Broad-scale sampling of primary freshwater fish populations reveals the role of intrinsic traits, inter-basin connectivity, drainage area and latitude on shaping contemporary patterns of genetic diversity

Abstract

Background. Worldwide predictions suggest that up to 75% of the freshwater fish species occurring in rivers with reduced discharge could be extinct by 2070 due to the combined effect of climate change and water abstraction. The Mediterranean region is considered to be a hotspot of freshwater fish diversity but also one of the regions where the effects of climate change will be more severe. Iberian cyprinids are currently highly endangered, with over 68% of the species raising some level of conservation concern.Methods. During the FISHATLAS project, the Portuguese hydrographical network was extensively covered (all the 34 river basins and 47 sub-basins) in order to contribute with valuable data on the genetic diversity distribution patterns of native cyprinid species. A total of 188 populations belonging to 16 cyprinid species of Squalius, Luciobarbus, Achondrostoma, Iberochondrostoma, Anaecypris and Pseudochondrostoma were characterized, for a total of 3,678 cytochrome b gene sequences.Results. When the genetic diversity of these populations was mapped, it highlighted differences among populations from the same species and between species with identical distribution areas. Factors shaping the contemporary patterns of genetic diversity were explored and the results revealed the role of latitude, inter-basin connectivity, migratory behaviour, species maximum size, species range and other species intrinsic traits in determining the genetic diversity of sampled populations. Contrastingly, drainage area and hydrological regime (permanent vs. temporary) seem to have no significant effect on genetic diversity. Species intrinsic traits, maximum size attained, inter-basin connectivity and latitude explained over 30% of the haplotype diversity variance and, generally, the levels of diversity were significantly higher for smaller sized species, from connected and southerly river basins.Discussion. Targeting multiple co-distributed species of primary freshwater fish allowed us to assess the relative role of historical versus contemporary factors affecting genetic diversity. Since different patterns were detected for species with identical distribution areas we postulate that contemporary determinants of genetic diversity (species’ intrinsic traits and landscape features) must have played a more significant role than historical factors. Implications for conservation in a context of climate change and highly disturbed habitats are detailed, namely the need to focus management and conservation actions on intraspecific genetic data and to frequently conduct combined genetic and demographic surveys.

Paleobiogeography of an Iberian endemic species,Luciobarbus sclateri(Günther, 1868) (Actinopterygii, Cyprinidae), inferred from mitochondrial and nuclear markers

“…In contrast, some large rivers, such as Guadiana and Guadalete, showed surprisingly low genetic diversity values in comparison with other large basins, as Guadalquivir Basin, which could be consequence of recent founder effects, as supported by the estimated divergence times. This lack of correlation between diversity indices and basin size has already been reported for other Iberian cyprinid fishes (Perea & Doadrio, ; Sousa‐Santos et al., ).…”

“…Other previous studies dealing with the genetic diversity of L. sclateri in Portuguese basins showed that the haplotype diversity was lower in comparison with other cyprinid species. In addition, the highest diversity was found in Guadiana River, the largest one considered in the study (Sousa-Santos et al, 2016). Previous genetic studies did not include many of the southern Spanish populations that comprise most of the distribution range of the species (Gante et al, 2009).…”

“…The complete mitochondrial cytochrome b gene (MT-CYB) (1140 pb) and a fragment (474 bp) of ribosomal protein S7 gene (RPS7) were amplified. Both genes have proved to be useful in resolving phylogenetic and phylogeographical relationships in cypriniformes (Mayden et al, 2009;Moyer, Remington, & Turner, 2009;Perea, Cobo-Simon, & Doadrio, 2016;Sch€ onhuth, Doadrio, Dom ınguez-Dom ınguez, Hillis, & Mayden, 2008;Sousa-Santos et al, 2016). The tetraploid condition of Luciobarbus, due to recent genome duplication, shows high sequence similarity between paralogs, especially protein-coding exons, which makes the use of nuclear genes a challenging issue (Gante, Alves, & Dowling, 2011).…”

Phylogeography and Conservation Genetics of the Ibero-Balearic Three-Spined Stickleback (Gasterosteus aculeatus)

“…Therefore, our preliminary conclusion is that the extinction of Penyscola was too abrupt to leave any genetic footprint. This scenario somehow resembles the case of the high nuclear (and mitochondrial) diversities critically reported for the endangered Iberian fish Anaecypris hispanica and attributed to recent fragmentation and decline of its populations [89, 93]. Overall, the loss of Penyscola did not substantially affect to the nuclear and mitochondrial diversity present in our 17 sampled sites.…”

“…This kind of watershed experiences a predictable annual cycle of autumn-winter floods and extended summer droughts. These changes result in a series of disconnected ponds during the dry season and affect biological community traits [88, 89]. This is illustrated by the earlier breeding season of G .…”