Demographic and Population Separation History Inference Based on Whole Genome Sequences.

Patterns of DNA sequence variation among present day individuals contain rich information about past population history. The recent availability of whole genome sequences provides challenges and opportunities for developing computational methods to infer detailed models of population history. The goal of this thesis is to extend current methodology and apply available techniques to answer questions about population history in human, gorilla and canine species. Recent methodologies based on the sequentially Markovian coalescent model permit the inference of population history using single or several whole genome sequences. However, these approaches fail to generate parametric estimates for split times, which are confounded by subsequent migration. Additionally, the effect of switch errors resulted from statistical phasing on split time estimation is largely unknown. We reconstructed phased haplotypes of nine individuals from diverse populations using fosmid pool sequencing. We analyzed population size and separation history using the Pairwise Sequentially Markovian Coalescent model (PSMC) and Multiple Sequentially Markovian Coalescent model (MSMC) and found that applying MSMC on statistically phased haplotypes results in more recent split time estimation compared with physically phased haplotypes due to switch errors. We further extended PSMC with Approximate Bayesian Computation to infer split time and migration rates under a standard isolation with migration model. We dated several key events in human separation history using these methods. Gorillas are human’s closet living relatives other than chimpanzees. We analyzed whole genome sequencing data of thirteen gorilla individuals and applied GPhoCS, a Bayesian coalescent-based approach to infer ancestral population sizes, divergence times and migration rates amongst three gorilla subspecies, shedding light on the evolutionary forces that have uniquely influenced patterns of gorilla genetic variation. The origins and dynamics of dog domestication has been a controversial and intriguing problem. We analyzed two ancient dog genomes from the Neolithic and over 100 contemporary canine genomes. While both dogs show signatures of admixture, they predominantly share ancestry with modern European dogs, contradicting a late Neolithic population replacement suggested by mitochondrial studies. By calibrating the mutation rate using our oldest dog, we narrowed the timing of dog domestication to a window of 20-40 kyrs ago.PhDBioinformaticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/133341/1/songsy_1.pd

Analysis on the interactions between the first introns and other introns in mitochondrial ribosomal protein genes

It is realized that the first intron plays a key role in regulating gene expression, and the interactions between the first introns and other introns must be related to the regulation of gene expression. In this paper, the sequences of mitochondrial ribosomal protein genes were selected as the samples, based on the Smith-Waterman method, the optimal matched segments between the first intron and the reverse complementary sequences of other introns of each gene were obtained, and the characteristics of the optimal matched segments were analyzed. The results showed that the lengths and the ranges of length distributions of the optimal matched segments are increased along with the evolution of eukaryotes. For the distributions of the optimal matched segments with different GC contents, the peak values are decreased along with the evolution of eukaryotes, but the corresponding GC content of the peak values are increased along with the evolution of eukaryotes, it means most introns of higher organisms interact with each other though weak bonds binding. By comparing the lengths and matching rates of optimal matched segments with those of siRNA and miRNA, it is found that some optimal matched segments may be related to non-coding RNA with special biological functions, just like siRNA and miRNA, they may play an important role in the process of gene expression and regulation. For the relative position of the optimal matched segments, the peaks of relative position distributions of optimal matched segments are increased during the evolution of eukaryotes, and the positions of the first two peaks exhibit significant conservatism

Phased haplotpyes -- callable regions

The .tar archive contains phasing information for each sample. The files *.mask.bed.gz, indicate the genomic regions for each sample deemed to be callable. Files are based on the GRCh37 reference genome assembly. This release contains phased data generated by Song et al. as well as reprocessing of previously published data (samples NA20847 (KITZMAN et al. 2011), HGDP01029 and HGDP00456 (MEYER et al. 2012)). Please see Song et al. 2016 for more information. The following files are included: HG02799.fosmid.phased.vcf.gz, HG02799.mask.bed.gz, HG03108.fosmid.phased.vcf.gz, HG03108.mask.bed.gz, HG03428.fosmid.phased.vcf.gz, HG03428.mask.bed.gz, HGDP00456.fosmid.phased.vcf.gz, HGDP00456.mask.bed.gz, HGDP01029.fosmid.phased.vcf.gz, HGDP01029.mask.bed.gz, NA12878.fosmid.phased.vcf.gz, NA12878.mask.bed.gz, NA19240.fosmid.phased.vcf.gz, NA19240.mask.bed.gz, NA20847.fosmid.phased.vcf.gz, NA20847.mask.bed.gz, NA21302.fosmid.phased.vcf.gz, NA21302.mask.bed.gz

