Population Structure, Diversity, and Phylogeography in the Near
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Population Structure
Population Structure Population Structure Nonrandom Mating HWE assumes that mating is random in the population Most natural populations deviate in some way from random mating There are various ways in which a species might deviate from random mating We will focus on the two most common departures from random mating: inbreeding population subdivision or substructure Population Structure Nonrandom Mating: Inbreeding Inbreeding occurs when individuals are more likely to mate with relatives than with randomly chosen individuals in the population Increases the probability that offspring are homozygous, and as a result the number of homozygous individuals at genetic markers in a population is increased Increase in homozygosity can lead to lower fitness in some species Increase in homozygosity can have a detrimental effect: For some species the decrease in fitness is dramatic with complete infertility or inviability after only a few generations of brother-sister mating Population Structure Nonrandom Mating: Population Subdivision For subdivided populations, individuals will appear to be inbred due to more homozygotes than expected under the assumption of random mating. Wahlund Effect: Reduction in observed heterozygosity (increased homozygosity) because of pooling discrete subpopulations with different allele frequencies that do not interbreed as a single randomly mating unit. Population Structure Wright's F Statistics Sewall Wright invented a set of measures called F statistics for departures from HWE for subdivided populations. F stands for fixation index, where fixation being increased homozygosity FIS is also known as the inbreeding coefficient. The correlation of uniting gametes relative to gametes drawn at random from within a subpopulation (Individual within the Subpopulation) FST is a measure of population substructure and is most useful for examining the overall genetic divergence among subpopulations Is defined as the correlation of gametes within subpopulations relative to gametes drawn at random from the entire population (Subpopulation within the Total population). -
Comparative Phylogeography As an Integrative Approach to Historical Biogeography
Journal of Biogeography, 28, 819±825 Comparative phylogeography as an integrative approach to historical biogeography ABSTRACT GUEST EDITORIAL Phylogeography has become a powerful approach for elucidating contemporary geographical patterns of evolutionary subdivision within species and species complexes. A recent extension of this approach is the comparison of phylogeographic patterns of multiple co-distributed taxonomic groups, or `comparative phylogeography.' Recent comparative phylogeographic studies have revealed pervasive and previously unrecognized biogeographic patterns which suggest that vicariance has played a more important role in the historical development of modern biotic assemblages than current taxonomy would indicate. Despite the utility of comparative phylogeography for uncovering such `cryptic vicariance', this approach has yet to be embraced by some researchers as a valuable complement to other approaches to historical biogeography. We address here some of the common misconceptions surrounding comparative phylogeography, provide an example of this approach based on the boreal mammal fauna of North America, and argue that together with other approaches, comparative phylogeography can contribute importantly to our understanding of the relationship between earth history and biotic diversi®cation. Keywords Area cladistics, comparative phylogeography, historical biogeography, vicariance. INTRODUCTION In a recent guest editorial Humphries (2000) presented an overview of historical biogeography. He concentrated largely on comparisons -
Genetic Diversity in Partially Selfing Populations with the Stepping-Stone Structure
Heredity 77 (1996) 469—475 Received 20 October 1995 Genetic diversity in partially selfing populations with the stepping-stone structure HIDENORI TACHIDA*t & HIROSHI YOSHIMARU tDepartment of Biology, Faculty of Science, Kyushu University 33, Fukuoka 812, Japan and tPopulation Genetics Laboratory, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305, Japan Amethod to compute identity coefficients of two genes in the stepping-stone model with partial selfing is developed. The identity coefficients in partially selfing populations are computed from those in populations without selfing as functions of s (selfing rate), m (migra- tion rate), N (subpopulation size), n (number of subpopulations) and u (mutation rate). For small m, 1/N and u, it is shown that approximate formulae for the identity coefficients of two genes from different individuals are the same as those in random mating populations if we replace N in the latter with N(1 —s12).Thus,the effects of selfing on genetic variability are summarized as reducing variation within subpopulations and increasing differentiation among subpopulations by reducing the subpopulation size. The extent of biparental inbreeding as measured by the genotypic correlation between truly outcrossed mates was computed in the one-dimensional stepping-stone model. The correlation was shown to be independent of the selfing rate and starts to fall off as the migration rate increases when mN is larger than 0.1. Keywords:biparentalinbreeding, fixation index, genetic variability, geographical differentia- tion, selfing, stepping-stone model. Introduction Model analysis Manyplant species are partially self-fertilizing Genesare defined to be identical by descent if they (Brown, 1990; Murawski & Hamrick, 1991, 1992; have a common ancestor gene and there is no muta- Kitamura et a!., 1994). -
