1. two approaches to population structure.
    traditional summary statistics and phylogeography
  2. traditional summary statistics. 
    mathematical approach using population genetic models.  examine patterns of DNA sequence variation and allele frequencies 
  3. phylogeography.
    phylogenetic approach (building phylogenetic trees of individuals and comparing to trees to geography)

    discipline concerned with relationships between gene genealogies, phylogenetics, and geography

    recognition that mtDNA lineages in natural populations often display distinct geographic orientations (expand to nuclear genes) 
  4. what type of markers do phylogeographic studies use?
    mitochondrial DNA markers 
  5. genealogical concordance. 
    as time since isolation incr., degree of agreement among characters within a gene incre.
  6. regional concordance. 
    geographyic placement of phylogenetic gaps agree across codistributed species 
  7. what are the comparative phylogeography?
    genealogical concordance and regional concordance. 
  8. mammals displays on phylogeographyic studies 
    • wide varity of phylogeographic outsomes, 
    • smalll mammals: strong population differentation
    • large: less population differentation 
    • marine: moderate popu. differentiation 
  9. birds display on phylogeographic studies 
    display wide variety of phylogeographic outcomes 
  10. most reptiles display on phylogeography studies 
    • sedentary and show strong population differentiation
    • marine turtles: highly mobile, but show population differentiation 
  11. freshwater and marine fishes on phylogeographic studies 
    • freshwater: strong differentiation 
    • marine: minimal differentiation 
  12. invertebrates of phylogeographic studies 
    display wide variety of phylogeographic outcomes 
  13. patterns in plants? 
    • fewer phylogeographic than animals 
    • lack useful genetic markers and technical limitations 
    • complex xbreeding system 
    • dispersal via seeds and pollen
    • comlicated cuz of hybridization and introgression with other species 
    • hybrid zones common in nature 
  14. phylogenetic trees - not enough resolution, so network approaches are used...
    • insufficient polymorphism
    • coexistence of ancestor and descendants 
    • rejoining of lineages 
  15. Haplotype networks
    • distance or parismony based. 
    • seize of circle represent frequency of haplotype 
    • hatch marks on connection represnt mutational steps 
  16. minimum spanning tree: parsimony networks
    - a common way of representing the inferred genealogythe number of mutational changes among alleles is minimizedby parsimony.

    - if homoplasy (mutational convergence or reversal) is infrequent,then a single minimum spanning tree can be inferred bymaximum parsimony searches

    Extant alleles (haplotypes) on a gene tree are oftenseparated by more than one mutational step.

    Why are intermediate alleles missing and need to be inferred?
  17. Statistical parsimony network:
    -links haplotypes to one another through a series ofevolutionary steps.

    - algorithm estimates (at 95% statistical confidence) themaximum number of base pair differences betweenhaplotypes [= the parsimony limit].

    -Haplotypes that differ by a single mutation are connected,followed by two mutations, then three . . … ..

    End product: a single network showing interrelationshipsof haplotypes that requires the smallest number of mutations. The connections represent coalescent events.

    Haplotypes that exceed the parsimony limit are not connected.
  18. predictions from parismony networks 
    1. High frequency haplotypes are likely to be old alleles.

    2. Old alleles are interior to the network, new are peripheral.

    3. Haplotypes with lots of connections likely to be old.

    4. Old haplotypes likely to be broad ranging (long time fordispersal).

    5. Haplotypes with one connection (singletons) likely to beconnected to haplotypes from their own population (not along time for dispersal).
  19. nested clade analysis.
    used to identify historical and geographical factors behind distribution of haplotypes.  tests specific hypotheses

    • first step: estimate haplotype network
    • ea. step long network represents one mutation change that was observed in data

    next: nested groups of haplotypes (clades) that are spearated from one another by one or more mutational steps are identified

    then: superimpose geography over clades 
  20. test of geographic structure determines.
    whether samples from same population are closer to each other in haplotype network than would be xpected by chance

    if evidence of geographic structure is found, relationships between mutational distance and geographical distance among haplotypes are interpreted using inference key of possible demographic factors 
  21. test and inferences rely on two calculated geographical distances
    wat does it look for?
    • Dc - clade distance 
    • Dn- nested clade distance

    looks for non-random association of haplotypes and geography
  22. Dc
    geographical range of a clade or avg distance of ea. member of a clade from its geographic center
  23. Dn
    avg geographic distance of all members of a clade from geographical centre of its higher-level nesting clade
  24. inference key is based on?
    • expected patterns of geographical assoicaton
    • restricted gene flow, range expansion and allopatric fragmentation 
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