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Italy hosts a large number of endemic freshwater fish species due to complex geological events which promoted genetic differentiation and allopatric speciation. Among them, the South European roach Sarmarutilus rubilio inhabits various freshwater environments in three different ichthyogeographic districts. We investigated the genetic diversity of S. rubilio using two different mitochondrial markers (COI and CR), aiming to define its relationship with other similar taxa from the Balkan area and, from a phylogeographic perspective, test the effects of past hydrogeological dynamics of Italian river basins on its genetic structure and demographic history. Our analysis highlighted a marked genetic divergence between S. rubilio and all other roach species and, among Italian samples, revealed the existence of three deeply divergent geographic haplogroups, named A, B and C. Haplogroup C likely corresponds to a new putative cryptic species and is located at the northern border of the South European roach range; haplogroup B is restricted to Southern Italy; and haplogroup A is widespread across the entire range and in some sites it is in co-occurrence with C or B. Their origin is probably related to the tectonic uplifting of the Apuan Alps in the north and of the Colli Albani Volcano in the south during the Pleistocene, which promoted isolation and vicariance followed by secondary contacts.

Italy hosts a large number of endemic freshwater fish species due to complex geological events which promoted genetic differentiation and allopatric speciation. Among them, the South European roach

The brook chub (Squalius lucumonis) is a freshwater fish, endemic of Central Italy, which is experiencing a rapid range decline so that it is presently listed as Critically Endangered in the Italian IUCN Red List. For effective conservation, information about the spatial pattern of genetic diversity is crucial. Therefore, we analysed the mitochondrial Control Region and nuclear (microsatellites) markers to investigate population genetic structure, demography and spatial diversity over the whole species distribution range. We revealed significant divergence among populations, even at the local spatial scale, according to the isolation by distance model. At the biogeographic spatial scale, genetic diversity was shaped by past hydrogeological and climatic events that isolated the principal drainage basins (Vara, Tiber and Arno) from each other. On the other hand, strong genetic differentiation within the Tiber drainage basin could be due to local factors that acted at single-stream scale, as recent barriers to fish dispersal and irregular seasonal flow rates typical of small Mediterranean streams. Our findings contribute to the basal data collection on S. lucumonis required by European Habitats Directive and necessary for planning protection actions. We recommend that the three river drainages and most of the sampling sites should be regarded as different Management Units (MUs) to preserve their genetic distinctiveness. A recovery plan for the brook chub should consider environmental intervention and creation of protected areas, as well as in situ/ex situ restocking activities with juveniles produced by breeders from the same MU, to preserve local (adaptive) diversity.

The role of the south-western Alps as a corridor for Mediterranean trout (Salmo trutta complex Linnaeus, 1758) was evaluated in order to understand the influence of the last glacial events in shaping the spatial distribution of the genetic diversity of this salmonid. For this, the allochthonous hypothesis of a man-mediated French origin (19th century) of the Mediterranean trout inhabiting the Po tributaries in the Italian side of the south-western Alps was tested. A total of 412 individuals were analysed at the mitochondrial control region. The phylogenetic classification was carried out by using a Median-Joining Network analysis. Mismatch pair-wise analysis, molecular dating and Kernel density distribution analysis of the main mitochondrial lineages were evaluated to compare past demographic dynamics with the current spatial distribution of genetic diversity. The main outcomes resulted strongly in agreement with a biogeographic scenario where the south-western Alps acted as a unidirectional corridor that permitted the colonization of the upper Durance (Rhône River basin) by trout from the Po River basin. Therefore, the Mediterranean trout should be considered as native also along the Italian side of the south-western Alps and the allochthonous hypothesis should be rejected.