scholarly journals Stairway Plot 2: demographic history inference with folded SNP frequency spectra

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaoming Liu ◽  
Yun-Xin Fu
Keyword(s):  
Demographic History ◽  
Genotyping By Sequencing ◽  
Program Package ◽  
Nonparametric Method ◽  
Conservation Genomics ◽  
Frequency Spectra ◽  
Sequencing Technologies ◽  
Cross Platform

AbstractInferring the demographic histories of populations has wide applications in population, ecological, and conservation genomics. We present Stairway Plot 2, a cross-platform program package for this task using SNP frequency spectra. It is based on a nonparametric method with the capability of handling folded SNP frequency spectra (that is, when the ancestral alleles of the SNPs are unknown) of thousands of samples produced with genotyping-by-sequencing technologies; therefore, it is particularly suitable for nonmodel organisms.

scholarly journals Author Correction: Stairway Plot 2: demographic history inference with folded SNP frequency spectra

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaoming Liu ◽  
Yun-Xin Fu
Keyword(s):  
Demographic History ◽  
Frequency Spectra

An amendment to this paper has been published and can be accessed via the original article.

scholarly journals Blockwise Site Frequency Spectra for Inferring Complex Population Histories and Recombination

2016 ◽  
Author(s):  
Champak R. Beeravolu ◽  
Michael J. Hickerson ◽  
Laurent A.F. Frantz ◽  
Konrad Lohse
Keyword(s):  
Demographic History ◽  
Composite Likelihood ◽  
Model Organisms ◽  
Secondary Contact ◽  
Parameter Estimates ◽  
Genome Sequences ◽  
Frequency Spectra ◽  
Genome Wide ◽  
Complex Population ◽  
History Of

AbstractWe introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel composite likelihood framework based on a recently introduced summary of sequence variation: the blockwise site frequency spectrum (bSFS). This simulation-based framework uses the the frequencies of bSFS configurations to jointly model demographic history and recombination and is explicitly designed to make inference using multiple whole genomes or genome-wide multi-locus data (e.g. RADSeq) catering to the needs of researchers studying model or non-model organisms respectively. The flexible nature of our method further allows for arbitrarily complex population histories using unphased and unpolarized whole genome sequences. In silico experiments demonstrate accurate parameter estimates across a range of divergence models with increasing complexity, and as a proof of principle, we infer the demographic history of the two species of orangutan from multiple genome sequences (over 160 Mbp in length) from each species. Our results indicate that the two orangutan species split approximately 650-950 thousand years ago but experienced a pulse of secondary contact much more recently, most likely during a period of low sea-level South East Asia (∼300,000 years ago). Unlike previous analyses we can reject a history of continuous gene flow and co-estimate genome-wide recombination. ABLE is available for download at https://github.com/champost/ABLE.

scholarly journals Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Yongmei Zhao ◽  
Li Tai Fang ◽  
Tsai-wei Shen ◽  
Sulbha Choudhari ◽  
Keyur Talsania ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Cancer Genomics ◽  
Data Sets ◽  
Precision Oncology ◽  
Whole Genome ◽  
Factors Affecting ◽  
Sequencing Technologies ◽  
Cross Platform ◽  
Sequencing Platforms ◽  
Reference Samples

AbstractWith the rapid advancement of sequencing technologies, next generation sequencing (NGS) analysis has been widely applied in cancer genomics research. More recently, NGS has been adopted in clinical oncology to advance personalized medicine. Clinical applications of precision oncology require accurate tests that can distinguish tumor-specific mutations from artifacts introduced during NGS processes or data analysis. Therefore, there is an urgent need to develop best practices in cancer mutation detection using NGS and the need for standard reference data sets for systematically measuring accuracy and reproducibility across platforms and methods. Within the SEQC2 consortium context, we established paired tumor-normal reference samples and generated whole-genome (WGS) and whole-exome sequencing (WES) data using sixteen library protocols, seven sequencing platforms at six different centers. We systematically interrogated somatic mutations in the reference samples to identify factors affecting detection reproducibility and accuracy in cancer genomes. These large cross-platform/site WGS and WES datasets using well-characterized reference samples will represent a powerful resource for benchmarking NGS technologies, bioinformatics pipelines, and for the cancer genomics studies.

