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During the Pleistocene, the saiga antelope, a nomadic, non-territorial, herding species, inhabited vast areas of Eurasia and North America; its distribution was at its maximum extent in the last glaciation. Now, it is restricted to a few isolated populations in Central Asia. Two main forms of saiga were recognised: Saiga borealis and S. tatarica . The former became extinct at the beginning of Holocene, the latter has survived since the Pleistocene to the present. They are regarded either as two species or as two subspecies of S . tatarica . Our comparison of skull and horn measurements of many Eurasian specimens, including literature data, revealed significant differences between these taxa. S . borealis was larger than S . tatarica in terms of some cranial measurements, whereas S . tatarica was characterised by a greater diameter of horncore base. However, the distinction involved only a few metric features and the ranges of all the analysed measurements overlapped at least partially, indicating that the two taxa may not be true species. Our analyses also showed that the skull of S . tatarica had become smaller since the Pleistocene in terms of several measurements, which was probably associated with the climate and palaeogeographical changes at the end of the last glaciation and a decrease in the population size. We found significant differences between the various geographical subgroups of S . borealis and S . tatarica only in some measurements. The observed dissimilarities between S . borealis and S . tatarica correspond most probably to subspecies level and may have resulted from a biogeographical differentiation of the saiga populations in the Pleistocene. [ABSTRACT FROM AUTHOR]

Aim Migrants of the Atlantic sturgeon, Acipenser oxyrinchus, from North America are thought to have founded the Baltic sturgeon population during the Little Ice Age around 1200 years ago, replacing the European sturgeon, Acipenser sturio. To test this hypothesis and to further elucidate the colonization of the Baltic Sea by A. oxyrinchus, we carried out DNA analyses of ancient and contemporary populations of both species. Location We analysed DNA from 188 specimens of sturgeons collected from archaeological sites and museums in Poland and of 225 contemporary specimens from North American and European populations. Methods Several mitochondrial DNA fragments were sequenced and eight microsatellite loci were genotyped for species identification, polymorphism and population structure analyses. Approximate Bayesian computation was used to estimate when the Baltic Sea was colonized. Results Of 125 ancient sturgeon specimens from the Baltic Sea, only four were classified as A. sturio, the remainder being A. oxyrinchus oxyrinchus. The ancient A. o. oxyrinchus population over two different time periods was highly polymorphic and genetically distant from contemporary populations of this taxon. The time of entry into the Baltic Sea was estimated to be 4000-5000 years ago. We also detected introgression of A. sturio into the A. o. oxyrinchus gene pool, caused by a prior hybridization event. Main conclusions For the past 2000 years at least, A. o. oxyrinchus has been the dominant sturgeon in the Baltic Sea, indicating a much earlier origin than previously suggested. The most similar extant sturgeon populations to the extinct Baltic stock are those from the St John and St Lawrence rivers in Canada. These populations should be considered the best source of breeding material for the ongoing sturgeon restitution programmes in Poland and Germany. [ABSTRACT FROM AUTHOR]

The standard genetic code (SGC) is a set of rules according to which 64 codons are assigned to 20 canonical amino acids and stop coding signal. As a consequence, the SGC is redundant because there is a greater number of codons than the number of encoded labels. This redundancy implies the existence of codons that encode the same genetic information. The size and organization of such synonymous codon blocks are important characteristics of the SGC structure whose evolution is still unclear. Therefore, we studied possible evolutionary mechanisms of the codon block structure. We conducted computer simulations assuming that coding systems at early stages of the SGC evolution were sets of ambiguous codon assignments with high entropy. We included three types of reading systems characterized by different inaccuracy and pattern of codon recognition. In contrast to the previous study, we allowed for evolution of the reading systems and their competition. The simulations performed under minimization of translational errors and reduction of coding ambiguity produced the coding system resistant to these errors. The reading system similar to that present in the SGC dominated the others very quickly. The survived system was also characterized by low entropy and possessed properties similar to that in the SGC. Our simulation show that the unambiguous SGC could emerged from a code with a lower level of ambiguity and the number of tRNAs increased during the evolution. [ABSTRACT FROM AUTHOR]

