scholarly journals mstree: A Multispecies Coalescent Approach for Estimating Ancestral Population Size and Divergence Time during Speciation with Gene Flow

2020 ◽  
Vol 12 (5) ◽  
pp. 715-719
Author(s):  
Junfeng Liu ◽  
Qiao Liu ◽  
Qingzhu Yang
Keyword(s):  
Gene Flow ◽  
Divergence Time ◽  
Ancestral Population ◽  
Migration Model ◽  
Isolation With Migration ◽  
Multispecies Coalescent ◽  
Coalescent Approach ◽  
Population Sizes ◽  
And Migration ◽  
The Relationship

Abstract Gene flow between species may cause variations in branch length and topology of gene tree, which are beyond the expected variations from ancestral processes. These additional variations make it difficult to estimate parameters during speciation with gene flow, as the pattern of these additional variations differs with the relationship between isolation and migration. As far as we know, most methods rely on the assumption about the relationship between isolation and migration by a given model, such as the isolation-with-migration model, when estimating parameters during speciation with gene flow. In this article, we develop a multispecies coalescent approach which does not rely on any assumption about the relationship between isolation and migration when estimating parameters and is called mstree. mstree is available at https://github.com/liujunfengtop/MStree/ and uses some mathematical inequalities among several factors, which include the species divergence time, the ancestral population size, and the number of gene trees, to estimate parameters during speciation with gene flow. Using simulations, we show that the estimated values of ancestral population sizes and species divergence times are close to the true values when analyzing the simulation data sets, which are generated based on the isolation-with-initial-migration model, secondary contact model, and isolation-with-migration model. Therefore, our method is able to estimate ancestral population sizes and speciation times in the presence of different modes of gene flow and may be helpful to test different theories of speciation.

scholarly journals Accounting for Gene Flow from Unsampled ‘Ghost’ Populations while Estimating Evolutionay History under the Isolation with Migration Model

2019 ◽  
Author(s):  
Arun Sethuraman ◽  
Melissa Lynch
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Population Genomics ◽  
Divergence Times ◽  
Effective Population ◽  
Migration Rates ◽  
Isolation With Migration ◽  
Population Sizes ◽  
And Migration ◽  
Erroneous Inferences

AbstractUnsampled or extinct ‘ghost’ populations leave signatures on the genomes of individuals from extant, sampled populations, especially if they have exchanged genes with them over evolutionary time. This gene flow from ‘ghost’ populations can introduce biases when estimating evolutionary history from genomic data, often leading to data misinterpretation and ambiguous results. Here we assess these biases while accounting, or not accounting for gene flow from ‘ghost’ populations under the Isolation with Migration (IM) model. We perform extensive simulations under five scenarios with no gene flow (Scenario A), to extensive gene flow to- and from- an unsampled ‘ghost’ population (Scenarios B, C, D, and E). Estimates of evolutionary history across all scenarios A-E (effective population sizes, divergence times, and migration rates) indicate consistent a) under-estimation of divergence times between sampled populations, (b) over-estimation of effective population sizes of sampled populations, and (c) under-estimation of migration rates between sampled populations, with increased gene flow from the unsampled ‘ghost’ population. Without accounting for an unsampled ‘ghost’, summary statistics like FST are under-estimated, and π is over-estimated with increased gene flow from the‘ghost’. To show this persistent issue in empirical data, we use a 355 locus dataset from African Hunter-Gatherer populations and discuss similar biases in estimating evolutionary history while not accounting for unsampled ‘ghosts’. Considering the large effects of gene flow from these ‘ghosts’, we propose a multi-pronged approach to account for the presence of unsampled ‘ghost’ populations in population genomics studies to reduce erroneous inferences.

scholarly journals On the estimation of ancestral population sizes of modern humans

1997 ◽  
Vol 69 (2) ◽  
pp. 111-116 ◽  
Author(s):  
ZIHENG YANG
Keyword(s):  
Population Size ◽  
Sequence Data ◽  
Divergence Time ◽  
Ancestral Population ◽  
Rate Variation ◽  
Effective Population ◽  
Modern Humans ◽  
Extant Species ◽  
Population Sizes ◽  
Highly Correlated

The theory developed by Takahata and colleagues for estimating the effective population size of ancestral species using homologous sequences from closely related extant species was extended to take account of variation of evolutionary rates among loci. Nuclear sequence data related to the evolution of modern humans were reanalysed and computer simulations were performed to examine the effect of rate variation on estimation of ancestral population sizes. It is found that the among-locus rate variation does not have a significant effect on estimation of the current population size when sequences from multiple loci are sampled from the same species, but does have a significant effect on estimation of the ancestral population size using sequences from different species. The effects of ancestral population size, species divergence time and among-locus rate variation are found to be highly correlated, and to achieve reliable estimates of the ancestral population size, effects of the other two factors should be estimated independently.

