Class Note for ECOL 406R at UA
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Date Created: 02/06/15
Conservation Lecture 18 19 Oct 2006 CH5 Paradigms CH6 Genetics Genetlcs Mlnlmulll Evaluuon imam1mm Yrm CH7 Populations umwmnmnmmmmn mm 1 9m nilmalame Conservation Biology ECOL 406Rl506R University of Arizona Fall 2006 Kevin Bonine Kathy Gerst Lab this week sewage treatment plant on 20 October web for readings 2729 October ORPI Pinacate CEDO Mexico food see website for lab readings Housekeeping 19 October 2006 506 Topic and References please Upcoming Readings today Text Ch6 Ch 5 and 7 PVA Puma concoor Tues 24 Oct Global Climate Change web for readings Thurs 26 Oct Guy McPherson Tues 31 Oct Ed Moll long web reading Thurs 02 Nov Exam Two Tues 07 Nov Don Falk web reading Short oral presentations 19 Oct Rachel Smith and Shea Cogswell 24 Oct Cori Dolan and Robert Johnson 26 Oct 31 Oct 02 Nov 07 Nov 16 Nov 21 Nov none Move Jon and Laura to 09 Nov Move Dan and Laneto 14 Nov Thursday October 19th at 730 pm Update on Mexican Gray Wolf Jaguar and other TampE species The Center for Biological Diversity invites the public to an illustrated presentation on the Endangered Species Act Thursday October 19th at 730 pm The event is free and will take place at Anjali 330 East 7th Street 12 block west of 4th Ave Michael Robinson the Center39s Predator Conservation Coordinator will give a slideshow about the Act the species that are protected by this important law the success stories of plants and animals that have persisted because of the Act39s protection as well as the current political threats to this law We will also provide information on how to become an effective advocate for endangered species Ed note Michael is a very good speaker and you are guaranteed to see great pictures and get good information The Arid Lands Resource Sciences Graduate Interdisciplinary Program invites you to the dissertation defense of doctoral candidate Maeveen Behan Who will present her dissertation entitled quotScience and Lore in Animal LaW39 on Monday October 23rd at 900 o39clock in the morning in room 113 of the Office of Arid Land Studies located at 1955 East Sixth Street All are encouraged to attend Visitor parking available along the back north fence Global Climate Change Lecture Series All lectures will take place at UA Centennial Hall All lecturesbegm anprn and are See 1e Lhepulzlllc Call 5211 6214an nrmuremfurmauun Tuesday ember 17 Glubal Cllmate Change The Emdenee Ma1eu1rn Hughes Prufessur uf Dendruenrennugy httpcos arizona educlimate Tuesday ember 24 Glubal curnaze Change What s Ahead Junathan OverpeelD1reetur quhe lnshtute fur the Study uf Planet Eann and Prufessur uf Geusnenees Tuesday oauber 31 Glubal Clxmate Change The Rule quryrng Thmgs Trams Huxman Ass1stant meessurufEculugy and Eyu1uuunary Bmlugy Tuesday Nuyember 7 Glubal Clxmate Change Ocean Impacts and Feedbacks lLlea Cale Assumate meessur ufGeusmenees Tuesday Nuyember 14 Glubal Clxmate Change Dlsease and Sneler Andrew cernne Dean quhe Graduate Cullege and Prufessur ufGeugaphy and Regunal Develupmmt Tuesday Nuyember 21 Glubal Clxmate Change Cuu1d Geuengneenng Reverse m Ruger Angel Regents meessur quSlXunumy Tuesday Nuyember 28 Glubal Clxmate Change Desxgqmg Fuhey Respunses Paul Fumey Dean ufthe Eller Cullege ufManagErnent and meessurufEeunumes 5 Shea and Rachel will speak for 10 minutes on Elasmobranchs httpwww fortusgs govresourceseducationbmbtsihome asp C haractu39isncs of the Brown Tree Snake I39EIE eyes 3mm x clh39puu pupils light to dark hrm 1 dursum 1 distinct Shadow 9 marlquot un lmuniumu Matches m 5L httpwww fortusgs govresourceseducationbmbtsihome asp GUAM m Saipan m mwm 1512 v g imiri m Cucus I nmcme suspemed mmem papmam httpwwwforLusgs govresourceseducationbtsbtsihome asp httpwwwf0rtusgs govresourceseducationbtsbtsihome asp Chapter 5 Paradigms Habitat Heterogeneity Disturbance Chap 6 Genetics of Conservation Biology 11 Habitat