University of Florida Thesis Or Dissertation Formatting
TOOLS FOR BIODIVERSITY ANALYSES USING NATURAL HISTORY COLLECTIONS AND REPOSITORIES: DATA MINING, MACHINE LEARNING AND PHYLODIVERSITY By CHANDRA EARL A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2020 1 . © 2020 Chandra Earl 2 . ACKNOWLEDGMENTS I thank my co-chairs and members of my supervisory committee for their mentoring and generous support, my collaborators and colleagues for their input and support and my parents and siblings for their loving encouragement and interest. 3 . TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 3 LIST OF TABLES ............................................................................................................ 5 LIST OF FIGURES .......................................................................................................... 6 ABSTRACT ..................................................................................................................... 8 CHAPTER 1 INTRODUCTION ...................................................................................................... 9 2 GENEDUMPER: A TOOL TO BUILD MEGAPHYLOGENIES FROM GENBANK DATA ...................................................................................................................... 12 Materials and Methods........................................................................................... -
Resolving Postglacial Phylogeography Using High-Throughput Sequencing
Resolving postglacial phylogeography using high-throughput sequencing Kevin J. Emerson1, Clayton R. Merz, Julian M. Catchen, Paul A. Hohenlohe, William A. Cresko, William E. Bradshaw, and Christina M. Holzapfel Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR 97403-5289 Edited by David L. Denlinger, Ohio State University, Columbus, OH, and approved August 4, 2010 (received for review May 11, 2010) The distinction between model and nonmodel organisms is becom- not useful for determining the genetic similarity in closely related ing increasingly blurred. High-throughput, second-generation se- populations of nonmodel species or species for which whole-genome quencing approaches are being applied to organisms based on their resequencing is not yet possible. interesting ecological, physiological, developmental, or evolutionary Phylogeography and phylogenetics have recently benefited from properties and not on the depth of genetic information available for genome-wide SNP detection methods to elucidate patterns of fi them. Here, we illustrate this point using a low-cost, ef cient tech- variation in model taxa or their close relatives (7, 13). The limiting fi nique to determine the ne-scale phylogenetic relationships among step in the applicability of multilocus datasets in nonmodel organ- recently diverged populations in a species. This application of restric- isms has been generating the genetic markers to be used (14). tion site-associated DNA tags (RAD tags) reveals previously unre- solved genetic structure and direction of evolution in the pitcher Baird et al. (4) developed a second generation sequencing ap- plant mosquito, Wyeomyia smithii, from a southern Appalachian proach that allowed for the simultaneous discovery and typing of Mountain refugium following recession of the Laurentide Ice Sheet thousands of SNPs throughout the genome (5). -
S41598-021-95872-0.Pdf
www.nature.com/scientificreports OPEN Phylogeography, colouration, and cryptic speciation across the Indo‑Pacifc in the sea urchin genus Echinothrix Simon E. Coppard1,2*, Holly Jessop1 & Harilaos A. Lessios1 The sea urchins Echinothrix calamaris and Echinothrix diadema have sympatric distributions throughout the Indo‑Pacifc. Diverse colour variation is reported in both species. To reconstruct the phylogeny of the genus and assess gene fow across the Indo‑Pacifc we sequenced mitochondrial 16S rDNA, ATPase‑6, and ATPase‑8, and nuclear 28S rDNA and the Calpain‑7 intron. Our analyses revealed that E. diadema formed a single trans‑Indo‑Pacifc clade, but E. calamaris contained three discrete clades. One clade was endemic to the Red Sea and the Gulf of Oman. A second clade occurred from Malaysia in the West to Moorea in the East. A third clade of E. calamaris was distributed across the entire Indo‑Pacifc biogeographic region. A fossil calibrated phylogeny revealed that the ancestor of E. diadema diverged from the ancestor of E. calamaris ~ 16.8 million years ago (Ma), and that the ancestor of the trans‑Indo‑Pacifc clade and Red Sea and Gulf of Oman clade split from the western and central Pacifc clade ~ 9.8 Ma. Time since divergence and genetic distances suggested species level diferentiation among clades of E. calamaris. Colour variation was extensive in E. calamaris, but not clade or locality specifc. There was little colour polymorphism in E. diadema. Interpreting phylogeographic patterns of marine species and understanding levels of connectivity among popula- tions across the World’s oceans is of increasing importance for informed conservation decisions 1–3. -