scholarly journals Divergence estimation in the presence of incomplete lineage sorting and migration

2017 ◽  
Author(s):  
Graham Jones
Keyword(s):  
Incomplete Lineage Sorting ◽  
Simulated Data ◽  
Species Tree ◽  
Lineage Sorting ◽  
Data Set ◽  
Migration Rates ◽  
Isolation With Migration ◽  
Multispecies Coalescent ◽  
Tree Inference ◽  
And Migration

AbstractThis paper focuses on the problem of estimating a species tree from multilocus data in the presence of incomplete lineage sorting and migration. We develop a mathematical model similar to IMa2 (Hey 2010) for the relevant evolutionary processes which allows both the the population size parameters and the migration rates between pairs of species tree branches to be integrated out. We then describe a BEAST2 package DENIM which based on this model, and which uses an approximation to sample from the posterior. The approximation is based on the assumption that migrations are rare, and it only samples from certain regions of the posterior which seem likely given this assumption. The method breaks down if there is a lot of migration. Using simulations, Leaché et al 2014 showed migration causes problems for species tree inference using the multispecies coalescent when migration is present but ignored. We re-analyze this simulated data to explore DENIM’s performance, and demonstrate substantial improvements over *BEAST. We also re-analyze an empirical data set. [isolation-with-migration; incomplete lineage sorting; multispecies coalescent; species tree; phylogenetic analysis; Bayesian; Markov chain Monte Carlo]

EXTRANUCLEAR DIFFERENTIATION AND GENE FLOW IN THE FINITE ISLAND MODEL

Genetics ◽  
1985 ◽  
Vol 109 (2) ◽  
pp. 441-457
Author(s):  
Naoyuki Takahata ◽  
Stephen R Palumbi
Keyword(s):  
Gene Flow ◽  
Natural Populations ◽  
Island Model ◽  
Published Data ◽  
Sequence Information ◽  
Restriction Maps ◽  
Mt Dna ◽  
Sequence Relatedness ◽  
And Migration ◽  
The Relationship

ABSTRACT Use of sequence information from extranuclear genomes to examine deme structure in natural populations has been hampered by lack of clear linkage between sequence relatedness and rates of mutation and migration among demes. Here, we approach this problem in two complementary ways. First, we develop a model of extranuclear genomes in a population divided into a finite number of demes. Sex-dependent migration, neutral mutation, unequal genetic contribution of separate sexes and random genetic drift in each deme are incorporated for generality. From this model, we derive the relationship between gene identity probabilities (between and within demes) and migration rate, mutation rate and effective deme size. Second, we show how within- and between-deme identity probabilities may be calculated from restriction maps of mitochondrial (mt) DNA. These results, when coupled with our results on gene flow and genetic differentiation, allow estimation of relative interdeme gene flow when deme sizes are constant and genetic variants are selectively neutral. We illustrate use of our results by reanalyzing published data on mtDNA in mouse populations from around the world and show that their geographic differentiation is consistent with an island model of deme structure.

scholarly journals Distinguishing gene flow between malaria parasite populations

2021 ◽  
Author(s):  
Tyler Steven Brown ◽  
Aimee R. Taylor ◽  
Olufunmilayo Arogbokun ◽  
Caroline O. Buckee ◽  
Hsiao-Han Chang
Keyword(s):  
Gene Flow ◽  
Malaria Parasite ◽  
Sequence Data ◽  
Simulated Data ◽  
Whole Genome Sequence ◽  
Effective Population ◽  
Migration Rates ◽  
Population Sizes ◽  
And Migration ◽  
Parasite Populations

Measuring gene flow between malaria parasite populations in different geographic locations can provide strategic information for malaria control interventions. Multiple important questions pertaining to the design of such studies remain unanswered, limiting efforts to operationalize genomic surveillance tools for routine public health use. This report evaluates numerically the ability to distinguish different levels of gene flow between malaria populations, using different amounts of real and simulated data, where data are simulated using parameters that approximate different epidemiological conditions. Specifically, using Plasmodium falciparum  whole genome sequence data and sequence data simulated for a metapopulation with different migration rates and effective population sizes, we compare two estimators of gene flow, explore the number of genetic markers and number of individuals required to reliably rank highly connected locations, and describe how these thresholds change given different effective population sizes and migration rates. Our results have implications for the design and implementation of malaria genomic surveillance efforts.

scholarly journals Defining Species When There is Gene Flow

2020 ◽  
Vol 70 (1) ◽  
pp. 108-119 ◽  
Author(s):  
Xiyun Jiao ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Migration Rates ◽  
Multispecies Coalescent ◽  
Hybridization Rate ◽  
Time Migration ◽  
Powerful Approach ◽  
Population Sizes ◽  
History Of ◽  
Definition Of ◽  
The Impact

