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 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 DILS: Demographic Inferences with Linked Selection by using ABC

2020 ◽  
Author(s):  
Christelle Fraïsse ◽  
Iva Popovic ◽  
Clément Mazoyer ◽  
Bruno Spataro ◽  
Stéphane Delmotte ◽  
...  
Keyword(s):  
Gene Flow ◽  
Published Data ◽  
Demographic Model ◽  
Size Change ◽  
Genetic Patterns ◽  
And Migration ◽  
Approximate Bayesian ◽  
Genomic Regions ◽  
Analysis Platform ◽  
Linked Selection

ABSTRACTWe present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single-population or two-population datasets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: 1) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, 2) the best genomic model to determine whether the effective size Ne and migration rate N.m are heterogeneously distributed along the genome (implying linked selection) and 3) loci in genomic regions most associated with barriers to gene flow. Also available via a web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations, and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.

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.

Two Gambling Women

2012 ◽  
Vol 5 (1) ◽  
pp. 39-49
Author(s):  
Tzu-Hui Chen
Keyword(s):  
Lived Experiences ◽  
Personal Experience ◽  
Cultural Context ◽  
Cross Cultural ◽  
Immigrant Population ◽  
The Other ◽  
Mail Order ◽  
Foreign Brides ◽  
And Migration ◽  
The Relationship

This narrative aims to explore the meaning and lived experiences of marriage that a unique immigrant population—“foreign brides” in Taiwan—possesses. This convergence narrative illustrates the dynamics and complexity of mail-order marriage and women's perseverance in a cross-cultural context. The relationship between marriage, race, and migration is analyzed. This narrative is comprised of and intertwined by two story lines. One is the story of two “foreign brides” in Taiwan. The other is my story about my cross-cultural relationship. All the dialogues are generated by 25 interviews of “foreign brides” in Taiwan and my personal experience.

Update on the Boundaries of the Curly Birch Range

2020 ◽  
pp. 9-21
Author(s):  
L.V. Vetchinnikova ◽  
◽  
A.F. Titov ◽  
◽  
Keyword(s):  
Population Size ◽  
Natural Populations ◽  
Forest Tree ◽  
Published Data ◽  
Population Approach ◽  
Key Factors ◽  
History Of ◽  
Individual Trees ◽  
Karelian Birch

The article reports on the application of the best known principles for mapping natural populations of curly (Karelian) birch Betula pendula Roth var. carelica (Mercklin) Hämet-Ahti – one of the most appealing representatives of the forest tree flora. Relying on the synthesis and analysis of the published data amassed over nearly 100 years and the data from own full-scale studies done in the past few decades almost throughout the area where curly birch has grown naturally, it is concluded that its range outlined in the middle of the 20th century and since then hardly revised is outdated. The key factors and reasons necessitating its revision are specified. Herewith it is suggested that the range is delineated using the population approach, and the key element will be the critical population size below which the population is no longer viable in the long term. This approach implies that the boundaries of the taxon range depend on the boundaries of local populations (rather than the locations of individual trees or small clumps of trees), the size of which should not be lower than the critical value, which is supposed to be around 100–500 trees for curly birch. A schematic map of the curly birch range delineated using this approach is provided. We specially address the problem of determining the minimum population size to secure genetic diversity maintenance. The advantages of the population approach to delineating the distribution range of curly birch with regard to its biological features are highlighted. The authors argue that it enables a more accurate delineation of the range; shows the natural evolutionary history of the taxon (although it is not yet officially recognized as a species) and its range; can be relatively easily updated (e.g. depending on the scope of reintroduction); should be taken into account when working on the strategy of conservation and other actions designed to maintain and regenerate this unique representative of the forest tree flora.

scholarly journals Intraspecific Latitudinal Variation in Nest Orientation Among Ground-Nesting Passerines: A Study Using Published Data

The Condor ◽  
2007 ◽  
Vol 109 (2) ◽  
pp. 441-446 ◽  
Author(s):  
Niall H.K. Burton
Keyword(s):  
Early Morning ◽  
Published Data ◽  
Nest Entrance ◽  
Clear Trend ◽  
European Species ◽  
Statistical Comparison ◽  
Species Comparisons ◽  
Nest Microclimate ◽  
The Relationship ◽  
Ground Nesting

Abstract The relationship between nest entrance orientation and latitude among ground-nesting passerines was reviewed using published information. Data were collated for seven North American and European species. Pooling within-species comparisons, there was a clear trend from a preference for north-facing nests at lower latitudes to eastward- or southward-facing nests farther north. Orientations differed significantly in eight of 12 cases for which statistical comparison was possible, means differing in the expected direction in six of these cases. These results highlight how the influence of solar radiation on nest microclimate typically delineates preferred nest orientation in these species, i.e., at lower latitudes, the need for shade results in a preference for northward orientations; at mid latitudes, eastward orientations predominate, reflecting a probable balance between the benefits of warmth in the early morning and shade in the afternoon; while at high latitudes, nests may be oriented southward to gain warmth throughout the day.

