Applications of Genetics to Conservation Biology -Molecular Taxonomy -Population Genetics and Gene Flow -Relatedness (Kins...
How can genetics minimize extinction? <ul><li>Understanding species biology </li></ul><ul><ul><li>Relatedness (kinship, pa...
How can genetics minimize extinction? (continued) <ul><li>Detect and minimize inbreeding and loss of genetic diversity </l...
Molecular Taxonomy -Using molecules   (ie. DNA based techniques such as mitochondrial DNA or nuclear DNA)  to define taxon...
Molecular Taxonomy: Molecules versus Morphology <ul><li>Cryptic species (sibling species) </li></ul><ul><li>Morphological ...
Molecular Taxonomy: Conservation Relevance <ul><li>Unrecognized species may go extinct </li></ul><ul><li>Incorrect species...
Population Genetics and Gene Flow -Compare genetic traits among populations -Resolve substructure among populations -Infer...
Population Genetics and  Gene Flow: Conservation Relevance <ul><li>Determine units for management </li></ul><ul><li>Hetero...
Relatedness (Kinship, Paternity and Individual ID) -Application of molecular genetic techniques (using hypervariable, repe...
Kinship, Paternity, Individual ID: <ul><li>Infer relatedness among individuals </li></ul><ul><ul><li>First order (siblings...
Kinship, Paternity, Individual ID: Conservation Relevance <ul><li>Knowledge to aid management </li></ul><ul><ul><li>Family...
Examples <ul><li>Taxonomy, Population Subdivision, Gene Flow </li></ul><ul><ul><li>Puma (cougar, mountain lion) </li></ul>...
Subspecies Taxonomy and Gene Flow: Puma (cougar, mountain lion)
32 Puma subspecies, as of the early 1900s
Objectives <ul><li>Does current population differentiation reflect </li></ul><ul><ul><li>Subspecies descriptions? </li></u...
Molecular Methods Used <ul><li>Mitochondrial gene sequencing </li></ul><ul><ul><li>3 genes </li></ul></ul><ul><li>Nuclear ...
Mitochondrial DNA Haplotypes (in a geographical cline)
Microsatellite Alleles at FCA008
-Geographic clustering  of individuals ~Six groups identified 2 distance methods agree
Major restrictions  to gene flow: -Amazon River -Rio Parana -Rio Negro -Andes?
Fossil Record versus Molecular Divergence Estimates <ul><li>Oldest fossils in North and South America are ~250,000 years o...
Historical Inferences <ul><li>Extant pumas originated in Brazillian Highlands (ancestral haplotypes) </li></ul><ul><li>Dis...
-Ancestor to puma crosses  land-bridge ~2-3 Mya -Puma origin in Brazillian  Highlands ~300,000 ya
2 Major historical radiations -One locally distributed -One broad ranging
Puma Bottlenecks <ul><li>Subspecies-level </li></ul><ul><ul><li>North America low overall genetic variation </li></ul></ul...
Conclusions <ul><li>Possible extirpation and recolonization in North America (Pleistocene age?) </li></ul><ul><li>Molecula...
Conservation Implications <ul><li>Maintain habitat connectivity within 6 large groups </li></ul><ul><li>Management should ...
Paternity Application: Madagascar Fish-Eagle Ruth Tingay, PhD candidate U of Nottingham,
Antsalova wetland region of  western Madagascar                                                                   
Background and Methods <ul><li>Endangered eagle in Madagascar </li></ul><ul><li>2-3 males, and one female, attend each nes...
DNA Fingerprinting Alleles at 4 nests (6 representative bands out of 34)
Conclusions <ul><li>At all nests  with young (n=3), subordinate males fathered all offspring </li></ul><ul><li>Dominant ma...
Conservation Implications <ul><li>Preliminary results, more samples needed </li></ul><ul><li>Advantageous to raise young o...
