PhD thesis: Diversification patterns and phylogeography in a genus subterranean amphipod (Pseudoniphargus melitidae)
Esporles, September 21, 2017. Morten Stokkan will defend his doctoral thesis led by Dr. Damià Jaume and Dr. Joan Pons, from IMEDEA (CSIC-UIB).
This thesis deals with the phylogeny and phylogeography of the aquatic crustacean amphipod genus Pseudoniphargus, Chevereux, 1901, an obligate inhabitant of continental subterranean waters. Special emphasis is placed on the origin of the genus, its extremely disjunct distribution on both sides of the Atlantic as well as in the Mediterranean Sea, and the processes underlying this distribution.
Both morphological and molecular approaches are used to investigate the species diversity and detect possible cases of morphological of convergence or of recently formed species hidden under cryptisism.
Additionally this thesis attempts to place the evolution genus in a space-temporal framework by using both fossils and palaeogeographical events as calibration dating points.
An ample sampling and collecting across the entire known distribution of the genus was undertaken and together with rigorous morphological analysis, molecular data was collected.
Sanger sequencing and Next Generation Sequencing (NGS) was utilized to obtain both individual short marker and entire mitochondrial genomes covering all the major clades of the genus. By using four different methods of species delimitation based on mitochondrial cox1sequences as well as morphology and geographical location we were able to assess the diversity attained by Pseudoniphargus across the vast majority of its current distribution.
Several potential cryptic species were encountered, highlighting both the presence of strong morphological convergence and the necessity of using a broad multiple methodological approach to fully investigate species diversification.
Two new species are formally described P. morenoi and P. gevi, both from gypsum caves ifrom southern Spain. We used NGS on 31 species covering the major clades and distribution of the genus to recover their mitochondrial genome.
The thesis presents a strongly supported, fully resolved phylogeny of the genus Pseudoniphargus identifying four main clades within the genus. By using both fossil data and palaeogeographical events we were able to place the genus in a temporal framework enabling to identify both vicariance and dispersal as contributing processes to explain the current distribution of the genus.
Age and origin of the genus is about 55 Ma, consistent with previous investigations and correlates with ancient Tethys Sea from the Eocene and its subsequent regression.
The mitogenomes also revealed the occurrence of an unprecedented level of gene rearrangements within the genome of various species, up to five, whereupon two of them involved protein coding genes that is rare event in metazoans, and particularly within a genus.
A detailed analysis of thenucleotide and aminoacid composition, and the secondary structure of both RNA and the control region shed light on the molecular patterns of evolution in mitochondrial genomes that in turn are crucial to implement accurate phylogenetic models including mitochondrial sequences.
The new mitochondrial genomes presented here in give an important possibility to establish further comparisons with other amphipods from identical habitats and showing similar distribution patterns to Pseudoniphargus.
Date: September 21, 2017
Source: IMEDEA (UIB-CSIC)