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This 15 page Class Notes was uploaded by Ross Lynch on Saturday October 3, 2015. The Class Notes belongs to BIOL 208 at Bucknell University taught by Staff in Fall. Since its upload, it has received 47 views. For similar materials see /class/218087/biol-208-bucknell-university in Biology at Bucknell University.
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Date Created: 10/03/15
Systematics is the study of biological diversity and its origins Itfocuses on understanding evolutionary relationships among organisms species higher taxa or other biological entities such as genes and the evolution of the properties of taxa including intrinsic traits ecological interactions and geographic distributions An important part of systematics is the development of methods for various aspects of phylogenetic inference and biological nomenclatureclassification Systematic Biology editorial board Systematics Study of the kinds and diversity of organisms WWWA the relationships among them taxonomy and systems of classification Effigia okeeffeae Archosaur 210 my Harpymimus okadnikovi ii quot Lil Dinosaur 120 my 1 A 0 V e K y F W Cnelumsnunn v p v as Hm y i quot a 2 yx o 47 ea ask 6 av c ca Phylogenetic Tree or cladogram Topology COW Hypothesis Horse Gecko Salamander Time Nodes Internal TIme Branch 4 TermInal l Branch or Tip I Taxon pl Taxa PHVLDGENV Cladogenesis Anagenesis 7 x Rotation of branches Horse Gecko Salamander No change in topology Gecko Cow Horse Salamander New topology Cow Gecko Horse Salamander Cow Horse Gecko Salamander Monophyletic group Natural group Clade Paraphyletic group Cow Horse Gecko Salamander The gecko is the sister axon to the mammals in this tree Steps in phylogen analys Step 1 Select characters for analysis and make data matrix Step 2 Select method and search for the best tree Steps in phylogenetic analysis Step 1 Select characters for analysis and make data matrix Step 2 Select method and search for the best tree Character 7 any heriiahie amihuie iii an nrgzn39sm charaeier state 7 any observed variaiinn iii a given character 17 charaeieis must he hnmnlngnus lie similar heeause nmeeenumm a common aneesmi Horse 1 V Cow 1 1 Gecko 1 1 ooHiIt39w coolImp Salamander Data matrix Steps in phylogenetic analysis Step 1 Select characters for analysis and make data matrix Step 2 Select method and search for the best tree Maximum parsimony Cladistics Simpler explanations are preferred over more complex ones Chooses the tree with the fewest evolutionary steps as best estimate of phylogeny Minimizes confusing effects of homoplasy convergent or analogous characters Fur or Lactation 2 Cow Horse Gecko Salamander Apomorphy derived character state Synapomorphy shared derived character state 22 Horns F Cow Horse Gecko Salamander Autapomorphy unshared derived character state Cow Veitebrae K 39 Horse I Gecko Salamander Plesiomorphy ancestral character state Symplesiomorphy shared ancestral character state 24 Fur Horns Lactation I Vertebrae I I I cow I Horse I Gecko I Salamander Alternate character mappinq method Fur Horns Lactation I Vertebrae I I I cow I Horse I Gecko I Salamander 4 step tree mrmnmrmnemmzwa laman mmn 2an tar10 mmnznmm mnm mom 02min nmm 0mm The 15 possible trees for 4 taxa No taxa No rooted trees 2 1 3 3 4 15 5 105 10 3 X 107 50 3 X 1077 1000 4 X 102864 Horns Fur Lactation I Cow Vertebrae I Gecko I I I Horse Salamander 6 step tree Fur H Lactation I Vertebrae I I I I 4 step tree OITIS Cow Horse Gecko Salamander 1 2 3 4 5 V F L H C Cow 1 1 1 1 1 Horse 1 1 1 0 0 Gecko 1 0 0 0 1 Salamander 1 0 0 0 0 Data matrix Fur H Lactation I Ve rtebrae Brown color Homoplasy OI39 Cow Horse Gecko Salamander 6 steQ tree 2 The Outgroup Used to root the phylogenetic tree Differentiate shared ancestral character states from shared derived ones A brief history of Systematics Phylogeny a branching diagram species or other taxa Kennedy 1929 VWIi Hennig David Swofford FSU 37 x I Today s Goals Construct a phylogeny of vertebrates using the vertebrate example data set Construct a phylogeny for eight primate species using skulls in the lab Using Mesquite Analysis of phylogeny amp character evolution 39ETTicacy oT new drugs a 39 Responses of cells To TreonenTs STrucTure oT a noTural communiTy Can39T examine response of My organism However we can examine a subseT ThaT represenTs The whole BUT ThaT subseT musT be drawn wiThouT Md insufficienlehJiwember licnble l0 elleSl Frequenle need To know WhaT species compose a communiTy How abundanT is each species How do species inTeracT Useful To develop Recovery plans for endangered species ConservaTion plans for naTural areas UndersTanding of succession Sampling Methods Method depends on organisms amp community Secre39ive animals mark 6 recapturequot or capture per unit effortquot methods Sessile organisms quotareaquot quotdistancequot or linetransectquot met ods l We will explore 1 Area sampling 2 Distance sampling What39s Measured Abundance