Data from: Modeling human population separation history using physically phased genomes

Phased haplotype sequences are a key component in many population genetic analyses since variation in haplotypes reflects the action of recombination, selection, and changes in population size. In humans, haplotypes are typically estimated from unphased sequence or genotyping data using statistical models applied to large reference panels. To assess the importance of correct haplotype phase on population history inference, we performed fosmid pool sequencing and resolved phased haplotypes of five individuals from diverse African populations (including Yoruba, Esan, Gambia, Maasai, and Mende). We physically phased 98% of heterozygous SNPs into haplotype-resolved blocks, obtaining a block N50 of 1 Mbp. We combined these data with additional phased genomes from San, Mbuti, Gujarati and CEPH European populations and analyzed population size and separation history using the Pairwise Sequentially Markovian Coalescent (PSMC) and Multiple Sequentially Markovian Coalescent (MSMC) models. We find that statistically phased haplotypes yield a more recent split-time estimation compared with experimentally phased haplotypes. To better interpret patterns of cross-population coalescence, we implemented an approximate Bayesian computation (ABC) approach to estimate population split times and migration rates by fitting the distribution of coalescent times inferred between two haplotypes, one from each population, to a standard Isolation-with-Migration model. We inferred that the separation between hunter-gather populations and other populations happened around 120,000 to 140,000 years ago with gene flow continuing until 30,000 to 40,000 years ago; separation between west African and out of African populations happened around 70,000 to 80,000 years ago, while the separation between Maasai and out of African populations happened around 50,000 years ago

Improved flame resistance and thermo-mechanical properties of epoxy resin nanocomposites from functionalized graphene oxide via self-assembly in water

The development of a green and facile strategy for fabricating ecofriendly, highly effective flame retardants has remain a major challenge. Herein, supermolecular aggregates of piperazine (PiP) and phytic acid (PA) have been self-assembled onto the graphene oxide (GO) surface in water to fabricate functionalized GO (PPGO). The chemical structure and morphology of PPGO are determined by the X-ray photoelectron spectroscopy, transmission electron microscopy and scanning electron microscopy along with the energy dispersive spectroscopy. Due to the introduction of organic component onto the surface of graphene oxide, the adhesion between PPGO and the epoxy resin (EP) matrix is enhanced. As a result, the storage modulus (E′) of EP composites is increased in addition to a better dispersion of PPGO. Compared with the pure EP, the flame resistance of EP/PPGO is significantly improved, exhibiting a 42% decrease in peak heat release rate (pHRR), 22% reduction in total heat release (THR). The reduced flammability of EP is attributed to the synergistic effects afforded by the gas dilution effect of piperazine, char-forming promotion effect of phytic acid and the creation of 'tortuous path' barrier effect of GO during burning. This work offers a green and facile approach for creating highly effective graphene-based flame retardants

Sulfonated Block Ionomers Enable Transparent, Fire-Resistant, Tough yet Strong Polycarbonate

Polycarbonate (PC) features high transparency and balanced mechanical properties, and thus is being growingly used for producing many high-end products, e.g., construction facades, sensors and 5G equipment. For these applications, PC is required to combine satisfactory fire retardancy and great toughness while retain its mechanical strength and optical transparency. However, existing either fire retardants or toughening agents fail to enable PC to achieve such a required performance portfolio due to their improper molecular designs. To overcome this challenge, we, herein, rationally design a series of sulfonated ionomeric fire retardants (sSEBS-M, M = Na+, Zn2+, Ce3+) by sulfonating and neutralizing styrene-ethylene-butylene-styrene (SEBS). The sSEBS-M can be well-dispersed within the PC matrix with phase domain sizes less than 500 nm. Chemical structures of sSEBS-M and their dispersion within the polymer matrix strongly correlate to their comprehensive performances in PC. Among three sSEBS-M ionomers, sSEBS-Ce endows PC with better comprehensive performances. With 1.5 wt% of sSEBS-Ce, the final PC achieves a high limiting oxygen index of 33.5% and a desired UL-94 V-0 rating, in addition to a 53% reduction in peak heat release rate and a comparable transparency to virgin PC. Moreover, its impact toughness and ductility are enhanced by 40% and 116% with tensile strength well-preserved. The integrated performance portfolios are superior to previous counterparts. This work offers a novel strategy for the design of multifunctional ionomer-based fire retardants for creating high-performance PC and reveals its structure-composition-property relationship in PC, which will enable PC to realize its practical applications in above-mentioned industries

A facile way to prepare phosphorus-Nitrogen-Functionalized graphene oxide for enhancing the flame retardancy of epoxy resin

