Dispersal models Continuous populations Isolation-by-distance Discrete populations Stepping-stone Island model

F ST, the fixation index, is the most important statistic used to measure the extent of population subdivision. Where : H t is the heterozygosity expected to be shown by an individual in a randomly-mating total population H S is the mean heterozygosity in subpopulation Heterozygosity: Where, m is the number of alleles and x i the frequency of the ith allele at the locus

Barber et al Fine scale genetic structure between populations Planktonic larvae: 4-6 weeks Dispersal potential: estimated at 600 km of the mantis schrimp Haptosquilla pulchella 213 individuals 106 haplotypes Minimum-spanning network A sharp genetic break between populations north and south of the Flores and Java seas, as close as 300 km

New approach in population genetics: the coalescent

The coalescent : The increasing amount of genetic polymorphism revealed at the level of DNA encouraged the use of gene genealogies in population genetics (the phylogenetic relationships of the sequences sampled from a population). Coalescence process : The n sequences in a phylogenetic tree coalesce first to n-1 ancestral sequences, then to n-2, and so on until finally to a single common ancestral sequence, the MRCA = most recent common ancestor. Under the assumption of genetic drift only, the probability that 2 alleles share a common ancestor in the previous generation is 1/2N. If the population maintained a constant size, the time back to the MRCA is 4N generations (as we go backward, there are less lineages left to coalesce, so that half the coalescence time will occur between the last 2 lineages). MRCA

Past

Coalescence events are more likely to occur in a small population, or if the allele is subject to positive selection. The relative distribution of the coalescent events along the tree, as well as the total coalescence time, give information about past and present evolutionary processes in the analyzed population.

How does speciation occur in the ocean ?

Molecular Phylogenetics

MOLECULAR PHYLOGENETICS : The reconstruction of the evolutionary history between reproductively isolated species. The first and crucial point is to compare orthologous genes. Then the following steps are required for the reconstruction of the phylogenetic tree: 1) Alignment of the DNA sequences –insertion of gaps. 2) Choice of the best model of DNA substitution fitting your DNA alignment. 3) Inference of the molecular tree using one or several of the 3 classical methods: distance, maximum parsimony (MP), or maximum likelihood (ML). 4) Statistical test of the robustness of the phylogenetic groups (i.e. Bootstrap); eventually test of alternating phylogenetic hypotheses (i.e. LRT, likelihood ratio test).

DNA sequences – Multiple Alignment

Assumptions of the model of nucleotide substitutions: 1) All nucleotide sites change independently 2) The substitution rate is constant over time and in different lineages 3) The base composition is at equilibrium 3) The conditional probabilities of nucleotide substitutions are the same for all sites and do not change over time