scholarly journals Genomic analysis reveals the genetic diversity, population structure, evolutionary history and relationships of Chinese pepper

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Shijing Feng ◽  
Zhenshan Liu ◽  
Yang Hu ◽  
Jieyun Tian ◽  
Tuxi Yang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Demographic History ◽  
Genomic Analysis ◽  
Genotyping By Sequencing ◽  
Gansu Province ◽  
Climatic Oscillations ◽  
Genome Wide ◽  
A Genome ◽  
Wild Accessions

Abstract Chinese pepper, mainly including Zanthoxylum bungeanum and Zanthoxylum armatum, is an economically important crop popular in Asian countries due to its unique taste characteristics and potential medical uses. Numerous cultivars of Chinese pepper have been developed in China through long-term domestication. To better understand the population structure, demographic history, and speciation of Chinese pepper, we performed a comprehensive analysis at a genome-wide level by analyzing 38,395 genomic SNPs that were identified in 112 cultivated and wild accessions using a high-throughput genome-wide genotyping-by-sequencing (GBS) approach. Our analysis provides genetic evidence of multiple splitting events occurring between and within species, resulting in at least four clades in Z. bungeanum and two clades in Z. armatum. Despite no evidence of recent admixture between species, we detected substantial gene flow within species. Estimates of demographic dynamics and species distribution modeling suggest that climatic oscillations during the Pleistocene (including the Penultimate Glaciation and the Last Glacial Maximum) and recent domestication events together shaped the demography and evolution of Chinese pepper. Our analyses also suggest that southeastern Gansu province is the most likely origin of Z. bungeanum in China. These findings provide comprehensive insights into genetic diversity, population structure, demography, and adaptation in Zanthoxylum.

scholarly journals Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild

2019 ◽  
Author(s):  
Emily Humble ◽  
Pavel Dobrynin ◽  
Helen Senn ◽  
Justin Chuven ◽  
Alan F. Scott ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Captive Breeding ◽  
Demographic History ◽  
High Genetic Diversity ◽  
Contact Mapping ◽  
Sequencing Technologies ◽  
Captive Populations ◽  
Recent Developments ◽  
In The Wild ◽  
Negative Impacts

AbstractCaptive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management planning. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes however, the transfer of these approaches to applied conservation has been slow. The scimitar-horned oryx (Oryx dammah) is a North African antelope that has been extinct in the wild since the early 1980s and is the focus of a long-term reintroduction project. To enable the selection of suitable founder individuals, facilitate post-release monitoring and improve captive breeding management, comprehensive genomic resources are required. Here, we used 10X Chromium sequencing together with Hi-C contact mapping to develop a chromosomal-level genome assembly for the species. The resulting assembly contained 29 chromosomes with a scaffold N50 of 100.4 Mb, and displayed strong chromosomal synteny with the cattle genome. Using resequencing data from six additional individuals, we demonstrated relatively high genetic diversity in the scimitar-horned oryx compared to other mammals, despite it having experienced a strong founding event in captivity. Additionally, the level of diversity across populations varied according to management strategy. Finally, we uncovered a dynamic demographic history that coincided with periods of climate variation during the Pleistocene. Overall, our study provides a clear example of how genomic data can uncover valuable insights into captive populations and contributes important resources to guide future management decisions of an endangered species.

scholarly journals Dynamic sampling bias and overdispersion induced by skewed offspring distributions

2021 ◽  
Author(s):  
Takashi Okada ◽  
Oskar Hallatschek
Keyword(s):  
Allele Frequency ◽  
Statistical Tests ◽  
Demographic History ◽  
Natural Populations ◽  
Sampling Bias ◽  
Coarse Grained ◽  
Frequency Spectra ◽  
Scaling Hypothesis ◽  
Frequency Fluctuations ◽  
Dynamic Sampling

