Inferring the demographic history from DNA sequences: An importance sampling approach based on non-homogeneous processes

2016 ◽  
Vol 111 ◽  
pp. 16-27
Author(s):  
S. Ait Kaci Azzou ◽  
F. Larribe ◽  
S. Froda
Keyword(s):  
Importance Sampling ◽  
Dna Sequences ◽  
Demographic History ◽  
Sampling Approach

scholarly journals Molecular characterization and genetic diversity of Ornithonyssus sylviarum in chickens (Gallus gallus) from Hainan Island, China

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Biswajit Bhowmick ◽  
Jianguo Zhao ◽  
Øivind Øines ◽  
Tianlin Bi ◽  
Chenghong Liao ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Genetic Diversity ◽  
Molecular Analysis ◽  
Dna Sequences ◽  
Demographic History ◽  
Asian Countries ◽  
Ornithonyssus Sylviarum ◽  
Private Haplotype ◽  
Northern Fowl Mite ◽  
Poultry Farms

Abstract Background The northern fowl mite (NFM), Ornithonyssus sylviarum, is an obligatory hematophagous ectoparasite of birds and one of the most important pests in the poultry industry on several continents. Although NFM poses a serious problem, it remains a neglected pest of poultry in China and other Asian countries. Therefore, a molecular analysis was conducted to provide baseline information on the occurrence, genetic diversity and emergence of NFM in poultry farms from China. Methods This study focused on morphological description and identification of adults based on electron microscopy, molecular sequencing of the mitochondrial cox1 gene and phylogenetic analysis. We have also used the DNA sequences of the cox1 gene to study the genetic diversity, population structure and demographic history. The neutrality tests were used to analyze signatures of historical demographic events. Results The mites collected were identified as the northern fowl mite Ornithonyssus sylviarum based on external morphological characterization using electron microscopy. Molecular analysis using a 756-bp long partial fragment of the cox1 gene revealed 99–100% sequence identity with NFM and phylogenetic inferences showed a bootstrap value of 99% indicating a well-supported monophyletic relationship. Molecular diversity indices showed high levels of haplotype diversity dominated by private haplotypes, but low nucleotide divergence between haplotypes. The Tajima’s D test and Fu’s Fs test showed negative value, indicating deviations from neutrality and both suggested recent population expansion of mite populations supported by a star-like topology of the isolates in the network analysis. Our genetic data are consistent with a single introduction of NFM infestations and the spread of NFM infestation in Hainan poultry farms and a private haplotype dominance, which suggest that infestations are recycled within the farms and transmission routes are limited between farms. Conclusions To our knowledge, this is the first time a molecular report of NFM in chicken from China including other Asian countries using DNA barcoding. The findings have potential implications with respect to understanding the transmission patterns, emergence and populations trends of parasitic infestations of poultry farms that will help for setting the parameters for integrated pest management (IPM) tactics against mite infestations.

Chance-constrained problems and rare events: an importance sampling approach

2015 ◽  
Vol 157 (1) ◽  
pp. 153-189 ◽  
Author(s):  
Javiera Barrera ◽  
Tito Homem-de-Mello ◽  
Eduardo Moreno ◽  
Bernardo K. Pagnoncelli ◽  
Gianpiero Canessa
Keyword(s):  
Importance Sampling ◽  
Rare Events ◽  
Constrained Problems ◽  
Sampling Approach

scholarly journals The geography of evolutionary divergence in the highly endemic avifauna from the Sierra Madre del Sur, Mexico

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Alberto Rocha-Méndez ◽  
Luis A. Sánchez-González ◽  
Clementina González ◽  
Adolfo G. Navarro-Sigüenza
Keyword(s):  
Hypothesis Testing ◽  
Dna Sequences ◽  
Demographic History ◽  
Central Valley ◽  
Evolutionary Divergence ◽  
Montane Forests ◽  
Historical Factors ◽  
Sierra Madre ◽  
Valley Of Oaxaca ◽  
Sierra Madre Del Sur