Heterogeneity Conserve Bigger Area Population Varla Conserve More Diverse HabitatS 5 Figure 523 Popuiaiiorrs of bush crrckei Weinopiem bicoor subunris exempiiiy ihai popuiairan size is iess variabie as heierogerreiiy increases Dark circies indiwie parches where iocai exirrrciiom occurred Whrre circies indicaie parches wiyh exiarrr popuioiiciis Papuiarran variabriiry was measured by he coeHicieni aivarrarrce CV of ioaai papuiaiicrr size and habiiai heierogerreih was measured using digirized irrhared aerrai phoiographs Each paich was assigned vaiues according ia haw much he paich deviaied ham ihe siaridard ievei or gray in ihe pherograpirs some After Kindval 199a Disturbances Endogenous Exogenous Tree Fall in Forest Beaver Dam on Stream AnSLVV is seen cwexedby sand asreadmts walk in mm hamesm mspeclthe darting byhuncane IvanWednzsday Sept 22 2mm mPensacalaEuch m Eeachxeadentswexe mawedta see 39heuhames m the mum ans m hurncanz AP thaAimomj coadapted gene Conservation Genetics eggt20MHCaIIeIes mplexeS polymorphic vs m monomorphic nuuinw mum Hinton C mm Puni i grrmiu rimNu heterozygosity u a f ii give 11 ilnu luiidnmuiiinlICUIxpnunrnnmiumxithml mam umLx mm n imlnnhml ii in ume 39mmpir mvni m wmm xiiiummlmn m umnWWm lcu39ncm mmm Humid mm a rwpniaimn imwnuniu hlmqi hu ill i 7 7 mumin nu Aihiiim xniuainirmiluu ilimululrivi1 i Mmmmm md pupulallmi Wm Groom Meffe ampCarroll 2006 How do we keep the gene pool from becoming a gene puddle Foose 1983 14 Allelic Variation Within and Among Populations m 3L i l 7 Gene Frequenzies a me Palyrnorphir laclln the Club Moss Lycopodium lucldulum Laws Niel Woo geCT Lichfx39zldCT EinghammnNV NewLehanonNv PGM u um n w 050 lulu ll min i no 0 Eli um i l l4 0 00 0 00 mm mm n 055 l an i an n 75 ll 0 32 mm um i 25 Gama ll 0 93 l on 082 091 ll n 07 mm m2 0 m L i l D Z l i no I uu 050 l w h min lull ll5u 0 Di mslnl u 50 um i an I use lulu ii an illim llim m Crepe w Gmum Me e e Carmll ZEIEIE Heterozygosity 1A B L E i i 3 Ecologiml and Life Hislary Correlates with Heterozygosity Ozmpancy of differem life mm Cusmupo n and mmpemm lmpiml gt lmplml gt mmperats gt Hth 13ng n endemim Sph clk s wih bmad geoglaphlc disuibulmn gt endemic species sumal imbim leqllilemmts Overgmuml gt minimal or aqlialic gt underground Degxnu uf specializahon Garwmllsis gt specialisls Climatic nondiliuns Species inhabiting ecological extremes gt legions nl hmmlm mimic variation Degree n 21riariallky Nnnlen39imi39ial gt lcrrimrial Body size Sum gt medium gt Ialge gt my large NUIU organisms lmrmg i given M mm mil In lha 1in r um symbol ml In H gmisi lwh mqgmlry llmn swims mm ll drillmm lllc lvlslnlv ii ilil right 0i me gt wmbiil mm mm waml Wm Gruum Me e e Carrull ZEIEIE Mean Total Heterozygosity HT and Proportion Due to AmongPopulation Differentiation DPW W Taxonomic Groups Number Number Taxon HT of species DPT of species Vertebrates Fishes L 51 195 0135 79 Amphibians 109 116 0315 33 Reptiles 78 85 0258 22 Mammals 67 172 0242 57 Birds 68 80 0076 16 Invertebrates Insects 137 170 0097 46 Crustaceans 52 80 0169 19 Molluscs 145 105 0263 44 Others 160 15 0060 5 Summ Ward et a1 1992 Groom Meffe amp Carroll 2006 17 Allelic Variation Among Populations TARLE 1 1 5 General Correlates of Genetic Variation among Population i 11 Gehe cwia riatior Witllianip cies will be positively correlated With pLoloulaliOn39size 39 L L L L nation b e fwsitiveljr correlated with habitat area 39 39 V miill belgieatet in Species with Wider39ranges 2 3 L 4 Ceneticiva ri animal Willb degatiVely correlated with bodyLsize L Ceneti Variation will b ne atively correlated With rate of chromosomal evolution L theticvariatioxi will be positjyely correlated with populetioh Lsiz f across species 7 Geneticv tiafibn will be lowe inyvertebr tesLtha t iii inv rtebrates planth 5 l6 8 Geneticyfari onshould belloWeirL islandpopulalio s than mainland populations 9 L 2 Genetic vanatlo willlpe Tow erZin endangered species than nonendan39gered