Phylodynamic inference for emerging viruses using segregating sites

Epidemiological models are commonly fit to case data to estimate model parameters and to infer unobserved disease dynamics. More recently, epidemiological models have also been fit to viral sequence data using phylodynamic inference approaches that generally rely on the reconstruction of viral phylogenies. However, especially early on in an expanding viral population, phylogenetic uncertainty can be substantial and methods that require integration over this uncertainty can be computationally intensive. Here, we present an alternative approach to phylodynamic inference that circumvents the need for phylogenetic tree reconstruction. Our "tree-free" approach instead relies on quantifying the number of segregating sites observed in sets of sequences over time and using this trajectory of segregating sites to infer epidemiological parameters within a Sequential Monte Carlo (SMC) framework. Using forward simulations, we first show that epidemiological parameters and processes leave characteristic signatures in segregating site trajectories, demonstrating that these trajectories have the potential to be used for phylodynamic inference. We then show using mock data that our proposed approach accurately recovers key epidemiological quantities such as the basic reproduction number and the timing of the index case. Finally, we apply our approach to SARS-CoV-2 sequence data from France, estimating a reproductive number of approximately 2.2 and an introduction time of mid-January 2021, consistent with estimates from epidemiological surveillance data. Our findings indicate that "tree-free?" phylodynamic inference approaches that rely on simple population genetic summary statistics can play an important role in estimating epidemiological parameters and reconstructing infectious disease dynamics, especially early on in an epidemic.

Genetic diversity of pituitary transcription factor 1 (PIT 1) gene in Nigerian local and exotic chicken

This study was carried out to investigate the genetic diversity of PIT1 gene in Nigerian local and exotic chicken breeds. Genomic DNA was extracted from the blood of Isa brown, Shika brown and Naked neck chickens which was used to amplify the PIT1 gene and later sequenced. Sequences were aligned and analyzed using Mega 6.0 and DNASp. The results revealed that Naked neck had 181 monomorphic sites and the least was observed in Isa brown (34). However, Isa brown had the highest number of polymorphic site (181) and the least was observed in Shika brown. Singleton variable sites also varied across breeds. Number of segregating sites was highest in Isa brown (174). The highest number of haplotypes was observed in Isa brown (11). Highest number of indel sites were observed in Isa brown (46) chickens. The highest estimates of average evolutionary divergence over sequence pairs within chicken breeds was observed in Isa brown (0.766) and the least in Shika brown (0.15). The highest genetic distance is between Isa brown and Naked neck and the least between Naked neck and Shika brown. The result obtained from this study revealed a clearer understanding of the genetic diversity in PIT1 gene across the different breeds. This information can be harnessed for better policies for conservation and breeding programs.

Proximate and Genetic Analysis of Blackfin Tuna (T. atlanticus)

ABSTRACTThe tuna meat is a nutritious food that possesses high content of protein, its low content of saturated fatty acids makes it a high demand food in the world. The Thunnus genus is composed of eight species, albacore (T. alalunga), bigeye (T. obesus), long tail tuna (T. tonggol), yellowfin tuna (T. albacares), pacific bluefin tuna (T. orientalis), bluefin tuna (T. maccoyii), Atlantic bluefin tuna (T. thynnus) and blackfin tuna (T. atlanticus). The blackfin tuna (BFT) (Thunnus atlanticus) represent the smallest species within the Thunnus genus. This species inhabits the warm waters of the West Atlantic Ocean, from the shore of Massachusetts in the north, to Rio De Janeiro in Brazil. The first objective of this study was to evaluate the nutritional composition of BFT captured in the Gulf of Mexico, we determined ash, moisture, fat, protein and carbohydrates in BFT muscle and compared the obtained data with the nutritional reports from commercial tuna species including yellowfin tuna, Atlantic bluefin tuna and salmon (Salmo salar).Secondly, we report the genetic diversity and genetic differentiation of BFT within its geographical distribution range using the Cytochrome Oxidase I (COI) and control region sequenced data and from specimens collected in the Gulf of Mexico. We observed a nucleotide diversity π=0.001, 24 segregating sites and 10 parsimony informative. Within the CR we found nine different haplotypes π=0.044, 39 segregating sites, 16 parsimony informative sites. We concluded that according with the haplotype distribution there are differences among the BFT from the Gulf of Mexico and the North Atlantic compared to the South Atlantic. The Caribbean Sea is a migration point of the BFT, where all except the South Atlantic haplotypes were found.

The third moments of the site frequency spectrum

The analysis of patterns of segregating (i.e. polymorphic) sites in aligned sequences is routine in population genetics. Quantities of interest include the total number of segregating sites and the number of sites with mutations of different frequencies, the so-called site frequency spectrum. For neutrally evolving sequences, some classical results are available, including the expected value and variance of the spectrum in the Kingman coalescent model without recombination as calculated by Fu (1995).In this work, we use similar techniques to compute the third moments of the site frequency spectrum without recombination. We also account for the linkage pattern of mutations, yielding the full haplotype spectrum of three polymorphic sites. Based on these results, we derive analytical results for the bias of Tajima’s D and other neutrality tests.As an application, we obtain the second moments of the spectrum of linked sites, which is related to the neutral spectrum of chromosomal inversions and other structural variants. These moments can be used for the normalisation of new neutrality tests relying on these spectra.