A Southern California Freeway Is a Physical and Social Barrier to Gene Flow in Carnivores
Molecular Ecology (2006) 15, 1733–1741 doi: 10.1111/j.1365-294X.2006.02907.x FAST-TRACKBlackwell Publishing Ltd A southern California freeway is a physical and social barrier to gene flow in carnivores SETH P. D. RILEY,*† JOHN P. POLLINGER,* RAYMOND M. SAUVAJOT,*† ERIC C. YORK,† CASSITY BROMLEY,† TODD K. FULLER‡ and ROBERT K. WAYNE* *Department of Ecology and Evolutionary Biology, 621 Charles Young Dr. South, University of California, Los Angeles, CA 90095, USA, †Santa Monica Mountains National Recreation Area, National Park Service, 401 W. Hillcrest Dr., Thousand Oaks, CA 91360, USA, ‡Department of Natural Resources Conservation, Holdsworth Natural Resources Center, 160 Holdsworth Way, Amherst, MA 01003-9285, USA Abstract Roads present formidable barriers to dispersal. We examine movements of two highly mobile carnivores across the Ventura Freeway near Los Angeles, one of the busiest highways in the United States. The two species, bobcats and coyotes, can disappear from habitats isolated and fragmented by roads, and their ability to disperse across the Ventura Freeway tests the limits of vertebrates to overcome anthropogenic obstacles. We combine radio- telemetry data and genetically based assignments to identify individuals that have crossed the freeway. Although the freeway is a significant barrier to dispersal, we find that carnivores can cross the freeway and that 5–32% of sampled carnivores crossed over a 7-year period. However, despite moderate levels of migration, populations on either side of the freeway are genetically differentiated, and coalescent modelling shows their genetic isolation is consistent with a migration fraction less than 0.5% per generation. These results imply that individuals that cross the freeway rarely reproduce. -
Population Structure, Genetic Diversity, and Gene Introgression of Two Closely Related Walnuts (Juglans Regia and J
Article Population Structure, Genetic Diversity, and Gene Introgression of Two Closely Related Walnuts (Juglans regia and J. sigillata) in Southwestern China Revealed by EST-SSR Markers Xiao-Ying Yuan, Yi-Wei Sun, Xu-Rong Bai, Meng Dang, Xiao-Jia Feng, Saman Zulfiqar and Peng Zhao * Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; [email protected] (X.-Y.Y.); [email protected] (Y.-W.S.); [email protected] (X.-R.B.); [email protected] (M.D.); [email protected] (X.-J.F.); [email protected] (S.Z.) * Correspondence: [email protected]; Tel./Fax: +86-29-88302411 Received: 20 September 2018; Accepted: 12 October 2018; Published: 16 October 2018 Abstract: The common walnut (Juglans regia L.) and iron walnut (J. sigillata Dode) are well-known economically important species cultivated for their edible nuts, high-quality wood, and medicinal properties and display a sympatric distribution in southwestern China. However, detailed research on the genetic diversity and introgression of these two closely related walnut species, especially in southwestern China, are lacking. In this study, we analyzed a total of 506 individuals from 28 populations of J. regia and J. sigillata using 25 EST-SSR markers to determine if their gene introgression was related to sympatric distribution. In addition, we compared the genetic diversity estimates between them. Our results indicated that all J. regia populations possess slightly higher genetic diversity than J. sigillata populations. The Geostatistical IDW technique (HO, PPL, NA and PrA) revealed that northern Yunnan and Guizhou provinces had high genetic diversity for J. -
The Comparison Between Wright's Fixation Index (FST) and The
Genetics: Published Articles Ahead of Print, published on March 4, 2007 as 10.1534/genetics.106.062901 The effect of dominance on the use of the QST-FST contrast to detect natural selection on quantitative traits Carlos López-Fanjul 1, Almudena Fernández 2 and Miguel A. Toro 2 1Departamento de Genética, Facultad de Ciencias Biológicas, Universidad Complutense, 28040 Madrid, Spain. 2Departamento de Mejora Genética Animal, SGIT-INIA, 28040 Madrid, Spain. Corresponding author: Carlos López-Fanjul Departamento de Genética, Facultad de Ciencias Biológicas, Universidad Complutense, 28040 Madrid, Spain. Phone No.: 34-1-394-4852 Fax No.: 34-1-394-4844 e-mail: [email protected] 1 The comparison between Wright’s among-population fixation index FST (a descriptor of the effect of the breeding structure on population diversity for neutral genes) and Spitze’s quantitative index of population divergence QST (defined as Vb/(Vb+2Vw), where Vb and Vw are, respectively, the between- and the additive within- population components of variance for the trait considered) is widely used to assess the relative importance of selection and drift as determinants of the genetic differentiation for quantitative traits. For neutral genes with additive gene action between and within loci, QST is the quantitative analogue of FST. Otherwise, divergent or convergent selection is invoked, respectively, as a cause of the observed increase (QST > FST) or decrease (QST < FST) of QST from its neutral expectation (QST = FST). However, the validity of the QST-FST contrast has been questioned, as neutral non-additive gene action (dominance and/or epistasis) can mimic the additive expectations under selection (LÓPEZ-FANJUL et al. -