It is assumed that at the early stage of cell evolution its translation machinery was characterized by high noise, i.e. ambiguous assignment of codons to amino acids in the genetic code, which initially encoded only few amino acids. Next, during its evolution new amino acids were added to this code. Taking into account this facts, we investigated theoretical models of genetic code's structure, which evolved from a set of ambiguous codons assignments into a coding system with a low level of uncertainty. We considered three types of translational inaccuracies assuming a different number of fixed codon positions. We applied a modified version of evolutionary algorithm for finding the genetic codes that the most effectively reduced the initial uncertainty in the assignment of codons to encoded labels, i.e. amino acids and a stop translation signal. We examined codes with the number of labels from four to 22. Our results indicated that the quality of genetic code structure is strongly dependent on the number of encoded labels as well as the type of translational mechanism. The more strict assignments of codon to the labels was preferred by the codes encoding more number of labels. The results showed that a smaller degeneracy of codes evolved from a more tolerant coding with the stepwise addition of coded amino acids to the genetic code. The distribution of codon groups in the standard genetic code corresponds well to the translation model assuming two fixed codon positions, whereas the six-codon groups can be relics form previous stages of evolution when the code characterized by a greater uncertainty. [ABSTRACT FROM AUTHOR]

The Pleistocene lion Panthera spelaea was not a homogenous taxon; it was represented by three chronoforms. The oldest one, from the Early and Middle Pleistocene, was P. s. fossilis , the youngest was the Late Pleistocene cave lion P. s. spelaea. The intermediate form between them was P. s. intermedia. The scarcity of stratigraphically old lion made it difficult to understand the evolution of this carnivore. Therefore, we revised the fossil material of the Pleistocene lion from Polish excavation sites. The analysis revealed the presence of P. s. fossilis in 7 sites: Tunel Wielki, Południowa, Wschodnia, Draby, Biśnik, Deszczowa and Wierzchowska Górna caves. The remains from these localities significantly differed in their average size and teeth proportions from the nominate younger chronoform, i.e. the cave lion. Using this material and all other available data, we compared the lion remains grouped into four palaeoclimate periods: MIS 17-12, MIS 11-9, MIS 8-6 and MIS 5-2. We found significant time-related trends in many morphometric features of dentition and limb bones. Between the first two periods, the lion became larger but from MIS 8, it gradually decreased in size. The teeth showed a much greater rate of changes than the metapodial bones, which in turn were characterised by more heterogeneous and mosaic evolution. The changes observed in the fossil material can result from in situ evolution of lion populations occupying Europe or immigration and replacement of the native forms by those from other regions, for example Asia. • P. s. fossilis differs from P. s. spelaea in larger size and teeth proportions. • Remains of P. s. fossilis are known in Poland from Tunel Wielki, Południowa, Draby, Biśnik and Wierzchowska Góra caves. • Dental features occurred more diagnostic and demonstrated more significant differences than the tarsal and metapodial bones. • The largest fraction of statistically discriminative traits had canine, P4, p4 and interestingly metatarsus V. • Generally, most measurements decreased over time, which indicates that the lion became smaller. • The limb bones usually increased in size and thickness, which could be relate to the better adaptation to confrontation with large preys. [ABSTRACT FROM AUTHOR]

This comprehensive study examines fossil remains from Niedźwiedzia Cave in the Eastern Sudetes, offering detailed insights into the palaeobiology and adversities encountered by the Pleistocene cave bear Ursus spelaeus ingressus. Emphasising habitual cave use for hibernation and a primarily herbivorous diet, the findings attribute mortality to resource scarcity during hibernation and habitat fragmentation amid climate shifts. Taphonomic analysis indicates that the cave was extensively used by successive generations of bears, virtually unexposed to the impact of predators. The study also reveals that alkaline conditions developed in the cave during the post-depositional taphonomic processes. Mortality patterns, notably among juveniles, imply dwindling resources, indicative of environmental instability. Skeletal examination reveals a high incidence of forelimb fractures, indicating risks during activities like digging or confrontations. Palaeopathological evidence unveils vulnerabilities to tuberculosis, abscesses, rickets, and injuries, elucidating mobility challenges. The cave's silts exhibit a high zinc concentration, potentially derived from successive bear generations consuming zinc-rich plants. This study illuminates the lives of late cave bears, elucidating unique environmental hurdles faced near their species' end., (© 2024. The Author(s).)

Targeting peptides or presequences are N-terminal extensions of proteins that encode information about their cellular localization. They include signal peptides (SP), which target proteins to the endoplasmic reticulum, and transit peptides (TP) directing proteins to the organelles of endosymbiotic origin: chloroplasts and mitochondria. TPs were hypothesized to have evolved from antimicrobial peptides (AMPs), which are responsible for the host defence against microorganisms, including bacteria, fungi and viruses. In this study, we performed comprehensive bioinformatic analyses of amino acid motifs of targeting peptides and AMPs using a curated set of experimentally verified proteins. We identified motifs frequently occurring in each type of presequence showing specific patterns associated with their amino acid composition, and investigated their position within the presequence. We also compared motif patterns among different taxonomic groups and identified taxon-specific features, providing some evolutionary insights. Considering the functional relevance and many practical applications of targeting peptides and AMPs, we believe that our analyses will prove useful for their design, and better understanding of protein import mechanism and presequence evolution., (© 2023. Springer Nature Limited.)