 
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Ppt molecular tax

  1. 1. Applications of Genetics to Conservation Biology -Molecular Taxonomy -Population Genetics and Gene Flow -Relatedness (Kinship, Paternity, Individual ID)
  2. 2. How can genetics minimize extinction? <ul><li>Understanding species biology </li></ul><ul><ul><li>Relatedness (kinship, paternity, individual ID) </li></ul></ul><ul><ul><li>Gene flow (migration, dispersal, movement patterns) </li></ul></ul><ul><li>Molecular Systematics </li></ul><ul><ul><li>Resolve taxonomic uncertainty </li></ul></ul><ul><ul><li>Resolve population structure </li></ul></ul><ul><ul><li>Define management units </li></ul></ul><ul><ul><li>Identify populations of conservation concern </li></ul></ul>
  3. 3. How can genetics minimize extinction? (continued) <ul><li>Detect and minimize inbreeding and loss of genetic diversity </li></ul><ul><li>Detect and minimize hybridization </li></ul><ul><li>Identify best population for reintroduction </li></ul>
  4. 4. Molecular Taxonomy -Using molecules (ie. DNA based techniques such as mitochondrial DNA or nuclear DNA) to define taxonomic units (species, subspecies, ESUs and MUs)
  5. 5. Molecular Taxonomy: Molecules versus Morphology <ul><li>Cryptic species (sibling species) </li></ul><ul><li>Morphological variation without genetic variation </li></ul>
  6. 6. Molecular Taxonomy: Conservation Relevance <ul><li>Unrecognized species may go extinct </li></ul><ul><li>Incorrect species recognition </li></ul><ul><ul><li>Non-optimal use of management resources </li></ul></ul><ul><ul><li>Problems with hybridization </li></ul></ul><ul><li>Incorrect subspecies or population recognition </li></ul><ul><ul><li>Non-optimal use of management resources </li></ul></ul><ul><ul><li>Problems with introgression </li></ul></ul>
  7. 7. Population Genetics and Gene Flow -Compare genetic traits among populations -Resolve substructure among populations -Infer movement patterns among individuals -Infer historical events for species
  8. 8. Population Genetics and Gene Flow: Conservation Relevance <ul><li>Determine units for management </li></ul><ul><li>Heterozygosity estimates </li></ul><ul><ul><li>Population bottlenecks </li></ul></ul><ul><ul><li>Hardy-Weinberg assumptions (mutation, migration, selection, drift, inbreeding) </li></ul></ul><ul><li>PVA (Population Viability Assessment) </li></ul><ul><li>MVP (Minimum Viable Population Size) </li></ul><ul><li>Effective population size </li></ul><ul><ul><li>Number of breeding individuals </li></ul></ul>
  9. 9. Relatedness (Kinship, Paternity and Individual ID) -Application of molecular genetic techniques (using hypervariable, repetitive DNA such as DNA fingerprinting and microsatellites) to questions of kinship, paternity, or individual ID
  10. 10. Kinship, Paternity, Individual ID: <ul><li>Infer relatedness among individuals </li></ul><ul><ul><li>First order (siblings), second order (cousins), etc. </li></ul></ul><ul><li>Infer paternity (maternity) </li></ul><ul><li>Reproductive success (male, female) </li></ul><ul><li>Interpret reproductive strategies </li></ul><ul><ul><li>Monogamy, harem, female choice, etc. </li></ul></ul><ul><li>Interpret behaviors </li></ul><ul><ul><li>Dispersal (male, female), care giving, others </li></ul></ul><ul><li>Individual ID </li></ul><ul><ul><li>Populations size estimates </li></ul></ul><ul><ul><li>Forensics </li></ul></ul>
  11. 11. Kinship, Paternity, Individual ID: Conservation Relevance <ul><li>Knowledge to aid management </li></ul><ul><ul><li>Family structure </li></ul></ul><ul><ul><li>Reproductive strategy </li></ul></ul><ul><ul><li>Behavior </li></ul></ul><ul><ul><li>Dispersal </li></ul></ul><ul><ul><li>Inbreeding </li></ul></ul><ul><ul><li>Forensics/law enforcement </li></ul></ul>
  12. 12. Examples <ul><li>Taxonomy, Population Subdivision, Gene Flow </li></ul><ul><ul><li>Puma (cougar, mountain lion) </li></ul></ul><ul><li>Kinship and Paternity </li></ul><ul><ul><li>Madagascar Fish-Eagle </li></ul></ul>
  13. 13. Subspecies Taxonomy and Gene Flow: Puma (cougar, mountain lion)
  14. 14. 32 Puma subspecies, as of the early 1900s
  15. 15. Objectives <ul><li>Does current population differentiation reflect </li></ul><ul><ul><li>Subspecies descriptions? </li></ul></ul><ul><ul><li>Physical or ecological barriers? </li></ul></ul><ul><ul><li>Geographic distance? </li></ul></ul><ul><li>Are current levels of genetic variation the same within each population? </li></ul><ul><li>Does population structure and genetic variation reflect </li></ul><ul><ul><li>Historic migrations, dispersals, and/or bottlenecks? </li></ul></ul>
  16. 16. Molecular Methods Used <ul><li>Mitochondrial gene sequencing </li></ul><ul><ul><li>3 genes </li></ul></ul><ul><li>Nuclear microsatellite length determination </li></ul><ul><ul><li>10 domestic cat microsatellite markers </li></ul></ul>
  17. 17. Mitochondrial DNA Haplotypes (in a geographical cline)
  18. 18. Microsatellite Alleles at FCA008
  19. 19. -Geographic clustering of individuals ~Six groups identified 2 distance methods agree
  20. 20. Major restrictions to gene flow: -Amazon River -Rio Parana -Rio Negro -Andes?
