Evolutionary history of the alpha2,8-sialyltransferase (ST8Sia) gene family: Tandem duplications in early deuterostomes explain most of the diversity found in the vertebrate ST8Sia genes

Background

The Salangid icefish Neosalanx taihuensis (Salangidae) is an economically important fish, which is endemic to China, restricted to large freshwater systems (e.g. lakes, large rivers and estuaries) and typically exhibit low vagility. The continuous distribution ranges from the temperate region of the Huai and Yellow River basins to the subtropical region of the Pearl River basin. This wide ranging distribution makes the species an ideal model for the study of palaeoclimatic effects on population genetic structure and phylogeography. Here, we aim to analyze population genetic differentiation within and between river basins and demographic history in order to understand how this species responded to severe climatic oscillations, decline of the sea levels during the Pleistocene ice ages and tectonic activity.

Results

We obtained the complete mtDNA cytochrome b sequences (1141 bp) of 354 individuals from 13 populations in the Pearl River, the Yangze River and the Huai River basin. Thirty-six haplotypes were detected. Haplotype frequency distributions were strongly skewed, with most haplotypes (n = 24) represented only in single samples each and thus restricted to a single population. The most common haplotype (H36) was found in 49.15% of all individuals. Analysis of molecular variance (AMOVA) revealed a random pattern in the distribution of genetic diversity, which is inconsistent with contemporary hydrological structure. Significant levels of genetic subdivision were detected among populations within basins rather than between the three basins. Demographic analysis revealed that the population size in the Pearl River basin has remained relatively constant whereas the populations in the Yangze River and the Huai River basins expanded about 221 and 190 kyr ago, respectively, with the majority of mutations occurring after the last glacial maximum (LGM).

Conclusion

The observed complex genetic pattern of N. taihuensis is coherent with a scenario of multiple unrelated founding events by long-distance colonization and dispersal combined with contiguous population expansion and locally restricted gene flow. We also found that this species was likely severely impacted by past glaciations. More favourable climate and the formation of large suitable habitations together facilitated population expansion after the late Quaternary (especially the LGM). We proposed that all populations should be managed and conserved separately, especially for habitat protection.     

Multi-trait evolution in a cave fish, Astyanax mexicanus

SUMMARY When surface species colonize caves, a characteristic suite of traits eventually evolves over time, regardless of species. The genetic basis of the inevitable appearance of these very similar phenotypes was investigated through quantitative trait loci (QTL) mapping of 12 traits that differ significantly between the recently evolved (<1 Myr). Mexican cave tetra and its surface conspecific. The traits were a representative set, including eye size, pigment cell numbers, chemical sensitivity, body and skull morphology, standard length, and metabolism. We used both single- and multi-trait models for QTL mapping. QTL effects of these traits were significantly clustered in the genome. We mapped 13 regions in the genome with QTL effects on from three to nine traits. These clusters could be multigenic or could represent single locus with pleiotropic alleles. Given the relatively short time available to construct clusters from unlinked genes through genomic rearrangement, and the counterintuitive polarities of some of the substitution effects, we argue that at least some of the clusters must have a pleiotropic basis.     

A new Ruscinian site in Europe: Baza-1 (Baza basin,Andalusia, Spain)

The Guadix–Baza depression (southeastern Spain) preserves one of the best continental Plio-Pleistocene records of the European continent. The new site, Baza-1, is the first Ruscinian locality with fauna of large vertebrates known in the basin. During the summer seasons of 2001, 2002, 2015 and 2016, systematic excavations were undertaken in the site over an area of 25 m², which provided > 400 fossil remains of Ruscinian mammals. The faunal assemblage is diverse, comprising 17 genera. Rodentia are represented by Ruscinomys sp., Apocricetus barrierei, Debruijnimys julii, Apodemus gorafensis, Castillomys gracilis, Occitanomys cf. brailloni, Paraethomys meini, Paraethomys aff. abaigari, Stephanomys cordii, Trilophomys cf. castroi and Eliomys aff. intermedius. Large mammals are represented by two proboscideans, Anancus arvernensis and Mammut borsoni, the rhino Stephanorhinus sp. cf. S. jeanvireti, the equid cf. Hipparion sp., two bovids, a large sized Alephis sp. and a small-to-middle sized Bovidae indet. (cf. Antilope sp.), and a middle sized deer, Cervinae indet. This record is completed by the presence of a chelonid, Testudinae indet. Biostratigraphic data from micro and macromammals suggest an age for the assemblage between 4 and 4.5 Ma.     

Quantitative study of a hippuritid rudist lithosome in a Santonian carbonate platform in the southern Central Pyrenees

The Santonian carbonate platform deposits of the Sant Corneli anticline in the southern Central Pyrenees contain distinctive lenticular to tabular lithosomes formed by congregations of slender hippuritid rudists. Here we make a quantitative study of one of the lithosomes in the Sant Pere de Vilanoveta Member, in the northern side of Sant Corneli. It is exposed over some 4 km, along a WNW–ESE section, and shows a remarkably persistent thickness up to a maximum of 5.15 m, though for the most part it is less than 3 m thick. In the lithosome, hippuritid shells are mostly preserved inclined about 30°–60° from the perpendicular with respect to bedding. The majority of inclined shells lean towards the southwestern to southeastern quadrants, the inferred principal downstream direction. Hippuritids are loosely clustered and supported in a fine bioclastic matrix. Percentage cover of hippuritids ranges from 19.8% at the base to 31.9% in the middle and top of the lithosome. The preliminary data on numerical densities (number of individuals per unit area) of hippuritids show some clustering around values of about 290–750 individuals per m². The inclined orientation of hippuritid shells seems original and the result of active growth by the animals. The high numerical density of hippuritids at the base of the lithosome may indicate that the hippuritid congregation grew rapidly. The congregation appears to have reached an optimal level of density by the middle of the lithosome and to have maintained it through time during the development of the rudist congregation. The lithosome lacks relief and has no evidence of any rigid framework.     

Operational strategies, monitoring and control of heterologous protein production in the methylotrophic yeast Pichia pastoris under different promoters: A review

The methylotrophic yeast Pichia pastoris has been widely reported as a suitable expression system for heterologous protein production. The use of different phenotypes under PAOX promoter, other alternative promoters, culture medium, and operational strategies with the objective to maximize either yield or productivity of the heterologous protein, but also to obtain a repetitive product batch to batch to get a robust process for the final industrial application have been reported. Medium composition, kinetics growth, fermentation operational strategies from fed-batch to continuous cultures using different phenotypes with the most common PAOX promoter and other novel promoters (GAP, FLD, ICL), the use of mixed substrates, on-line monitoring of the key fermentation parameters (methanol) and control algorithms applied to the bioprocess are reviewed and discussed in detail.