Class Note for ECOL 406R with Professor Bonine at UA 2
Class Note for ECOL 406R with Professor Bonine at UA 2
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Date Created: 02/06/15
Lecture 15 11 October 2005 Conservation Biology ECOL 406R506R University of Arizona Fall 2005 Kevin Bonine Kathy Gerst Conservation Biolo 406 506R 1 Conservation Genetics Ch6 2 Populations Ch7 3 Thank Rob Robichaux 4 Holldobler talk Mannan Talk LAB In Field Friday 12301600h LAB Field Trip Friday gt Sunday 2123 October Reminder Seminar Wednesday 12 October 2005 This week39s seminar will be presented by Dr William Mannan Professor ofWildlife Ecology School of Natural Resources University of Arizona Topic quotIdentifying habitat sinks a case study of Cooper39s hawks in an urban environmentquot Date time and location 12 October 2005 100200pm NOTE NEW TIME Room 225 Biological Sciences East All are encouraged to attend Introgression RED WOLF Can395 rufus Coyotes Gray wolves Dogs Applications of Genetics to Conservation Biology Molecular Taxonomy Populations Gene Flow Phylogeography Dr Melanie Culver SN39R UA Molecular Taxonomy Using molecules ie DNAbased techniques for systematic study or to define taxonomic units species subspecies ESUs and MUS Molecular Taxonomy Molecules versus Morphology Cryptic species sibling species Morphological variation Without genetic variation Molecular Taxonomy Conservation Relevance 0 Unrecognized species may go extinct Incorrect species recognition Nonoptimal partitioning of management resources Problems with hybridization Incorrect subspecies or population recognition Nonoptimal partitioning of management resources Problems with introgression Populations Gene Flow Phylo geography Compare genetic traits among populations Resolve substructure among populations Infer movement patterns among individuals Infer historical events for species Population Gene Flow Phylogeography Conservation Relevance Determine units for management Heterozygosity estimates 7 Population bottlenecks 7 HardyWeinberg assumptions mutation migration selection drift inbreeding PVA Population Viability Analysis MVP Minimum Viable Population Size Effective population size 7 Number of breeding individuals 10 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 11 Kinship Paternity Individual ID Infer relatedness among individuals 7 First order second order etc Infer patemity maternity Reproductive success male female Interpret reproductive strategies 7 Monogamy harem female choice etc Interpret behaviors 7 Dispersal male female care giving others Individual ID 7 Populations size estimates 7 Forensics 12 Kinship Paternity Individual ID Conservation Relevance Knowledge to aid management 7 Family structure 7 Reproductive strategy 7 Behavior 7 Dispersal 7 Inbreeding 7 Forensicslaw enforcement 13 Important Techniques Phylogenetic Analysis 0 Resolve evolutionary relationships species subspecies populations individuals 0 Tool used to determine Evolutionarin Significant Units ESUS Also resolves Management Units MUS 14 Phylogenetic tree With ESUs and MUS ESU l ESU 2 MU 15 Phylogenetic Analysis Phylogeography Combines phylogeny with geographical locations of populations 0 Three likely outcomes for geographical populations Equally different branches of tree Shallow structure Monophyletic group 16 Phylogenetic Analysis Phylogeography Equally Divergent Shallow and Monophyletic 17 NonInvasive Sampling Allows sampling without disturbance to individual 0 Rare or hard to capture species 0 Examples hair scat feathers salivacheek swab regurgitated pellets dried blood biopsy dart museum tissues 18 NonInvasive Sampling Applications Species ID Individual ID SeX Determination SeX Ratio Gene Flow Previously described applications for genetics in conservation biology 19 NonInvasive Sampling Pros and Cons Allow studies that are not possible by other methods Errorfailure rates associated with having very minimal amount of DNA Use fresh tissues when possible to avoid potential errors 20 10 Examples Taxonomy Population Subdivision Gene Flow Phylogeography 7 Puma cougar mountain lion Kinship and Paternity 7 Madagascar FishEagle Species Inventory 7 Mammals at SNP using noninvasive methods 21 Subspecies Taxonomy Phylogeography Gene Flow Puma cougar mountain lion 11 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 24 12 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 26 13 Mitochondrial DNA Haplotypes in a geographical cline HAMInca V W A u n n I u u Mlnlmum Spannan Network 155Nn5m1a genes comhlnod Absolul Number o Dmemnc Ancestral haplotypes 2 historical radiations mum mm in mm m mm Alumna NA is most recently founded population Scumu um m k mm mm m m m quotmm H n wmmmsm A amnle Flnlmulll l4 Microsatellite Alleles at FCA008 222 an 59 an a Mlnlmum Evolulicn Neighbor Joining Tree 10 Mlcrosalelllles and 252 individuals