Abstract Background Mesoamerica is a remarkable region with a high geological and ecological complexity. Within northern Mesoamerica, the biotic province of the Sierra Madre del Sur (SMS) in southwestern Mexico harbors exceptionally high avian endemism and diversity. Herein, we searched for spatially and temporally concordant phylogeographic patterns, in four bird genera from three distinct avian orders co-distributed across Mesoamerica and investigated their causes through hypothesis testing regarding historical processes. Selected species include endemic and differentiated populations across the montane forests of Mesoamerica, and particularly within the SMS. Results We gathered mitochondrial DNA sequences for at least one locus from 177 individuals across all species. We assessed genetic structure, demographic history, and defined a framework for the coalescent simulations used in biogeographic hypothesis testing temporal and spatial co-variance. Our analyses suggested shared phylogeographic breaks in areas corresponding to the SMS populations, and between the main montane systems in Mesoamerica, with the Central Valley of Oaxaca and the Nicaragua Depression being the most frequently shared breaks among analyzed taxa. Nevertheless, dating analyses and divergence patterns observed were consistent with the hypothesis of broad vicariance across Mesoamerica derived from mechanisms operating at distinct times across taxa in the SMS. Conclusions Our study provides a framework for understanding the evolutionary origins and historical factors enhancing speciation in well-defined regions within Mesoamerica, indicating that the evolutionary history of extant biota inhabiting montane forests is complex and often idiosyncratic.

Importance sampling on coalescent histories. II: Subdivided population models

2004 ◽  
Vol 36 (2) ◽  
pp. 434-454 ◽  
Author(s):  
Maria De Iorio ◽  
Robert C. Griffiths
Keyword(s):  
Importance Sampling ◽  
Dna Sequences ◽  
Sampling Technique ◽  
Population Models ◽  
Gene Trees ◽  
Gene Frequencies ◽  
Sample Distribution ◽  
Subdivided Population ◽  
Importance Sampling Technique ◽  
Ancestral Inference

De Iorio and Griffiths (2004) developed a new method of constructing sequential importance-sampling proposal distributions on coalescent histories of a sample of genes for computing the likelihood of a type configuration of genes in the sample by simulation. The method is based on approximating the diffusion-process generator describing the distribution of population gene frequencies, leading to an approximate sample distribution and finally to importance-sampling proposal distributions. This paper applies that method to construct an importance-sampling algorithm for computing the likelihood of samples of genes in subdivided population models. The importance-sampling technique of Stephens and Donnelly (2000) is thus extended to models with a Markov chain mutation mechanism between gene types and migration of genes between subpopulations. An algorithm for computing the likelihood of a sample configuration of genes from a subdivided population in an infinitely-many-alleles model of mutation is derived, extending Ewens's (1972) sampling formula in a single population. Likelihood calculation and ancestral inference in gene trees constructed from DNA sequences under the infinitely-many-sites model are also studied. The Griffiths-Tavaré method of likelihood calculation in gene trees of Bahlo and Griffiths (2000) is improved for subdivided populations.

scholarly journals The geography of evolutionary divergence in the highly endemic avifauna from the Sierra Madre del Sur, Mexico

2019 ◽  
Author(s):  
Alberto Rocha-Méndez ◽  
LUIS A. SÁNCHEZ-GONZÁLEZ ◽  
CLEMENTINA GONZÁLEZ ◽  
ADOLFO G. NAVARRO-SIGÜENZA
Keyword(s):  
Hypothesis Testing ◽  
Dna Sequences ◽  
Demographic History ◽  
Central Valley ◽  
Evolutionary Divergence ◽  
Montane Forests ◽  
Historical Factors ◽  
Sierra Madre ◽  
Valley Of Oaxaca ◽  
Sierra Madre Del Sur

Abstract Background Mesoamerica is a remarkable region with a high geological and ecological complexity. Within northern Mesoamerica, the biotic province of the Sierra Madre del Sur (SMS) in southwestern Mexico harbors exceptionally high avian endemism and diversity. Herein, we searched for spatially and temporally concordant phylogeographic patterns, in four bird genera from three distinct avian orders co-distributed across Mesoamerica and investigated their causes through hypothesis testing regarding historical processes. Selected species include endemic and differentiated populations across the montane forests of Mesoamerica, and particularly within the SMS. Results We gathered mitochondrial DNA sequences for at least one locus from 177 individuals across all species. We assessed genetic structure, demographic history, and defined a framework for the coalescent simulations used in biogeographic hypothesis testing temporal and spatial co-variance. Our analyses suggested shared phylogeographic breaks in areas corresponding to the SMS populations, and between the main montane systems in Mesoamerica, with the Central Valley of Oaxaca and the Nicaragua Depression being the most frequently shared breaks among analyzed taxa. Nevertheless, dating analyses and divergence patterns observed were consistent with the hypothesis of broad vicariance across Mesoamerica derived from mechanisms operating at distinct times across taxa in the SMS. Conclusions Our study provides a framework for understanding the evolutionary origins and historical factors enhancing speciation in well-defined regions within Mesoamerica, indicating that the evolutionary history of extant biota inhabiting montane forests is complex and often idiosyncratic.

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