Lactoferrin, an iron-binding glycoprotein, plays a significant role in the innate immune system, with antibacterial, antivirial, antifungal, anticancer, antioxidant and immunomodulatory functions reported. It is worth emphasizing that not only the whole protein but also its derived fragments possess antimicrobial peptide (AMP) activity. Using AmpGram, a top-performing AMP classifier, we generated three novel human lactoferrin (hLF) fragments: hLF 397-412, hLF 448-464 and hLF 668-683, predicted with high probability as AMPs. For comparative studies, we included hLF 1-11, previously confirmed to kill some bacteria. With the four peptides, we treated three Gram-negative and three Gram-positive bacterial strains. Our results indicate that none of the three new lactoferrin fragments have antimicrobial properties for the bacteria tested, but hLF 1-11 was lethal against Pseudomonas aeruginosa . The addition of serine protease inhibitors with the hLF fragments did not enhance their activity, except for hLF 1-11 against P. aeruginosa , which MIC dropped from 128 to 64 µg/mL. Furthermore, we investigated the impact of EDTA with/without serine protease inhibitors and the hLF peptides on selected bacteria. We stress the importance of reporting non-AMP sequences for the development of next-generation AMP prediction models, which suffer from the lack of experimentally validated negative dataset for training and benchmarking.

Due to their complex history, plastids possess proteins encoded in the nuclear and plastid genome. Moreover, these proteins localize to various subplastid compartments. Since protein localization is associated with its function, prediction of subplastid localization is one of the most important steps in plastid protein annotation, providing insight into their potential function. Therefore, we create a novel manually curated data set of plastid proteins and build an ensemble model for prediction of protein subplastid localization. Moreover, we discuss problems associated with the task, e.g. data set sizes and homology reduction. PlastoGram classifies proteins as nuclear- or plastid-encoded and predicts their localization considering: envelope, stroma, thylakoid membrane or thylakoid lumen; for the latter, the import pathway is also predicted. We also provide an additional function to differentiate nuclear-encoded inner and outer membrane proteins. PlastoGram is available as a web server at https://biogenies.info/PlastoGram and as an R package at https://github.com/BioGenies/PlastoGram . The code used for described analyses is available at https://github.com/BioGenies/PlastoGram-analysis ., (© 2023. The Author(s).)

Synonymous codon usage can be influenced by mutations and/or selection, e.g., for speed of protein translation and correct folding. However, this codon bias can also be affected by a general selection at the amino acid level due to differences in the acceptance of the loss and generation of these codons. To assess the importance of this effect, we constructed a mutation-selection model model, in which we generated almost 90,000 stationary nucleotide distributions produced by mutational processes and applied a selection based on differences in physicochemical properties of amino acids. Under these conditions, we calculated the usage of fourfold degenerated (4FD) codons and compared it with the usage characteristic of the pure mutations. We considered both the standard genetic code (SGC) and alternative genetic codes (AGCs). The analyses showed that a majority of AGCs produced a greater 4FD codon bias than the SGC. The mutations producing more thymine or adenine than guanine and cytosine increased the differences in usage. On the other hand, the mutational pressures generating a lot of cytosine or guanine with a low content of adenine and thymine decreased this bias because the nucleotide content of most 4FD codons stayed in the compositional equilibrium with these pressures. The comparison of the theoretical results with those for real protein coding sequences showed that the influence of selection at the amino acid level on the synonymous codon usage cannot be neglected. The analyses indicate that the effect of amino acid selection cannot be disregarded and that it can interfere with other selection factors influencing codon usage, especially in AT-rich genomes, in which AGCs are usually used.