species Source After Frankham 1996 Groom Meffe amp Carroll 2006 18 Conservation Genetics 1 Maintain genetic diversity Future response to environmental change Speciation 2 Tools for population monitoring and assessment Conservation Planning 19 Genetic Issues Inbreeding depression Loss of genetic diversity can t respond to change Fragmentation loss of gene flow Genetic drift gt natural selection Mutational meltdown Genetic adaptation to captivity reintroduction Taxonomic uncertainties Define management units MUs Forensics Understand species biology Outbreeding depression 20 10 Effective Population Size and Genetic Variance Bottleneck size IIlUrl Inn lll ll 7n on 393 ui quot er Ill Ill ll exV39Wm Groom Meffe amp Carroll 2006 figure 3 lr 1a1ljol CQl Ll gClf genclin varinnxze remain ingovrr IU generations in a thenretiml idealized populalion nl various genetically l vtivo population sinus N l r arim 21 lion is lost rnnrlomly llimugh genetic drift r 10 ND 10 Average heterozygosily quoto Growth Rate r l l l l Recovery of Variation 102 104 10quot 108 Time in generations Figure 115 After a bottleneck genetic variation as meaSlt ured by average heterozygosity very slowly recovers Recov ery is quickest when populations have a high growth rate r 10 and when the bottleneck is less severe founding number N0 10 or greater Modi ed from Nei 1975 Groom Meffe amp Carroll 2006 11 Rare Alleles and Ne 20 15 m 3393 5 10 H 0 l a a 05 u l l I I l 10 100 1000 10000 100000 N Groom Meffe ampCarroll 2006 Figure 116 Rare alleles are lost from small isolated popula tions of an endangered daisy Rutidosis Ieplorrhynchaides in Australia Modified from Young et a1 1999 23 Inbreeding 6 Outbreeding Depression HL39IA39l uq llllbruxllm lllrp mam lulumlmu llvmwun lm mm mm lw 39 epol39l 59mm Lmlmnl pxlo ltulnnxlums m parents Figure 9 Ollxprmg IIIVNgt x5 ull lmnnd by llu dmm ur n lnlvdnl nl pmnls lowly nvlml parcnb Pludllu inlulul lmllg um an l m than lllmu m llnn39lllll39d plll39unblul llw samv spams lumllllg l quotlnbrccdmg lepmamnx39 Wlmll par l39lllull39vullnIdh39xllilxl1l lu xll lllinghl39lllld39glll llr hvl Un39sls As pdlunh IrL39 mom dblmm wl mll le39 lwlim um um um mulr nlltbru dingduprcsslun and usually u 3mm pnml ullspl39lllg um c vs belnwu Sp u are far lxl39lquottll tl rxlll c 1 um u 1 pm 0 mm m Groom Me ey ampCarr 2006 24 um m1 AM we Mm mic um wmph39 m Samplv wax um my w vam u mk mm mu mmm 1mylc m A hm wlmlc Vth Aunan 39 Hun p wwmmmm mm mum a w h m mm mm mm Mm hm mm Noun Y39mnt sampun m Salupk u Snmyln m w Fm Wm w 5m umlnlhchndl s ulmlvbvnlvm anb Ammo mm vlmlv wwmm ngumk 1 g lkm mm hmrmul IX w sperm M 2m k n ir mw x4 gm 1m Mmuswnlumv mhrm mg mum nf39 nlphm m quotnuke whale mom mva lvgmllv wm m 1mm mm H mm fum aptnrmm wum 1mm whalr yumsllulhn mme awn zmbhvnalU7hlvurwmmnrknmdasMm mm dmyhm onmnm VMadinud mm Bakerund V39alumhu mm Introgression RED WOLF Can395 rufus Coyotes Gray wolves Dogs Forensics Gruum Me e e CarruH ZEIEIE 13 Applications of Genetics to Conservation Biology MoecuarTaxonomy Populations Gene Flow Phylogeography Relatedness Paternity Individual ID Molecular Taxonomy Molecules versus Morphology Cryptic species sibling species Morphological variation without genetic variation 28 14 Relatedness Kinship Paternity and Individual ID Application of molecular genetic techniques using hypervariable repetitive DNA ie microsatellites minisatellites to questions of kinship paternity or individual ID 29 Populations Gene Flow Phylogeography Compare genetic traits among populations Resolve substructure among populations lnfer movement patterns among individuals lnfer historical events for species 15 NonInvasive Sampling Allows sampling without disturbance to individual Rare or hard to capture species Examples hair scat feathers salivacheek swab regurgitated pellets dried blood biopsy dart museum tissues 31 Subspecies Taxonomy Phylogeography Gene Flow Puma cougar mountain lion 16 32 Puma subspecies as of the early 