In this paper, we have reported a facile way to functionalize graphene oxide (GO) via assembling a supermolecular aggregate of piperazine (PiP) and phytic acid (PA) onto the GO surface (PPGO) without using any organic solvent. The functionalization of GO is confirmed by the X-ray photoelectron spectrum (XPS), transmission electron micrographs (TEM) and Raman spectrum. The introduction of 3 wt% PPGO into epoxy resin (EP/PPGO3) results in notable suppression on the fire risk of epoxy resin. In addition, cone calorimeter tests showed that the peak heat release rate (pHRR) was decreased from 727.4 kW/m2 to 367.5 kW/m2 (49%), and the peak smoke production rate (pSPR) was decreased from 0.2316 m2/s to 0.1379 g/s (40%). The improved flame-retardant performance of EP nanocomposites is most likely due to a tripartite cooperative effect from the key components (piperizine, phytic acid, and GO). This strategy demonstrates a facile and efficient approach for fabricating highly effective graphene-based flame retardants for polymers

A hyperbranched P/N/B-containing oligomer as multifunctional flame retardant for epoxy resins

Flame-retardant epoxy resins (EPs) with superior optical, mechanical and dielectric properties are highly desired in high-tech industries. In this work, a multifunctional hyperbranched additive (BDHDP) was synthesized for EPs. Our results showed that BDHDP catalyzed the curing of epoxy resin because of its tertiary amine and hydroxyl groups. At a low addition level (<3.0 wt%), BDHDP increased the glass-transition temperature and maintained the optical transmittance of epoxy thermoset. Meanwhile, BDHDP improved the mechanical strength and toughness, and reduced the dielectric constant and loss of EP because of the rigid phosphaphenanthrene groups and intra-molecular cavities. Moreover, BDHDP reduced the heat release and smoke generation during the EP combustion. Adding 1.5 wt% of BDHDP led to a UL-94 V-0 rating, and reduced the total smoke production by 16.4%. Hence, this study offers an effective method to create transparent EP thermosets with outstanding mechanical, dielectric and fire-retardant properties via incorporating a P/N/B-containing hyperbranched oligomer

Synthesis of decorated graphene with P, N-containing compounds and its flame retardancy and smoke suppression effects on polylactic acid

Functionalized graphene (PNFR@RGO) has been fabricated by decorating chemically reduced graphene oxide (RGO) with 9,10-dihydro-9-oxa-10-phosphaphenanthrene-10-oxide (DOPO) and branched polyethylenimine (BPEI) in this work. PNFR@RGO is then used to reduce the flammability of polylactic acid (PLA) via a melt compounding protocol. X-ray photoelectron spectroscopy (XPS) and Infrared spectroscopy (IR) have confirmed the successful fabrication of the target PNFR@RGO. The chemical decoration introduces phosphorus and nitrogen elements to the GO which can combine the formation of compact char barriers from graphene nanosheets and the elimination of free radicals when ignited or heated. The results show that the degradation temperature in air is increased and the heat release rate (HRR) is reduced. With the addition of 4 wt% PNFR@RGO, the average specific extinction area (ASEA) and the total smoke release (TSR) of PLA are noticeably suppressed by 92% and 79%, respectively. This is attributed to the combination of the corridor barrier functions of RGO and the radical-scavenging effects of PNFR

A bio-based ionic complex with different oxidation states of phosphorus for reducing flammability and smoke release of epoxy resins

Developing high efficient, environmentally friendly and bio-based flame retardants for combustible polymers has gained increasing interest. Herein, a novel highly efficient biomass-derived flame retardant (EHPP@PA) with different oxidation state phosphorus is prepared via neutralization of phytic acid (PA) and phenylphosphonate-based compound (EHPP). Due to synergistic effect between PA and EHPP, the incorporation of EHPP@PA significantly improves the flame-retardant performances of epoxy resin (EP), bringing about 64% reduction in peak heat release rate (pHRR) and 16% reduction in total heat release (THR). Additionally, EP/EHPP@PA also displays excellent smoke suppression performance, exhibiting 45% reduction in peak CO production (pCOP), 61% reduction in peak smoke release production rate (pSPR), and 21% reduction in total smoke production (TSP). The flame-retardant mechanism of EHPP@PA is further investigated, indicating that EHPP@PA effectively exerts flame-retardant effect in the condensed and gaseous phases during combustion. In the condensed phase, phytic acid facilitates the formation of a protective char shield, while in the gas phase, EHPP releases PO· and NO· to quench active radicals and inhibits the combustion