ITS sequence variation supports the hybrid origin of Malus toringoides Hughes

2007 ◽  
Vol 85 (7) ◽  
pp. 659-666 ◽  
Author(s):  
Ting-Ting Feng ◽  
Zhi-Qin Zhou ◽  
Jian-Min Tang ◽  
Ming-Hao Cheng ◽  
Shi-Liang Zhou
Keyword(s):  
Sequence Variation ◽  
Gene Tree ◽  
Natural Populations ◽  
Its Sequences ◽  
Nuclear Ribosomal Dna ◽  
Hybrid Origin ◽  
Putative Hybrid ◽  
Molecular Evidence ◽  
Sequence Information ◽  
Aflp Data

Malus toringoides (Rehd.) Hughes was suggested to have originated from hybridization between Malus transitoria Schneid. and Malus kansuensis Rehd., followed by repeated backcrossing to one of the putative parents. In the present study, the sequence information of the internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA) was used to re-examine the origin of this species. A total of 69 accessions from three natural populations (Maerkang, Xiaba and Kehe, Aba Autonomous Region, Sichuan, China) of M. toringoides and 10 accessions of its putative parents were analyzed. Using Malus angustifolia (Ait.) Michx., Malus ioensis (Wood) Britt. and Malus doumeri Chev. as outgroups, our phylogenetic analysis of the ITS sequences of M. toringoides and its putative parents showed that M. toringoides was not monophyletic, and two different types of ITS sequences which were obtained from each of the six accessions of M. toringoides were found to have clustered separately with those of the two putative parent species on the gene tree. A comparison of the sequence variation between M. toringoides and its putative parents revealed an additive variation pattern of ITS sequences in the putative hybrid species. These results are consistent with the previous morphological and amplified fragment length polymorphism (AFLP) data which suggested that M. toringoides was of hybrid origin. Our ITS data provide new molecular evidence for the hybrid origin hypothesis of M. toringoides and these results are of great importance for future study on hybridization, polyploid speciation and evolution of the genus Malus Miller.

scholarly journals AHA1 upregulates IDH1 and metabolic activity to promote growth and metastasis and predicts prognosis in osteosarcoma

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Diwei Zheng ◽  
Weihai Liu ◽  
Wenlin Xie ◽  
Guanyu Huang ◽  
Qiwei Jiang ◽  
...  
Keyword(s):  
Metabolic Activity ◽  
Cancer Metabolism ◽  
Cancer Metastasis ◽  
Isocitrate Dehydrogenase 1 ◽  
Cell Growth And Migration ◽  
And Migration ◽  
The Relationship ◽  
Common Primary Malignant Bone

AbstractOsteosarcoma (OS) is the most common primary malignant bone tumor in children and adolescents. Although activator of HSP90 ATPase activity 1 (AHA1) is reported to be a potential oncogene, its role in osteosarcoma progression remains largely unclear. Since metabolism reprogramming is involved in tumorigenesis and cancer metastasis, the relationship between AHA1 and cancer metabolism is unknown. In this study, we found that AHA1 is significantly overexpressed in osteosarcoma and related to the prognosis of osteosarcoma patients. AHA1 promotes the growth and metastasis of osteosarcoma both in vitro and in vivo. Mechanistically, AHA1 upregulates the metabolic activity to meet cellular bioenergetic needs in osteosarcoma. Notably, we identified that isocitrate dehydrogenase 1 (IDH1) is a novel client protein of Hsp90-AHA1. Furthermore, the IDH1 protein level was positively correlated with AHA1 in osteosarcoma. And IDH1 overexpression could partially reverse the effect of AHA1 knockdown on cell growth and migration of osteosarcoma. Moreover, high IDH1 level was also associated with poor prognosis of osteosarcoma patients. This study demonstrates that AHA1 positively regulates IDH1 and metabolic activity to promote osteosarcoma growth and metastasis, which provides novel prognostic biomarkers and promising therapeutic targets for osteosarcoma patients.

An ecological explanation for hyperallometric scaling of reproduction

2021 ◽  
Author(s):  
Tomos Potter ◽  
Anja Felmy
Keyword(s):  
Body Size ◽  
Reproductive Output ◽  
Resource Competition ◽  
Natural Populations ◽  
Scaling Exponent ◽  
Wild Populations ◽  
Wet Season ◽  
Size Dependent ◽  
In The Wild ◽  
The Relationship

AbstractIn wild populations, large individuals have disproportionately higher reproductive output than smaller individuals. We suggest an ecological explanation for this observation: asymmetry within populations in rates of resource assimilation, where greater assimilation causes both increased reproduction and body size. We assessed how the relationship between size and reproduction differs between wild and lab-reared Trinidadian guppies. We show that (i) reproduction increased disproportionately with body size in the wild but not in the lab, where effects of resource competition were eliminated; (ii) in the wild, the scaling exponent was greatest during the wet season, when resource competition is strongest; and (iii) detection of hyperallometric scaling of reproduction is inevitable if individual differences in assimilation are ignored. We propose that variation among individuals in assimilation – caused by size-dependent resource competition, niche expansion, and chance – can explain patterns of hyperallometric scaling of reproduction in natural populations.

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