Genetic Coalescence in North American White Pines - PowerPoint PPT Presentation

1 / 30
About This Presentation
Title:

Genetic Coalescence in North American White Pines

Description:

Coalescence is the pattern of common ancestry. ... Primers Anneal. Taq Polymerase builds. a complementary copy. Polymerase Chain Reaction (PCR) ... – PowerPoint PPT presentation

Number of Views:56
Avg rating:3.0/5.0
Slides: 31
Provided by: FSDef214
Category:

less

Transcript and Presenter's Notes

Title: Genetic Coalescence in North American White Pines


1
Genetic Coalescence in North American White Pines
  • Kathleen Farrell
  • Dr. Aaron Liston, Dr. Richard Cronn,
  • John Syring

P. strobus
2
Coalescence is the pattern of common ancestry.
Coalescence theory At some point all alleles in
the population will be traceable to a single
common ancestral allele that existed in the
population at time t0.
  • Factors
  • Gene flow
  • Hybridization
  • Selection
  • Population size

3
Objective to find low copy nuclear genes that
accurately demonstrate the relationships
(phylogeny) between closely related species,
North American White Pines.
Why low copy genes? Orthologs vs. Paralogs
4
Objective to find low copy nuclear genes that
accurately demonstrate the relationships
(phylogeny) between closely related species,
North American White Pines.
Why low copy genes? Orthologs vs. Paralogs
5
Species Sampled North American White Pines P.
albicaulis Whitebark Pine P. ayacahuite Mexican
White Pine P. chiapensis Chiapas White Pine P.
flexilis Limber Pine P. lambertiana Sugar
Pine P. monticola Western White Pine P.
strobiformis Southwestern White Pine P.
strobus Eastern White Pine
P. flexilis
P. lambertiana
P. albicaulis
P. ayacahuite
Outgroups P. monophylla Singleleaf Pinyon P.
longaeva Bristlecone Pine
P. monophylla
P. longaeva
6
Methods and Approach
DNA Extraction from the megagametophyte tissue.
megagametophyte (1n)
embryo (2n) shoot end
embryo root tip (radicle)
7
Polymerase Chain Reaction (PCR)
  • How it works
  • DNA Denatures
  • Primers Anneal
  • Taq Polymerase builds a complementary copy.

8
Polymerase Chain Reaction (PCR)
  • How it works
  • DNA Denatures
  • Primers Anneal
  • Taq Polymerase builds a complementary copy.

9
Polymerase Chain Reaction (PCR)
Results Gel Electrophoresis
IFG8612 Optimization MONTICOLA 02S1
Temperature (C) ? 56 57 58 59 60
61
Temperature (C) ? 56 57 58 59 60
61
Control
Control
62 63 64 65 66 67 68
62 63 64 65 66 67 68
2.0 mM MgCl
1.5 mM MgCl
10
Polymerase Chain Reaction (PCR)
Results Gel Electrophoresis
IFG8612 Optimization MONTICOLA 02S1
Temperature (C) ? 56 57 58 59 60
61
Temperature (C) ? 56 57 58 59 60
61
Control
Control
62 63 64 65 66 67 68
62 63 64 65 66 67 68
2.0 mM MgCl
1.5 mM MgCl
11
Polymerase Chain Reaction (PCR)
Results Gel Electrophoresis
IFG8612 Optimization MONTICOLA 02S1
Temperature (C) ? 56 57 58 59 60
61
Temperature (C) ? 56 57 58 59 60
61
Control
Control
62 63 64 65 66 67 68
62 63 64 65 66 67 68
2.0 mM MgCl
1.5 mM MgCl
12
Cycle Sequencing
Capillary Gel
13
Cycle Sequencing
Analyzing Results
Clean Sequence
Sequence Noise
Alignment and Editing
------------------------GTAATT----AGATTTGAATGGCATG
GAATGAATGGAAA -GCaGGAtaTTGTCATTTCTTTCAGTAATT----AG
ATTTGAATGGCATGGAATGAATGGAAA ----GGAtaTTATCATTTTTTT
CaGTAATTAATTAGATTTGAATGGCATGGAATGAATGGAAA -GCaGGAt
ATTGTCATTTCTTTCAGTAATT----AGATTTGAATGGCATGGAATGAAT
GGAAA
14
Developing a Phylogenetic Tree
  • Export alignments to PAUP
  • Search for phylogenetic trees based on maximum
    parsimony using the branch and bound algorithm.
  • Calculate bootstrap values (measure of confidence
    for each branch) and branch length (measure of
    relative divergence).

15
Results
IFG8898
IFG8612
Cinnamyl Alcohol Dehydrogenase
16
Results
IFG8898
IFG8612
Cinnamyl Alcohol Dehydrogenase
17
Results
IFG8898
IFG8612
Cinnamyl Alcohol Dehydrogenase
18
IFG8612 alignment
19
IFG8612 alignment
20
IFG8612 alignment
21
IFG8612 alignment
22
Phylogenetic Tree
23
Phylogenetic Tree
Outgroups
Bootstrap Support ()
24
Phylogenetic Tree
25
Phylogenetic Tree
26
Phylogenetic Tree
27
Phylogenetic Tree
FLEXILIS JVS
28
Phylogenetic Tree
FLEXILIS JVS
29
Future Research
  • Continue screening low copy, nuclear genes to
    compare phylogenetic patterns across the genome.
  • Increase sampling to five individuals from each
    species that represent the geographic
    distribution of the species.
  • Extend research to include Asian White Pines.

30
Special Thanks to Howard Hughes Medical
Institute Portland Garden Club Undergraduate
Research, Innovation, Scholarship, and Creativity
(URISC) National Science Foundation
P. strobus
Write a Comment
User Comments (0)
About PowerShow.com