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Summary: The vast biodiversity of the microbial world and how little is known about it, has already been revealed by extensive metagenomics analyses. Our rudimentary knowledge of microbes stems from difficulties concerning their isolation and culture in laboratory conditions, which is necessary for describing their phenotype, among other things, for biotechnological purposes. An important component of the understudied ecosystems is methanogens, archaea producing a potent greenhouse‐effect gas methane. Therefore, we created PhyMet2, the first database that combines descriptions of methanogens and their culturing conditions with genetic information. The database contains a set of utilities that facilitate interactive data browsing, data comparison, phylogeny exploration and searching for sequence homologues. The most unique feature of the database is the web server MethanoGram, which can be used to significantly reduce the time and cost of searching for the optimal culturing conditions of methanogens by predicting them based on 16S RNA sequences. The database will aid many researchers in exploring the world of methanogens and their applications in biotechnological processes. PhyMet2 with the MethanoGram predictor is available at http://metanogen.biotech.uni.wroc.pl [ABSTRACT FROM AUTHOR]

The present distribution of many species is a result of climatic changes during the Pleistocene and human activity. The impact of climate has been accompanied by restrictions of populations into refugia during glacial periods, and subsequent expansions during more favourable conditions, whereas human influence has been associated with hunting practices and translocations. One mammalian species that has been subject to such transformations is the red deer, Cervus elaphus, but the exact nature of these changes has been difficult to determine using only modern DNA. In this study, we obtained new cytochrome b sequences from subfossil remains of deer found in the Crimean Peninsula. A comparison of these sequences with the available recent and ancient sequences allowed to us to reconstruct phylogeographic relationships between Cervus lineages and to determine their potential migration routes at both local and Eurasian scales. Our analyses showed that the Crimean Peninsula was not a glacial refugium for red deer, but rather that red deer colonized Crimea in three independent waves from both Western and Eastern red deer populations. The immigrations were related to local extinctions and replacements of native populations. [ABSTRACT FROM AUTHOR]

Although cave bear remains have been described since the end of 18th century, recent discoveries and methods provide new knowledge about the typical representative of Pleistocene megafauna, which did not survive the Last Glacial Maximum. Genetic studies supplemented by morphometric analyses showed that this mammal differentiated in the Late Pleistocene into two main forms called Ursus spelaeus and U. ingressus. The latter is regarded more expansive and replaced the native U. spelaeus in some areas of Western Europe. Taking into account the differences between these bears, it is interesting to determine if these forms became extinct at different or similar times. Therefore, we assessed their extinction times, applying seven methods using 205 dated records of cave bear ascribed to these two forms. The average extinction time of U. spelaeus was about 25,600 cal. yr BP (Before Present) and of U. ingressus about 24,800 cal. yr BP. The estimations showed that that U. ingressus could survive up to ca. 1,000 years longer than its relative U. spelaeus. The longer survival of the former could be related to its greater morphological variability and better adaptation to arid continental environments, as well as a stronger tendency to occasional omnivory. Both bears became extinct within the coldest phase of the last glacial period, Greenland Stadial 3, which implies that climate cooling was the main factor of their extinction. The climate deterioration decreased vegetation productivity, and could also have had negative consequences on the prolonged hibernation period when the bears were more susceptible to the activity of humans and predators. [ABSTRACT FROM AUTHOR]

Morphological variation of snails from the genus Trochulus is so huge that their taxonomy is unclear. The greatest variability concerns forms hispidus and sericeus/plebeius, which are often considered as separate species. To evidence the species barriers, we carried out crossbreeding experiments between these two sympatric morphs. Moreover, we compared the shell morphology of laboratory-bred offspring with their wild parents to test if the variation can be explained by the phenotypic plasticity model. We found that the two Trochulus morphs show no reproductive barriers. The fecundity rates, the mean clutch size, and F1 viability observed for all crosses were not significantly different. In hybrid crosses (in F2 generation), we also recorded reproduction compatibility, similar fecundity, and hatching success as in their parents. Accordingly, phylogenetic analyses revealed the significant grouping of sequences from these different morphs and supported no constrains in reproduction between them. Comparison of shell morphology between wild and laboratory samples showed that various characters appeared highly plastic. The average shell shape of the hispidus morph changed significantly from flat with wide umbilicus to elevated with narrower umbilicus such as in the sericeus/plebeius morph. All these findings indicate that the examined morphs do not represent separate biological species and the evolutionary process is not advanced enough to separate their genetic pool. Therefore, phenotypic plasticity has played a significant role in the evolution of Trochulus shell polymorphism. The two morphs can evolve independently in separate phylogenetic lineages under the influence of local environmental conditions. [ABSTRACT FROM AUTHOR]