Natural populations often show enhanced genetic drift consistent with a strong skew in their offspring number distribution. The skew arises because the variability of family sizes is either inherently strong or amplified by population expansions, leading to so-called ‘jackpot’ events. The resulting allele frequency fluctuations are large and, therefore, challenge standard models of population genetics, which assume sufficiently narrow offspring distributions. While the neutral dynamics backward in time can be readily analyzed using coalescent approaches, we still know little about the effect of broad offspring distributions on the dynamics forward in time, especially with selection. Here, we employ an exact asymptotic analysis combined with a scaling hypothesis to demonstrate that over-dispersed frequency trajectories emerge from the competition of conventional forces, such as selection or mutations, with an emerging time-dependent sampling bias against the minor allele. The sampling bias arises from the characteristic time-dependence of the largest sampled family size within each allelic type. Using this insight, we establish simple scaling relations for allele frequency fluctuations, fixation probabilities, extinction times, and the site frequency spectra that arise when offspring numbers are distributed according to a power law n−(1+α). To demonstrate that this coarse-grained model captures a wide variety of non-equilibrium dynamics, we validate our results in traveling waves, where the phenomenon of ‘gene surfing’ can produce any exponent 1 < α < 2. We argue that the concept of a dynamic sampling bias is useful generally to develop both intuition and statistical tests for the unusual dynamics of populations with skewed offspring distributions, which can confound commonly used tests for selection or demographic history.

scholarly journals Examination of signatures of recent positive selection on genes involved in human sialic acid biology

2017 ◽  
Author(s):  
Jiyun M. Moon ◽  
David M. Aronoff ◽  
John A. Capra ◽  
Patrick Abbot ◽  
Antonis Rokas
Keyword(s):  
Sialic Acid ◽  
Positive Selection ◽  
Transfer Functions ◽  
Demographic History ◽  
Neutral Evolution ◽  
Human Lineage ◽  
Selective Sweeps ◽  
Frequency Spectra ◽  
Recent Positive Selection ◽  
Soft Selective Sweeps

AbstractSialic acids are nine carbon sugars ubiquitously found on the surfaces of vertebrate cells and are involved in various immune response-related processes. In humans, at least 58 genes spanning diverse functions, from biosynthesis and activation to recycling and degradation, are involved in sialic acid biology. Because of their role in immunity, sialic acid biology genes have been hypothesized to exhibit elevated rates of evolutionary change. Consistent with this hypothesis, several genes involved in sialic acid biology have experienced higher rates of non-synonymous substitutions in the human lineage than their counterparts in other great apes, perhaps in response to ancient pathogens that infected hominins millions of years ago (paleopathogens). To test whether sialic acid biology genes have also experienced more recent positive selection during the evolution of the modern human lineage, reflecting adaptation to contemporary cosmopolitan or geographically-restricted pathogens, we examined whether their protein-coding regions showed evidence of recent hard and soft selective sweeps. This examination involved the calculation of four measures that quantify changes in allele frequency spectra, extent of population differentiation, and haplotype homozygosity caused by recent hard and soft selective sweeps for 55 sialic acid biology genes using publicly available whole genome sequencing data from 1,668 humans from three ethnic groups. To disentangle evidence for selection from confounding demographic effects, we compared the observed patterns in sialic acid biology genes to simulated sequences of the same length under a model of neutral evolution that takes into account human demographic history. We found that the patterns of genetic variation of most sialic acid biology genes did not significantly deviate from neutral expectations and were not significantly different among genes belonging to different functional categories. Those few sialic acid biology genes that significantly deviated from neutrality either experienced soft sweeps or population-specific hard sweeps. Interestingly, while most hard sweeps occurred on genes involved in sialic acid recognition, most soft sweeps involved genes associated with recycling, degradation and activation, transport, and transfer functions. We propose that the lack of signatures of recent positive selection for the majority of the sialic acid biology genes is consistent with the view that these genes regulate immune responses against ancient rather than contemporary cosmopolitan or geographically restricted pathogens.

Tigers of the World: Genomics and Conservation

2019 ◽  
Vol 7 (1) ◽  
pp. 521-548 ◽  
Author(s):  
Shu-Jin Luo ◽  
Yue-Chen Liu ◽  
Xiao Xu
Keyword(s):  
Demographic History ◽  
Morphological Diversity ◽  
Survival Strategies ◽  
Ex Situ ◽  
Sequencing Technologies ◽  
Genomic Tools ◽  
Genetic Patterns ◽  
The World ◽  
Tiger Conservation