1900s Objectives 0 Does current population differentiation re ect 7 Trinomial descriptions 7 Physical or ecological barriers 7 Isolation by distance 0 Are current levels of genetic variation the same Within each population 0 Does population structure and genetic variation re ect 7 Historic migrations 7 Historic dispersals 7 Historic bottlenecks 34 17 Modern and museum puma samples collected total of 3 15 I Historic Current Contemporary Museum Molecular Methods Used Mitochondrial gene sequencing 7 l6SrRNA 7 NADH5 7 ATPaseS Nuclear microsatellite length determination 7 10 domestic cat microsatellite loci 36 18 Neutral Markers often studied Relevance to natural selection and adaptation Ultimately source of all variation is mutation mutation rate 10394 10396 37 Mitochondrial DNA Haplotypes in a geographical Cline n x a x i 5 u 1 1 s 19 Mlnlmum Spannan Network 155Nn5m1a genes comhlnod Absoluu Number or Different Ancestral haplotypes 2 historical radiations Wm NA is most recently founded population sung um m k mm mm m m m unm u quot2 wwnmmsmo onka mmm Microsatellite Alleles at FCA008 HBH L39UEI 2 20 mum Evolution NeighbnrJoining Tree in Microsaieiiiies and 252 individuals Piaponion oi Shared Alleles distance Geographic clustering of individuals Norm Amerlca mm NSiX groups identi ed 2 distance methods agree Minlmum Evalution Neighborsloining Tree 10 Micmsaieimes and 29 Suhapecles Propanlon ol snared Allelzs dlstancl Subspecies associate into same 6 groups Statistical support from bootstrap values 2 distance methods agree Calculation of FStati comma umHHtmw Muvaleruwu FISI IITI IST mm mm or mum mm may by aLwVH wuqhx Hun we ma mm t man My Mum Haw gvnnmv man 0 mm g 5w mm vmn WWWMHW 1 Wmmhywhewunecattu quotXquot n pmrhrhMulwnuvnryuihmmoly WWWMMMW m m m hmkm n rm 4 nnuuvwl um mm MGMAmi m sullpuvuhnmws nn mum mm Imerqu dumnn mm mmquot WNW yumm 3 SHAWL m5 Immuva out 2 ame mm m nmqnunllhrohwrvrz mama n new m 7 u man mwam Am muv mm Huwmv Wm m Wm my wr vhwnvvnnnnm WWWW mumcamwuw quot quotquotquot quot Gmum Me e seam zuua mum mp mm mvtwmm m wfwlnuw V ight s Fst Estimates and Slatkin s h gration Estimates Fst near 0 little divergence nicmsatallitas 22 Summary 6 groups identi ed using microsatellites mtDNA haplotypes overlayed onto map supports 6 groups Location of 2 ancestral haplotypes Canlrgr America Monhem Major restrictions South America to gene ow Eastern Amazon River Southern Rio Parana X r CenIral R10 Negro 5 And 9 L America es Fossil Record versus Molecular Divergence Estimates Oldest fossils in North and South America date to 0203 Mya From mtDNA mutation rate of l 15 My divergence for extant puma lineages is 390000 years ago From mutation rate of 5 X 10399yr for microsatellite anking regions pumas are less than 230000 years old 45 23 Historical Inferences Extant pumas originated in Brazillian Highlands ancestral haplotypes Fossil record suggests dispersal to NA soon after the common origin in Brazil 2 historical radiation events occurred 47 Ancestor to puma crosses landbridge 23 Mya Puma origin in Brazilian Highlands 300000 ya 24 2 Maj or historical radiations One locally distributed One broad ranging quotmmquot Puma Radiations Puma Bottlenecks Subspecieslevel North America low overall genetic variation Populationlevel Florida monomorphic at 810 microsatellite loci Olympic Peninsula and Vancouver Island monomorphic at 510 microsatellite loci 50 25 Puma Conclusions Pumas originated in Brazil approximately 300000 years ago Possible extirpation and recolonization in North America Pleistocene age Molecular data does not support 32 subdivisions instead 6 groups Pumas are fairly panmictic Within 6 groups 51 Conservation Implications Maintain habitat connectivity within 6 large groups Management should consider effects of bottlenecked populations Eastem cougar Florida panther and Yuma puma management take into account revised subspecies 52 26
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