Measures D ensity individualsarea Dominance total basal area per unit area Frequency o of samples with given species What39s Measured Abundance Measures Importance O to 300 Relative density relative dominance relative frequency Importance as a percentage 0100 o Relative contribution 1 of a species to entire community Importance3 Where to Sample Three primary approaches 1 Haphazard or convenience sampling 2 Random sampling or stratifiedrandom sampling 3 Systematic sampling What39s Measured Abundance Measures Relative Densit density sp X as X of total density Relative Dominance basal area sp X as o of total dominance Relative Frequency frequency sp X as lo of total frequency m What39s Measured Diversity Measures Species richness of species in a community Evenness or equitability distribution of individuals among species Species diversit typically combo richness amp evenness Species Diversity Reflects Community Structure Communities w Lion diversity 4 have complex network of trophic pathways Communities w Iow diversity have fewer species a fewer interactions Species Diversity ssume two communities each with 10 species S 100 individuals Cummunity A Community B Sp 1 10 indivtduals l 91 individuals Sp z iu inoiwouais bp 4 i individual Spa 10 individuals Spa 1 mleldual Sp 10 10 indiwduais Sp 10 1 individual H 230 H 050 Species richness 10 Species richness 10 Pielou evenness 10 Pielou evenness 02 5 Species Diversity 3 H27 Zia Inp speciesii Range of values 0 gt a community of only one species 3 or less gt mixed mesophy tic forest of Allegheny Mts 7 or more gt rich forests of Siskiyou Mts of Oregon S California Species Diversity Shannon Wiener Index 5 H39 7 2 p In 19 speciesi1 where1pi n N umber of IncM f1 Total number of 1 Species Diversity coninbuiion in H z Reiaiwe canii What39s Measured Dispersion Measure Individuals distributed in community as Random no relation of one individual to another Uniform regular spacing eg orc ard Clumped individuals of a given species are aggregated N W Spatial Distribution Duspersuon 3 possible arrangements Unlfornl clumped Regular Aggregated Hyperdispersed Underdispersed Morisito Index Id nZX27NNNs1j Range of Values A O gt uniform dispersion 1 gt random dispersion gtgt1gt clumped dispersion Succession M Temporal Variation 1 Primary Succession Occurs on a site previously unoccupied by a community 2 Secondary Succession Occurs on a site previously occupied by a community Dispersion Morisi la Index Id nEsz iNNN71 where n quadrats ptsN totalindividuals 2x2 squares of individuals per quadmupls Succession Temporal Variation Early successional species to late successional Species generate a successional sequence 7 Calle d o Sere Serol stages Veer Alla Cullivllion 22 Secondary Succession M Succession often appears directional with a dynamic equilibrium endpoint 29 hardwood forest or hemlock forest Succession ofan abandoned mu in eastern North Amer ca 2 Succession Within succession can we predict the future success of s ecies m analyze age or sizeclass distributions ciicumierence Classr s Succession Within succession can we predict the future success of species auyiz succuszuu wwcclssrm smiu iiimmune Ciasses mum ui39 Vegetation on Slopes M Typz amp disiribuiion souwacmg slopes g Wnst viig kmwi Succession Within succession can we predict the ture success of species mi Cumlersnce ClassI s Succession Within succession can we predict the ture success of species 84 2 Virtual Forests M Mohn Mill Natural Area SnyderMiddleswar th Natural Area H 91 httg wwwdeuurtments bucknzll edu blclog courses corg blolzos ndex h tml wm We39ll Do Sample forest communities via haphazard random amp systematic sampling using m amp distance methods tstlmate species abundances Examine dispersion richness amp diversity Determine successional trends See environmental effects on species distributions eg N vs Sfacing slopes 31 Assignments Investigate bias in sampling Compare area amp distance sampling Explore spatial distribution amp succession Examine community attributes diversity Understand environmental influences on species distributions Write up answers to 18 questions Population structure Size Human Demography 7 Rate Age structure 7 ohorts 7 Age classes P0 ulationincreases in a eometric ratio p g Populatlon Size N Subsistence increasesin an arithmetic ratio a Nb d pnwmmc m imam um a m Em bases 5 uaalaamuariauueamm Lmuiauyiyamaas g u Dem de rldsri M 0 me mammal 4a In ii Life history tables Age structure k my Age class x Number ofindividualsin an age class nx Probability of surviving to x 1X b ing in an interval ax Probability of dying q Other life history components q 2 Number ofindjviduals alive at interval quot1 midpoint LX X Ages mm e x dx qx Total number ofyears still to be lived TX Life expectancy at age x ex T 29 Survivorship cmves e L L x Lx TX ex 1 900 2550 283 a E 2 700 1650 236 g H e 3 500 950 19 4 300 450 15 5 125 150 12 Whammy awe Mmemum 5 25 25 1 3 mamquot quot
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