Molecular Phylogenetics: Principles and Practice
REVIEWS STUDY DESIGNS Molecular phylogenetics: principles and practice Ziheng Yang1,2 and Bruce Rannala1,3 Abstract | Phylogenies are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection and the demographic changes and migration patterns of species. The advancement of sequencing technologies has taken phylogenetic analysis to a new height. Phylogenies have permeated nearly every branch of biology, and the plethora of phylogenetic methods and software packages that are now available may seem daunting to an experimental biologist. Here, we review the major methods of phylogenetic analysis, including parsimony, distance, likelihood and Bayesian methods. We discuss their strengths and weaknesses and provide guidance for their use. statistical Systematics Before the advent of DNA sequencing technologies, phylogenetics, creating the emerging field of 2,18,19 The inference of phylogenetic phylogenetic trees were used almost exclusively to phylogeography. In species tree methods , the gene relationships among species describe relationships among species in systematics and trees at individual loci may not be of direct interest and and the use of such information taxonomy. Today, phylogenies are used in almost every may be in conflict with the species tree. By averaging to classify species. branch of biology. Besides representing the relation- over the unobserved gene trees under the multi-species 20 Taxonomy ships among species on the tree of life, phylogenies -
Definition and Estimation of Higher-Order Gene Fixation Indices
Copyright 0 1987 by the Genetics Society of America Definition and Estimation of Higher-Order Gene Fixation Indices Kermit Ritland Department of Botany, University of Toronto, Toronto, M5S IAl Canada Manuscript received March 26, 1987 Revised copy accepted August 15, 1987 ABSTRACT Fixation indices summarize the associations between genes that arise from the joint effects of inbreeding and selection. In this paper, fixation indices are derived for pairs, triplets and quadruplets of genes at a single multiallelic locus. The fixation indices are obtained by dividing cumulants by constants; the cumulants describe the statistical distribution of alleles and the constants are functions of gene frequency. The use of cumulants instead of moments is necessary only for four-gene indices, when the fourth cumulant is used. A second type of four-gene index is also required, and this index is based upon the covariation of second-order cumulants. At multiallelic loci, a large number of indices is possible. If alleles are selectively neutral, the number of indices is reduced and the relationship between gene identity and gene cumulants is shown.-Two-gene indices can always be estimated from genotypic frequency data at a single polymorphic locus. Three-gene indices are also estimable except when allele frequency equals one-half. Four-gene indices are not estimable unless selection is assumed to have an equal effect upon each allele (such as under selective neutrality) and the locus contains at least three alleles of unequal frequency. For diallelic or selected loci, an alternative four- gene fixation index is proposed. This index incorporates both types of four-gene associations but cannot be related to gene identity. -
Phylogeography of Three Heteromyid Taxa: Insight on the Evolution of a North American Arid Grassland Rodent Guild
UNLV Theses, Dissertations, Professional Papers, and Capstones 5-2011 Phylogeography of three heteromyid taxa: Insight on the evolution of a North American arid grassland rodent guild Sean A. Neiswenter University of Nevada, Las Vegas Follow this and additional works at: https://digitalscholarship.unlv.edu/thesesdissertations Part of the Biology Commons, and the Desert Ecology Commons Repository Citation Neiswenter, Sean A., "Phylogeography of three heteromyid taxa: Insight on the evolution of a North American arid grassland rodent guild" (2011). UNLV Theses, Dissertations, Professional Papers, and Capstones. 1013. http://dx.doi.org/10.34917/2354145 This Dissertation is protected by copyright and/or related rights. It has been brought to you by Digital Scholarship@UNLV with permission from the rights-holder(s). You are free to use this Dissertation in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/or on the work itself. This Dissertation has been accepted for inclusion in UNLV Theses, Dissertations, Professional Papers, and Capstones by an authorized administrator of Digital Scholarship@UNLV. For more information, please contact [email protected]. PHYLOGEOGRAPHY OF THREE HETEROMYID TAXA: INSIGHTS ON THE EVOLUTION OF A NORTH AMERICAN ARID GRASSLAND RODENT GUILD by Sean Adam Neiswenter Bachelor of Science Angelo State University 2002 Master of Science Angelo State University 2004 A dissertation submitted in partial fulfillment of the requirements for the Doctor of Philosophy in Biological Sciences College of Sciences Graduate Department University of Nevada, Las Vegas May 2011 Copyright by Sean A.