dna variation in ecology and evolution iii- examples of application of molecular markers
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Maria Eugenia D’Amato. DNA variation in Ecology and Evolution III- Examples of application of molecular markers. BCB 703: Scientific Methodology. Gene flow and phylogeography Agama atra in Southern Africa. Phylogeographic reconstruction: Cytochrome b (540 bp) 16S rDNA (476 bp). - PowerPoint PPT PresentationTRANSCRIPT
Available at http://planet.uwc.ac.za/nislBCB 703:Scientific Methodology
Maria Eugenia D’Amato
DNA variation in Ecology and EvolutionIII- Examples of application of molecular markers
1. Gene flow and phylogeographyAgama atra in Southern Africa
Phylogeographic reconstruction: Cytochrome b (540 bp)
16S rDNA (476 bp)
Phylogeography of Agama atra
MP tree ML tree
Pachydactilus rugosus
Phylogeography of Agama atraCoincident pattern with other rock-dwelling species
Pronolagus rupestris
Vicariant event cycles of dry-humid period during glacial –interglacial produced fragmentation of habitat
2.a. Gene flow between species: the problem of hybrids
Tilapias
Hybrids in the wild?
O. aureus O. niloticus
Tilapias hybridization
Nuclear Mitochondrial
Haplotypes common to both species
O.aureus*
*
Cluster of population
Cluster of haplotypesSenegal
Nile
Niger
Tilapias hybridization
Main results• shallow mtDNA divergence between species in Sudano- Sahelian zone• large divergence between Nile- western Africa
Retention of ancestral polymorphisms?
Secondary contact + introgression?
hypotheses
2.b. Tilapias hybridization in South Africa
Kasinthula
O. mossambicus
O. andersoniiO. mortimeri O. karongae
Parsimony network of mtDNA control region
Cluster 1 O.urolepis-aureus
2a
Cluster 3 O . malagarasi
2b
Cluster 2 O. mossambicus
Cluster 4 O. karongae
Cluster 5 O. niloticus
Cluster 6 O. andersonii
O.urolepis O. aureus
6a 6b
6c
2c
3. Phylogeny of Abalone with nuclear sequences
HaliotidaeFissurellidae
260 MY
350 MY paralogs
Orthologs ~ 65% identity
Duplication event
Phylogeny of abalonesorthologs
orthologs
paralogs
65 % identity
80-95 % identity
4. Population structure- introduced forms
Japanese Chinese OverallMuroto Sukumo Shizuoka Nagasaki Shimane Mean Chinese1 Chinese2 Mean mean
Aver. no. of alleles/locus 8.8 11 9.3 10.8 9.8 9.9 9 11 10 10Ho 0.782 0.773 0.783 0.756 0.739 0.767 0.803 0.772 0.787 0.773He 0.777 0.756 0.76 0.76 0.753 0.761 0.762 0.768 0.765 0.762
Chinese threeline grunt
Population structure analysis with 4 microsatellites lociJapanese samples
Test Japanese Chinese TotalFst 0 0.015 0.013P 0.399 0 0
significant
Pairwise Fst between populations
Population structure in the threeline Chinese grunt
significant
LocationJapanese ChineseMuroto Sukumo Nagasaki Shizuoka Shimane Chinese1 Chinese2
MurotoSukumo -0.0005
Nagasaki -0.0044 0.0012
Shizuoka 0.0002 -0.0001 0.002
Shimane 0.0024 -0.0005 -0.0035 0.0027
Chinese1 0.0301a 0.0272 0.0272 0.0203 0.0249a
Chinese2 0.0216a 0.0129 0.0236 0.0147 0.0150a 0.0150a