Of all the big cats, or perhaps of all the endangered wildlife, the tiger may be both the most charismatic and most well-recognized flagship species in the world. The rapidly changing field of molecular genetics, particularly advances in genome sequencing technologies, has provided new tools to reconstruct what characterizes a tiger. Here we review how applications of molecular genomic tools have been used to depict the tiger's ancestral roots, phylogenetic hierarchy, demographic history, morphological diversity, and genetic patterns of diversification on both temporal and geographical scales. Tiger conservation, stabilization, and management are important areas that benefit from use of these genome resources for developing survival strategies for this charismatic megafauna both in situ and ex situ.

scholarly journals Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations

2020 ◽  
Author(s):  
Yann Bourgeois ◽  
Robert Ruggiero ◽  
Imtiyaz Hariyani ◽  
Stéphane Boissinot
Keyword(s):  
Transposable Elements ◽  
Demographic History ◽  
Ltr Retrotransposons ◽  
Frequency Spectra ◽  
Dna Transposons ◽  
Genomic Landscape ◽  
Demographic Processes ◽  
History Of ◽  
Recent Phase ◽  
Positive Correlations

AbstractBackgroundThe interactions between transposable elements (TEs) and their hosts constitute one of the most profound co-evolutionary processes found in nature. The population dynamics of TEs depends on factors specific to each TE families, such as the rate of transposition and insertional preference, the demographic history of the host and the genomic landscape. How these factors interact has yet to be investigated holistically. Here we are addressing this question in the green anole (Anolis carolinensis) whose genome contains an extraordinary diversity of TEs (including non-LTR retrotransposons, SINEs, LTR-retrotransposons and DNA transposons).ResultsWe observe a positive correlation between recombination rate and TEs frequencies and densities for LINEs, SINEs and DNA transposons. For these elements, there was a clear impact of demography on TE frequency and abundance, with a loss of polymorphic elements and skewed frequency spectra in recently expanded populations. On the other hand, some LTR-retrotransposons displayed patterns consistent with a very recent phase of intense amplification. To determine how demography, genomic features and intrinsic properties of TEs interact we ran simulations using SLiM3. We determined that i) short TE insertions are not strongly counter-selected, but long ones are, ii) neutral demographic processes, linked selection and preferential insertion may explain positive correlations between average TE frequency and recombination, iii) TE insertions are unlikely to have been massively recruited in recent adaptation..ConclusionsWe demonstrate that deterministic and stochastic processes have different effects on categories of TEs and that a combination of empirical analyses and simulations can disentangle the effects of these processes.

scholarly journals Dynamic Sampling Bias and Overdispersion Induced by Skewed Offspring Distributions

Genetics ◽  
2021 ◽  
Author(s):  
Takashi Okada ◽  
Oskar Hallatschek
Keyword(s):  
Allele Frequency ◽  
Evolutionary Dynamics ◽  
Statistical Tests ◽  
Demographic History ◽  
Sampling Bias ◽  
Coarse Grained ◽  
Frequency Spectra ◽  
Scaling Hypothesis ◽  
Frequency Fluctuations ◽  
Dynamic Sampling

Abstract Natural populations often show enhanced genetic drift consistent with a strong skew in their offspring number distribution. The skew arises because the variability of family sizes is either inherently strong or amplified by population expansions. The resulting allele-frequency fluctuations are large and, therefore, challenge standard models of population genetics, which assume sufficiently narrow offspring distributions. While the neutral dynamics backward in time can be readily analyzed using coalescent approaches, we still know little about the effect of broad offspring distributions on the forward-in-time dynamics, especially with selection. Here, we employ an asymptotic analysis combined with a scaling hypothesis to demonstrate that over-dispersed frequency trajectories emerge from the competition of conventional forces, such as selection or mutations, with an emerging time-dependent sampling bias against the minor allele. The sampling bias arises from the characteristic time-dependence of the largest sampled family size within each allelic type. Using this insight, we establish simple scaling relations for allele-frequency fluctuations, fixation probabilities, extinction times, and the site frequency spectra that arise when offspring numbers are distributed according to a power law n−(1+α). To demonstrate that this coarse-grained model captures a wide variety of evolutionary dynamics, we validate our results in traveling waves, where the phenomenon of ’gene surfing’ can produce any exponent 1 &lt; α &lt; 2. We argue that the concept of a dynamic sampling bias is useful to develop both intuition and statistical tests for the unusual dynamics of populations with skewed offspring distributions, which can confound commonly used tests for selection or demographic history.

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