Mitochondrial DNA hyperdiversity and population genetics in the periwinkle Melarhaphe neritoides (Mollusca: Gastropoda)

• Main Author: Fourdrilis, Severine
• Other Authors: Mardulyn, Patrick, Backeljau, Thierry, Noret, Nausicaa, Flot, Jean-François, Derycke, Sofie, Kochzius, Marc
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: Universite Libre de Bruxelles 2017
• Subjects: Sciences exactes et naturelles; Population genetics; Phylogenetics; Gene flow; Population genetic differentiation; North East Atlantic; Marine snail
• Online Access: http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/252992; https://dipot.ulb.ac.be/dspace/bitstream/2013/252992/4/Table_of_content.pdf; https://dipot.ulb.ac.be/dspace/bitstream/2013/252992/3/PhD_thesis_FOURDRILIS.pdf; https://dipot.ulb.ac.be/dspace/bitstream/2013/252992/5/ContratDIFourdrilis.pdf

This PhD thesis studies the evolution of the peculiar mitochondrial DNA (mtDNA) in the mollusc Melarhaphe neritoides. We measured mtDNA diversity and elucidated the evolutionary forces that shape the evolution of the organelle.The mtDNA in M. neritoides harbours a remarkable amount of polymorphism at selectively neutral nucleotide sites (π_syn = 6.8 %), called hyperdiversity when above the threshold of 5 %. We revealed that an elevated mutation rate (µ = 5.8 × 10-5 per site per year at the COI locus), which is 1000 fold higher than in other metazoans, is likely the primary force generating mtDNA hyperdiversity. Such mtDNA hyperdiversity may be more common across other phyla and more frequently linked to high µ values, than currently appreciated.Natural selection is a second force, which shapes mtDNA hyperdiversity. Positive selection influences the overall mtDNA polymorphism in the 16S, COI and Cytb genes, including synonymous sites at which mtDNA hyperdiversity is calculated. Therefore, synonymous sites in M. neritoides are not neutral but possibly positively selected. Strong purifying selection maintains a low non-synonymous polymorphism in the 13 protein-coding genes of the mitogenome, so that a very few changes in nucleotide sequence induce changes in amino acid sequence. The effective population size of this planktonic-dispersing species is surprisingly small in the North East Atlantic (Ne = 1303), likely biased by selection, and for this reason, Ne is a poor indicator of mtDNA hyperdiversity.Migration is a third force, which homogenises the gene pool of the species through high rates of gene flow, predominantly eastward, and results in high connectivity and panmixia over the entire North East Atlantic.Genetic drift, the fourth force, is not sufficient in M. neritoides to lower mtDNA diversity, and populations show no differentiation.This thesis also highlights an important pitfall. The use of hyperdiverse markers may easily lead to erroneous interpretations of differentiation statistics and connectivity ...