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