Pmponion ul glared Alleles distance Geographic clustering quotom Amerlm of individuals 531 mm NSlX groups identi ed 2 distance methods agree Cnnlml South Amerlca39 may mwun 15 Minlmum Evolutlon Neighbor Joining Tree 10 Mlcmsalelllles and 29 Suhapecles Propanlon ol snared Alleles dlmncn Subspecies associate into same 6 groups Statistical support from bootstrap values 2 distance methods agree right s Fst Estimates and Slatkin s Migration Estimates Fst near 1 little divergence nicrosatallites CA 16 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 01d 17 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 35 Ancestor to puma crosses landbridge 23 Mya Puma origin in Brazilian Highlands 300000 ya 18 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 38 19 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 39 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 40 20 1 13mlquot FIND 42 21 I go tree nurh mnwmmluwn as rsaso zdEIBQlqsnlwnm39m39MMMduu 43 wnrhltr nch 7 Hand Mockingbird hatham Mockingbird harlcs Mockingbird http wwwriledurhrsbiGalapagosl agesmockingbirdhhnl 44 46 23 Galapagos Marine Iguana Iguanidae Only lizard to feed at sea algae smweed Up in 10 or 12 m deep Up in a hourlong divs for large mals Darwin shipmate Highly social 8000 indivs km of coast 15 islands Cold upwelling water nourishs algae FernandinaIsabela WWW W s mals to 10 kg femals to almost 3 kg G WhY Water temperam re and enovesa current sn39ength mals only to 1 kg 47 females to lt 1kg Mm mm Prirmelm 48 24 KatrirTa Mangin Mm mm Punzelm 25 Galapagos Marine Iguana lguanidae Galapagos Marine Iguana lguanidae El Nine 9 lack of food Why Starvation bc high cost of salt excretion Animals may lose 15 body length bone absorption Only adult vertebrate known to regularly shrink astronauts Largest animals die sexual selection natural selection Amerhyndms distal5 Marun Vwkelski Winoeton 51 Marnn Wkelskl Princeton 26 What is population Viability analysis PVA Thanks to Margaret Evans 2003 53 Population Viability analysis is a quantitative analysis of population dynamics with the goal of assessing extinction risk Demographic Mathematical Prediction of Data Analysis extinction risk survival and fertility matrix model opopulation growth throughout an time series analysis rate A organism s life cycle branching process extinction population size over stochastic birth probability time death process otime to extinction obirth and death rates reactiondiffusion ofuture population equation size or structure Simulation VS Summary Statistics role of sampling endangered species 27 H 11 anemia uses of PVA pmduns category of Ilse Spud1 1 me minim Assessment at Assassin the extmetmn isk Shaffer 19m Slialfer and exiinmtitt mt cl 3 sing c population snnisan was unde lam Comparing mlalivv nski or Manges mu Falsman ei 1 Mo or inme papulnlinns 1Alllndcrfnal1997 Analyzing and synthesizing Mensa and Comm ms monlmnng am Gerber et al 1999 Guiding identitying key iiie stages Crown et ni I987 management or dmograplnc pmmsscs as management targets Dck lmlnmg how large a Shaffer 1931 Armbmsur and reserve needs to be to yin Land 1993 a desired level at protection imm extineiian Determining how mnny Eustirname 19 Heweiis duals m eiesse to and Edwards Jvnzs 1997 a new populalinn Mushall and sawstd Jonrs 1998 South exal 2mm Setting in aka item a Enpulalion el al 1995 Caswell et al 1998 units on itte hmm Namel etai 1995 Eastman that ate tompati ie with its Tutto c a 1999 continucd existente Deciding how mny popula Menges won iindenmyet lions renamed u Pmtcct a and Pusstllytaln rm spec from mglnnal or globzl exunc on 55 Why do we do population viability analysis U S Endangered Species Act 1973 codi es in law a national policy of avoiding the extinction of species U S National Forest Management Act 1976 ish and wildlife habitat shall be managed to maintain viable populations of existing native and desired nonnative vertebrate species in the planning area In order to insure that viable populations will be maintained habitat must be provided to support at least a minimum number of reproductive individuals and the habitat must be well distributed so that those individuals can interact with others in the planning area U S Marine Mammal Protection Act 1994 amendments stock assessment process 56 28 What do I mean by population dynamics Grizzly bears Yellow stone National Park Number of sheep millions populations are dynamic not static an 45 40 35 E5imnvd number of adult funulus w 1955 1953 1953 I973 197 1953 x988 Year 57 populations are dynamic not static Sheep on the island of Tasmania N o 1820 3940 3960 3980 1900 3920 Year 58 29 lemmings per heclave 40 27 populations are dynamic not static A a J is I 1929 1930 1931 1932 1933 1934 1935 1936 1937 1938 1939 1940 1941 1942 1943 year Lemmings 59 30
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