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Data from: First evidence of a genetic basis for thermal adaptation in a schistosome host snail
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Data from: Adaptive division of growth and development between hosts in helminths with two-host life cycles
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Data from: A host-adapted auxotrophic gut symbiont induces mucosal immunodeficiency (Part I)
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The role of evolving niche choice in herbivore adaptation to host plants: Literature survey data and R scripts for simulations
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A host-adapted auxotrophic gut symbiont induces mucosal immunodeficiency (Part II)
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An experimental test of parasite adaptation to common vs. rare host genotypes
<p>A core hypothesis in coevolutionary theory proposes that parasites adapt to specifically infect common host genotypes. Under this hypothesis, parasites function as agents of negative frequency-dependent selection, favoring rare host genotypes. This parasite-mediated advantage of rarity is key to the idea that parasites maintain genetic variation and select for outcrossing in host populations. Here, we report the results of an experimental test of parasite adaptation to common vs. rare host genotypes. We selected the bacterial parasite <i>Serratia marcescens</i> to kill <i>C. elegans</i> hosts in uneven mixtures of host genotypes. To examine the effect of commonness itself, independent of host identity, each of four host genotypes was represented as common or rare in experimental host mixtures. After experimental selection, we evaluated a parasite line's change in virulence, the selected fitness trait, on its rare and common host genotypes. Our results were consistent with a slight advantage for rare host genotypes: on average, parasites lost virulence against rare genotypes but not against common genotypes. The response varied substantially, however, with distinct patterns across host genotype mixtures. These findings support the potential for parasites to impose negative frequency-dependent selection, while emphasizing that the cost of being common may vary with host genotype.</p>
Data from: Combining experimental evolution and genomics to understand how seed beetles adapt to a marginal host plant
<p>Genes that affect adaptive traits have been identified, but our knowledge of the genetic basis of adaptation in a more general sense (across multiple traits) remains limited. We combined population-genomic analyses of evolve and resequence experiments, genome-wide association mapping of performance traits, and analyses of gene expression to fill this knowledge gap, and shed light on the genomics of adaptation to a marginal host (lentil) by the seed beetle <em>Callosobruchus maculatus</em>. Using population-genomic approaches, we detected modest parallelism in allele frequency change across replicate lines during adaptation to lentil. Mapping populations derived from each lentil-adapted line revealed a polygenic basis for two host-specific performance traits (weight and development time), which had low to modest heritabilities. We found less evidence of parallelism in genotype-phenotype associations across these lines than in allele frequency changes during the experiments. Differential gene expression caused by differences in recent evolutionary history exceeded that caused by immediate rearing host. Together, the three genomic data sets suggest that genes affecting traits other than weight and development time are likely to be the main causes of parallel evolution, and that detoxification genes (especially cytochrome P450s and beta-glucosidase) could be especially important for colonization of lentil by <em>C. maculatus</em>.</p>
Functions of the Sulfatase-Modifying Factor 1 (HaSumf1) in the development and host glucosinolates adaptation of Helicoverpa armigera
<p>In this study, we detailed the indicators of development of <em>H. armigera</em>, such as growth and development period, number of surviving larvae, body weight, pupa weight, and number, as well as the relative expression levels of <em>HaSumf1</em> gene at different instars, and the third- and fifth-instars after feeding with glucosinolates and /or ds<em>Sumf1</em>.</p>
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