Abstract Whatever one’s definition of species, it is generally expected that individuals of the same species should be genetically more similar to each other than they are to individuals of another species. Here, we show that in the presence of cross-species gene flow, this expectation may be incorrect. We use the multispecies coalescent model with continuous-time migration or episodic introgression to study the impact of gene flow on genetic differences within and between species and highlight a surprising but plausible scenario in which different population sizes and asymmetrical migration rates cause a genetic sequence to be on average more closely related to a sequence from another species than to a sequence from the same species. Our results highlight the extraordinary impact that even a small amount of gene flow may have on the genetic history of the species. We suggest that contrasting long-term migration rate and short-term hybridization rate, both of which can be estimated using genetic data, may be a powerful approach to detecting the presence of reproductive barriers and to define species boundaries.[Gene flow; introgression; migration; multispecies coalescent; species concept; species delimitation.]

scholarly journals Historical and current introgression in a Mesoamerican hummingbird species complex: a biogeographic perspective

PeerJ ◽  
2015 ◽  
Vol 4 ◽  
pp. e1556 ◽  
Author(s):  
Rosa Alicia Jiménez ◽  
Juan Francisco Ornelas
Keyword(s):  
Gene Flow ◽  
Species Complex ◽  
Evolutionary History ◽  
Divergence Time ◽  
Haplotype Network ◽  
Genetic Admixture ◽  
Isolation With Migration ◽  
History Of ◽  
Isthmus Of Tehuantepec ◽  
Assignment Analysis

The influence of geologic and Pleistocene glacial cycles might result in morphological and genetic complex scenarios in the biota of the Mesoamerican region. We tested whether berylline, blue-tailed and steely-blue hummingbirds,Amazilia beryllina,Amazilia cyanuraandAmazilia saucerottei, show evidence of historical or current introgression as their plumage colour variation might suggest. We also analysed the role of past and present climatic events in promoting genetic introgression and species diversification. We collected mitochondrial DNA (mtDNA) sequence data and microsatellite loci scores for populations throughout the range of the threeAmaziliaspecies, as well as morphological and ecological data. Haplotype network, Bayesian phylogenetic and divergence time inference, historical demography, palaeodistribution modelling, and niche divergence tests were used to reconstruct the evolutionary history of thisAmaziliaspecies complex. An isolation-with-migration coalescent model and Bayesian assignment analysis were assessed to determine historical introgression and current genetic admixture. mtDNA haplotypes were geographically unstructured, with haplotypes from disparate areas interdispersed on a shallow tree and an unresolved haplotype network. Assignment analysis of the nuclear genome (nuDNA) supported three genetic groups with signs of genetic admixture, corresponding to: (1)A. beryllinapopulations located west of the Isthmus of Tehuantepec; (2)A. cyanurapopulations between the Isthmus of Tehuantepec and the Nicaraguan Depression (Nuclear Central America); and (3)A. saucerotteipopulations southeast of the Nicaraguan Depression. Gene flow and divergence time estimates, and demographic and palaeodistribution patterns suggest an evolutionary history of introgression mediated by Quaternary climatic fluctuations. High levels of gene flow were indicated by mtDNA and asymmetrical isolation-with-migration, whereas the microsatellite analyses found evidence for three genetic clusters with distributions corresponding to isolation by the Isthmus of Tehuantepec and the Nicaraguan Depression and signs of admixture. Historical levels of migration between genetically distinct groups estimated using microsatellites were higher than contemporary levels of migration. These results support the scenario of secondary contact and range contact during the glacial periods of the Pleistocene and strongly imply that the high levels of structure currently observed are a consequence of the limited dispersal of these hummingbirds across the isthmus and depression barriers.

Credit constraints and Rural Migration: Evidence from Six Villages in Uttar Pradesh

2018 ◽  
Vol 15 (3) ◽  
pp. 389-398
Author(s):  
Ruchi Singh
Keyword(s):  
Credit Constraints ◽  
Uttar Pradesh ◽  
Binary Logistic Regression ◽  
Binary Logistic Regression Model ◽  
Male Migration ◽  
Rural Economies ◽  
And Migration ◽  
The Relationship ◽  
The Empirical Analysis

Rural economies in developing countries are often characterized by credit constraints. Although few attempts have been made to understand the trends and patterns of male out-migration from Uttar Pradesh (UP), there is dearth of literature on the linkage between credit accessibility and male migration in rural Uttar Pradesh. The present study tries to fill this gap. The objective of this study is to assess the role of credit accessibility in determining rural male migration. A primary survey of 370 households was conducted in six villages of Jaunpur district in Uttar Pradesh. Simple statistical tools and a binary logistic regression model were used for analyzing the data. The result of the empirical analysis shows that various sources of credit and accessibility to them play a very important role in male migration in rural Uttar Pradesh. The study also found that the relationship between credit constraints and migration varies across various social groups in UP.

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