Biology subjects

Harkness, A.

Publications and source records attributed to Harkness, A..

5 recordsLinked to original sources

bioRxiv2022

Optimization of universal primer set for the identification of all Influenza A viruses using real-time PCR

Avian Influenza Virus (AIV) occurs worldwide among aquatic wild and may mutate into a strain capable of efficient human-to-human transmission and cause a pandemic that could kill a large fraction of the human population. The purpose of this study is to efficiently identify and diagnose the virus for immediate treatment and prevention. Real-Time Reverse Transcription-Polymerase Chain Reaction (RRT-PCR or qPCR) was identified as the most efficient way to detect AIV in previous laboratory research, however only one pair of primers was used. In order to further optimize the test and make it commercially available in the future, we first tested an eight pair primer set via RRT-PCR by using standard AIV isolates from Dr.Gaimbrones lab (Auburn University). Using the AIV isolates, the optimal cDNA and primer concentrations were determined, this aided in the identification of the most sensitive primer set. Primers PA, HA, NP, and NA were able to detect the cDNA of positive AIV isolates at a low concentration of 0.0039 mg/ml. AIV cDNA were detected by primers M and HA at its lowest concentration of 0.0001 and 0.01 pmol/l. In order to further test our lab results, 20 fecal samples from aquatic wild birds were collected from Alabama Shakespeare Park located in Montgomery, Alabama during the winter season. The samples were analyzed using RRT-PCR. HA primer set detected 10 positive samples for Avian Influenza and is the most sensitive primer set to be used in RRT-PCR. The field sample detection confirmed laboratory results and revealed that local aquatic birds are actively shedding low pathogenic avian influenza virus(LPAIV). The optimization of all primer sets used in this study will aid in disease surveillance, facilitate quick diagnosis of Influenza A viruses, and implement an effective prevention of flu pandemic.

microbiology↗

bioRxiv2020

Nonself-recognition-based self-incompatibility canalternatively promote or prevent introgression

1O_LITraditionally, we expect that self-incompatibility alleles (S-alleles), which prevent self-fertilization, should benefit from negative-frequency dependent selection and rise to high frequency when introduced to a new population through gene flow. However, the most taxonomically widespread form of self-incompatibility, the ribonuclease-based system ancestral to the core eudicots, functions through nonself-recognition, which drastically alters the process of S-allele diversification. C_LIO_LIWe analyze a model of S-allele evolution in two populations connected by migration, focusing on comparisons among the fates of S-alleles originally unique to each population and those shared among populations. C_LIO_LIWe find that both shared and unique S-alleles originating from the population with more unique S-alleles were usually fitter than S-alleles from the population with fewer. Resident S-alleles were often driven extinct and replaced by migrant S-alleles, though this outcome could be averted by pollen limitation or biased migration. C_LIO_LINonself-recognition-based self-incompatibility will usually either disfavor introgression of S-alleles or result in the whole-sale replacement of S-alleles from one population with those from another. C_LI

evolutionary biology↗

bioRxiv2020

Diversification or collapse of self-incompatibility haplotypes as a rescue process

In angiosperm self-incompatibility systems, pollen with an allele matching the pollen recipient at the self-incompatibility locus is rejected. Extreme allelic polymorphism is maintained by frequency-dependent selection favoring rare alleles. However, two challenges limit the spread of a new allele (a tightly linked haplotype in this case) under the widespread "collaborative non-self recognition" mechanism. First, there is no obvious selective benefit for pollen compatible with non-existent stylar incompatibilities, which themselves cannot spread if no pollen can fertilize them. However, a pistil-function mutation complementary to a previously neutral pollen mutation may spread if it restores self-incompatibility to a self-compatible intermediate. Second, we show that novel haplotypes can drive elimination of existing ones with fewer siring opportunities. We calculate relative probabilities of increase and collapse in haplotype number given the initial collection of incompatibility haplotypes and the population gene conversion rate. Expansion in haplotype number is possible when population gene conversion rate is large, but large contractions are likely otherwise. A Markov chain model derived from these expansion and collapse probabilities generates a stable haplotype number distribution in the realistic range of 10-40 under plausible parameters. However, smaller populations might lose many haplotypes beyond those lost by chance during bottlenecks.

evolutionary biology↗

bioRxiv2019

Diversification or collapse of self-incompatibility haplotypes as outcomes of evolutionary rescue

Self-incompatibility systems in angiosperms are exemplars of extreme allelic polymorphism maintained by long-term balancing selection. Pollen that shares an allele with the pollen recipient at the self-incompatibility locus is rejected, and this rejection favors rare alleles as well as preventing self-fertilization. Advances in molecular genetics reveal that an ancient, deeply conserved, and well-studied incompatibility system functions through multiple tightly linked genes encoding separate pollen-expressed F-box proteins and pistil-expressed ribonucleases. We show that certain recombinant haplotypes at the incompatibility locus can drive collapse in the number of incompatibility types. We use a modified evolutionary rescue model to calculate the relative probabilities of increase and collapse in number of incompatibility types given the initial collection of incompatibility haplotypes and the population rate of gene conversion. We find that expansion in haplotype number is possible when population size or the rate of gene conversion is large, but large contractions are likely otherwise. By iterating a Markov chain model derived from these expansion and collapse probabilities, we find that a stable haplotype number distribution in the realistic range of 10-40 is possible under plausible parameters. However, small or moderate-sized populations should be susceptible to substantial additional loss of haplotypes beyond those lost by chance during bottlenecks. The same processes that can generate many incompatibility haplotypes in large populations may therefore be crushing haplotype diversity in smaller populations.

evolutionary biology↗

bioRxiv2018

Heterosis from local drift load is likely insufficient to favor reversions to outcrossing

The evolutionary trajectory from cross-to self-fertilization is widely documented in nature, but results from several taxa also suggest that outcrossing may evolve in a formerly selfing population. Population genetic theory explains that selfing can evolve when its advantages overcome its immediate cost of inbreeding depression, but that this process will not run in reverse because a self-fertilizing population purges itself of inbreeding depression. That is, the primary short-term advantage of cross-fertilization over self-fertilization depends on the existence of deleterious alleles exposed upon inbreeding. Here, we explore whether outcrossing can evolve in selfing populations if allelic variation exists as divergence among populations. We consider two monomorphic populations of entirely self-fertilizing individuals, introduce a modifier allele that increases the rate of cross-fertilization, and investigate whether the heterosis among populations is sufficient for the modifier to invade and fix. We find that, despite an initial increase in the frequency of the outcrossing modifier, its fixation is possible only when populations harbor extremely large unique fixed genetic loads. These rare reversions to outcrossing become more likely as the load becomes more polygenic, or when the modifier appears on a rare background, such as by dispersal of an outcrossing genotype into a selfing population.

evolutionary biology↗