Polymorphism in the major histocompatibility complex (MHC class II B) genes of the Rufous-backed Bunting (Emberiza jankowskii)

Genetic diversity is one of the pillars of conservation biology research. High genetic diversity and abundant genetic variation in an organism may be suggestive of capacity to adapt to various environmental changes. The major histocompatibility complex (MHC) is known to be highly polymorphic and plays an important role in immune function. It is also considered an ideal model system to investigate genetic diversity in wildlife populations. The Rufous-backed Bunting (Emberiza jankowskii) is an endangered species that has experienced a sharp decline in both population and habitat size. Many historically significant populations are no longer present in previously populated regions, with only three breeding populations present in Inner Mongolia (i.e., the Aolunhua, Gahaitu and Lubei557 populations). Efforts focused on facilitating the conservation of the Rufous-backed Bunting (Emberiza jankowskii) are becoming increasingly important. However, the genetic diversity ofE. jankowskiihas not been investigated. In the present study, polymorphism in exon 2 of the MHCIIB ofE. jankowskiiwas investigated. This polymorphism was subsequently compared with a related species, the Meadow Bunting (Emberiza cioides). A total of 1.59 alleles/individual were detected inE. jankowskiiand 1.73 alleles/individual were identified inE.cioides. The maximum number of alleles per individual from the threeE. jankowskiipopulations suggest the existence of at least three functional loci, while the maximum number of alleles per individual from the threeE. cioidespopulations suggest the presence of at least four functional loci. Two of the alleles were shared between theE. jankowskiiandE. cioides. Among the 12 unique alleles identified inE. jankowskii, 10.17 segregating sites per allele were detected, and the nucleotide diversity was 0.1865. Among the 17 unique alleles identified inE. cioides, eight segregating sites per allele were detected, and the nucleotide diversity was 0.1667. Overall, compared to other passerine birds, a relatively low level of MHC polymorphism was revealed inE. jankowskii, which was similar to that inE. cioides. Positive selection was detected by PAML/SLAC/FEL analyses in the region encoding the peptide-binding region in both species, and no recombination was detected. Phylogenetic analysis showed that the alleles fromE. jankowskiiandE. cioidesbelong to the same clade and the two species shared similar alleles, suggesting the occurrence of a trans-species polymorphism between the twoEmberizaspecies.

Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum

The sample frequency spectrum (SFS) of DNA sequences from a collection of individuals is a summary statistic that is commonly used for parametric inference in population genetics. Despite the popularity of SFS-based inference methods, little is currently known about the information theoretic limit on the estimation accuracy as a function of sample size. Here, we show that using the SFS to estimate the size history of a population has a minimax error of at least O(1/log s), where s is the number of independent segregating sites used in the analysis. This rate is exponentially worse than known convergence rates for many classical estimation problems in statistics. Another surprising aspect of our theoretical bound is that it does not depend on the dimension of the SFS, which is related to the number of sampled individuals. This means that, for a fixed number s of segregating sites considered, using more individuals does not help to reduce the minimax error bound. Our result pertains to populations that have experienced a bottleneck, and we argue that it can be expected to apply to many populations in nature.

Genetic variability of porcine circovirus 2 in vaccinating and non-vaccinating commercial farms

Vaccines against porcine circovirus 2 (PCV2) are now widely used to control the diseases caused by the virus. Although the vaccines protect pigs against the disease, they do not lead to sterilizing immunity and therefore infections with PCV2 continue in farms. It is expected that, due to its high evolutionary rate, PCV2 can adapt quickly to environmental pressures such as vaccination. The goal of this study was to elucidate the molecular variation of PCV2 in relation to vaccination. PCV2 variability was investigated from samples of infected pigs from five farms where vaccination had never been applied and two farms where pigs had been vaccinated for at least 2 years. For the genetic analysis, full PCV2 genomes were amplified and subsequently pooled by vaccination status from serum of eight vaccinated, infected pigs and 16 non-vaccinated, infected pigs. Variability of viral populations was quantified using next-generation sequencing and subsequent bioinformatics analysis. The number of segregating sites was similar in the non-vaccinated (n = 109) and vaccinated pools (n = 96), but the distribution of these sites in the genome differed. Most notably, in the capsid gene, the number of segregating sites was observed only in the non-vaccinated population. Based on the structural analysis, it is expected that some low-frequency amino acids result in biologically low-fit viruses. On the contrary, D294 in replicase represents a novel amino acid which was dominant and unique in the vaccinated pool. This work showed that variable PCV2 populations were circulating in commercial farms, and that this variability was different in samples obtained from vaccinating and non-vaccinating farms.

Genomic changes under rapid evolution: selection for parasitoid resistance

In this study, we characterize changes in the genome during a swift evolutionary adaptation, by combining experimental selection with high-throughput sequencing. We imposed strong experimental selection on an ecologically relevant trait, parasitoid resistance in Drosophila melanogaster against Asobara tabida. Replicated selection lines rapidly evolved towards enhanced immunity. Larval survival after parasitization increased twofold after just five generations of selection. Whole-genome sequencing revealed that the fast and strong selection response in innate immunity produced multiple, highly localized genomic changes. We identified narrow genomic regions carrying a significant signature of selection, which were present across all chromosomes and covered in total less than 5% of the whole D. melanogaster genome. We identified segregating sites with highly significant changes in frequency between control and selection lines that fell within these narrow ‘selected regions’. These segregating sites were associated with 42 genes that constitute possible targets of selection. A region on chromosome 2R was highly enriched in significant segregating sites and may be of major effect on parasitoid defence. The high genetic variability and small linkage blocks in our base population are likely responsible for allowing this complex trait to evolve without causing widespread erosive effects in the genome, even under such a fast and strong selective regime.