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89 results for “genotypic diversity”

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zenodo36/100

Figure 3 in PCR-RFLP Based genetic diversity of Plasmodium vivax genotypes in district Mardan, Pakistan

Figure 3. Prevalence of three different alleles of Pvmsp-3β (A, B, C) from PCR-RFLP.

opencc-by-4.0Dec 2022View details →

dryad36/100

Diversity in CRISPR-based immunity protects susceptible genotypes by restricting phage spread and evolution

Diversity in host resistance often associates with reduced pathogen spread. This may result from ecological and evolutionary processes, likely with feedback between them. Theory and experiments on bacteria-phage interactions have shown that genetic diversity of the bacterial adaptive immune system can limit phage evolution to overcome resistance. Using the CRISPR-Cas bacterial immune system and lytic phage, we engineered a host-pathogen system where each bacterial host genotype could be infected by only one phage genotype. With this model system, we explored how CRISPR diversity impacts the spread of phage when they can overcome a resistance allele, how immune diversity affects the evolution of the phage to increase its host range, and if there was feedback between these processes. We show that increasing CRISPR diversity benefits susceptible bacteria via a dilution effect, which limits the spread of the phage. We suggest that this ecological effect impacts the evolution of novel phage genotypes, which then feeds back into phage population dynamics.

opencc-zeroMay 2020View details →

dryad36/100

Data from: CHIIMP: an automated high-throughput microsatellite genotyping approach reveals greater allelic diversity in wild chimpanzees

Short tandem repeats (STRs), also known as microsatellites, are commonly used to non-invasively genotype wild-living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq-based approach and tested its performance using previously genotyped fecal samples from long-term studied chimpanzees in Gombe National Park, Tanzania. Using data from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus-specific files and automatically calls alleles after filtering stutter sequences and other PCR artifacts. Applying this method to the entire Gombe population, we confirmed previously reported genotypes, but also identified 31 new alleles that had been missed due to sequence differences and size homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one case of an ambiguous paternity. Using both singleplex and multiplex locus amplification, we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem in Tanzania, demonstrating the utility of the MiSeq-based approach for genotyping non-habituated populations and performing comparative analyses across field sites. The new automated high-throughput analysis platform (available at https://github.com/ShawHahnLab/chiimp) will allow biologists to more accurately and effectively determine wildlife population size and structure, and thus obtain information critical for conservation efforts.

opencc-zeroDec 2017View details →

dryad36/100

Data from: A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates

Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods. Our phylogenetic analyses robustly reconstructed three monophyletic clades corresponding to the three families of extant platyrrhines (Atelidae, Pitheciidae and Cebidae), with Pitheciidae as basal within the radiation. At the genus level, our results conformed well with previous phylogenetic studies and provide additional information relevant to the problematic position of the owl monkey (Aotus) within the family Cebidae, suggesting a need for further exploration of incomplete lineage sorting and other explanations for phylogenetic discordance, including introgression. Our study additionally provides one of the first applications of next-generation sequencing methods to the inference of phylogenetic history across an old, diverse radiation of mammals and highlights the broad promise and utility of ddRAD-seq data for molecular primatology.

opencc-zeroDec 2017View details →

dryad36/100

Ecological consequences of plant genotypic diversity within a foundation plant, Spartina alterniflora, are pervasive but not universal across multiple stress gradients

<ol> <li>Plant genotypic diversity can influence population- and community-level processes, yet we have a limited understanding of how these effects vary across environmental gradients that are ubiquitous in nature. </li> <li>We conducted a 2-year field experiment manipulating plant (Spartina alterniflora) genotypic diversity across a natural stress gradient in tidal elevation, both with and without the addition of nutrients. </li> <li> Spartina diversity increased stem production, but the magnitude of this effect was reduced at both the most stressful and most benign endpoints of the combined elevation and nutrient gradient, consistent with recent species diversity studies. Complementarity among individuals likely underpins the observed benefit of Spartina diversity. </li> <li> Spartina diversity also affected the associated marsh community, with higher consumer (Littoraria irrorata) abundance in more diverse plots, owing to both greater Spartina density and increased variation in Spartina traits.</li> <li> Synthesis: The positive effects of Spartina diversity on population- and community-level responses under most environmental conditions highlights the ecological importance of plant genotypic diversity for the maintenance of function across the marsh landscape. </li> </ol>

opencc-zeroJun 2023View details →

zenodo36/100

Fig. 1 in Genotype diversity, phylogenetic analysis and seasonality of isolates of Acanthamoeba spp. in swimming pools in Kafrelsheikh, Egypt

Fig. 1. Fresh unstained trophozoites (A) and cysts (B–D) of Acanthamoeba spp.

opencc-by-4.0Dec 2022View details →

dryad36/100

Data From: Effects of measurement methods and growing conditions on phenotypic expression of photosynthesis in seven diverse rice genotypes

Introduction: Light response curves are widely used to quantify phenotypic expression of photosynthesis by measuring a single sample and sequentially altering light intensity within a chamber (sequential method) or by measuring different samples that are each acclimated to a different light level (nonsequential method). Both methods are often conducted in controlled environments to achieve steady-state results, and neither method involves equilibrating the entire plant to the specific light level. Methods: Here, we compare sequential and non-sequential methods in controlled (greenhouse), semi-controlled (plant grown in growth chamber and acclimated to field conditions 2-3 days before measurements), and field environments. We selected seven diverse rice genotypes (five genotypes from the USDA rice minicore collection: 310588, 310723, 311644, 311677, 311795; and 2 additional genotypes: Nagina 22 and Zhe 733) to understand (1) the limitations of different methods, and (2) phenotypic plasticity of photosynthesis in rice grown under different environments. Results: Our results show that the non-sequential method was time-efficient and captured more variability of field conditions than the sequential method, but the model parameters were generally similar between the two methods except for the maximum photosynthesis rate (Amax). Amax was significantly lower across all genotypes under greenhouse conditions compared to the growth chamber and field conditions consistent with prior work, but surprisingly the apparent quantum yield (α) and the mitochondrial respiration (Rd) were generally not different among growing environments or measurement methods. Discussion: Our results suggest that field conditions are best suited to quantify phenotypic differences across different genotypes, and the nonsequential method was better at capturing the variability in photosynthesis.

opencc-zeroSep 2023View details →

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