  21. 21. Fossil Record versus Molecular Divergence Estimates <ul><li>Oldest fossils in North and South America are ~250,000 years old </li></ul><ul><li>From mtDNA markers, puma are ~390,000 years old </li></ul><ul><li>From microsatellite markers, pumas are ~230,000 years old </li></ul>
  22. 22. Historical Inferences <ul><li>Extant pumas originated in Brazillian Highlands (ancestral haplotypes) </li></ul><ul><li>Dispersal to NA soon after the common origin in Brazil </li></ul><ul><li>2 historical radiation (movement) events </li></ul>
  23. 23. -Ancestor to puma crosses land-bridge ~2-3 Mya -Puma origin in Brazillian Highlands ~300,000 ya
  24. 24. 2 Major historical radiations -One locally distributed -One broad ranging
  25. 25. Puma Bottlenecks <ul><li>Subspecies-level </li></ul><ul><ul><li>North America low overall genetic variation </li></ul></ul><ul><li>Population-level </li></ul><ul><ul><li>Florida has no variation at 8/10 microsatellites </li></ul></ul><ul><ul><li>Olympic Peninsula and Vancouver Island, no variation at 5/10 microsatellites </li></ul></ul>
  26. 26. Conclusions <ul><li>Possible extirpation and recolonization in North America (Pleistocene age?) </li></ul><ul><li>Molecular data does not support 32 subdivisions, instead 6 groups </li></ul><ul><li>Pumas are fairly panmictic within 6 groups </li></ul>
  27. 27. Conservation Implications <ul><li>Maintain habitat connectivity within 6 large groups </li></ul><ul><li>Management should consider effects of bottlenecked populations </li></ul><ul><li>Endangered populations (Eastern cougar, Florida panther and Yuma puma) should be managed using revised subspecies </li></ul>
  28. 28. Paternity Application: Madagascar Fish-Eagle Ruth Tingay, PhD candidate U of Nottingham,
  29. 29. Antsalova wetland region of western Madagascar                                                                
  30. 30. Background and Methods <ul><li>Endangered eagle in Madagascar </li></ul><ul><li>2-3 males, and one female, attend each nest (cooperative breeding) </li></ul><ul><li>Dominance hierarchy among males at nest </li></ul><ul><li>Multi-locus DNA fingerprinting used to infer potential fathers, and estimate adult relatedness among and between nests </li></ul>
  31. 31. DNA Fingerprinting Alleles at 4 nests (6 representative bands out of 34)
  32. 32. Conclusions <ul><li>At all nests with young (n=3), subordinate males fathered all offspring </li></ul><ul><li>Dominant males have higher energy investment </li></ul><ul><li>Dominant male may be first-order relative to adult female </li></ul><ul><li>One dominant male may have full-sib within nest </li></ul>
  33. 33. Conservation Implications <ul><li>Preliminary results, more samples needed </li></ul><ul><li>Advantageous to raise young of full-sib </li></ul><ul><li>Conservation management may consider </li></ul><ul><ul><li>Adult relatedness in area </li></ul></ul><ul><ul><li>Number of males that successfully breed </li></ul></ul>

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