Mitochondrial DNA (mtDNA) lineages are recognized as important components of intra- and interspecific biodiversity, and allow to reveal colonization routes and phylogeographic structure of many taxa. Among these is the genus Cervus that is widely distributed across the Holarctic. We obtained sequences of complete mitochondrial genomes from 13 Cervus taxa and included them in global phylogenetic analyses of 71 Cervinae mitogenomes. The well-resolved phylogenetic trees confirmed Cervus to be monophyletic. Molecular dating based on several fossil calibration points revealed that ca. 2.6 Mya two main mitochondrial lineages of Cervus separated in Central Asia, the Western (including C. hanglu and C. elaphus) and the Eastern (comprising C. albirostris, C. canadensis and C. nippon). We also observed convergent changes in the composition of some mitochondrial genes in C. hanglu of the Western lineage and representatives of the Eastern lineage. Several subspecies of C. nippon and C. hanglu have accumulated a large portion of deleterious substitutions in their mitochondrial protein-coding genes, probably due to drift in the wake of decreasing population size. In contrast to previous studies, we found that the relic haplogroup B of C. elaphus was sister to all other red deer lineages and that the Middle-Eastern haplogroup E shared a common ancestor with the Balkan haplogroup C. Comparison of the mtDNA phylogenetic tree with a published nuclear genome tree may imply ancient introgressions of mtDNA between different Cervus species as well as from the common ancestor of South Asian deer, Rusa timorensis and R. unicolor, to the Cervus clade., (© 2022. The Author(s).)

Background: Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans., Results: Therefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication., Conclusions: The duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications.

Compounds including non-canonical amino acids (ncAAs) or other artificially designed molecules can find a lot of applications in medicine, industry and biotechnology. They can be produced thanks to the modification or extension of the standard genetic code (SGC). Such peptides or proteins including the ncAAs can be constantly delivered in a stable way by organisms with the customized genetic code. Among several methods of engineering the code, using non-canonical base pairs is especially promising, because it enables generating many new codons, which can be used to encode any new amino acid. Since even one pair of new bases can extend the SGC up to 216 codons generated by a six-letter nucleotide alphabet, the extension of the SGC can be achieved in many ways. Here, we proposed a stepwise procedure of the SGC extension with one pair of non-canonical bases to minimize the consequences of point mutations. We reported relationships between codons in the framework of graph theory. All 216 codons were represented as nodes of the graph, whereas its edges were induced by all possible single nucleotide mutations occurring between codons. Therefore, every set of canonical and newly added codons induces a specific subgraph. We characterized the properties of the induced subgraphs generated by selected sets of codons. Thanks to that, we were able to describe a procedure for incremental addition of the set of meaningful codons up to the full coding system consisting of three pairs of bases. The procedure of gradual extension of the SGC makes the whole system robust to changing genetic information due to mutations and is compatible with the views assuming that codons and amino acids were added successively to the primordial SGC, which evolved minimizing harmful consequences of mutations or mistranslations of encoded proteins., Competing Interests: The authors declare that they have no competing interests., (© 2020 The Authors.)

Paulinella photosynthetic species are unicellular, silica shell-forming amoebas classified into the supergroup Rhizaria. They crawl at the bottom of freshwater and brackish environments with the help of filose pseudopodia. These protists have drawn the attention of the scientific community because of two photosynthetic bodies, called chromatophores, that fill up their cells permitting fully photoautotrophic existence. Paulinella chromatophores, similarly to primary plastids of the Archaeplastida supergroup (including glaucophytes, red algae as well as green algae and land plants), evolved from free-living cyanobacteria in the process of endosymbiosis. Interestingly, these both cyanobacterial acquisitions occurred independently, thereby undermining the paradigm of the rarity of endosymbiotic events. Chromatophores were derived from α-cyanobacteria relatively recently 60-140 million years ago, whereas primary plastids originated from β-cyanobacteria more than 1.5 billion years ago. Since their acquisition, chromatophore genomes have undergone substantial reduction but not to the extent of primary plastid genomes. Consequently, they have also developed mechanisms for transport of metabolites and nuclear-encoded proteins along with appropriate targeting signals. Therefore, chromatophores of Paulinella photosynthetic species, similarly to primary plastids, are true cellular organelles. They not only show that endosymbiotic events might not be so rare but also make a perfect model for studying the process of organellogenesis. In this chapter, we summarize the current knowledge and retrace the fascinating adventure of Paulinella species on their way to become photoautotrophic organisms.

Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

The distinct structure and universality of the standard genetic code (SGC) have fascinated the scientists ever since the first amino acid assignments were discovered. There are several hypotheses trying to explain the origin and evolution of this code. One of them postulates that the SGC evolved to minimize harmful effects of amino acid replacements in proteins, caused by mutations and translational errors. Many investigations concerning this hypothesis have already been carried out, but they were focused mainly on the consequences of single-point mutations. Therefore, we decided to check the influence of other types of mutations, i.e. insertions and deletions, on the robustness to amino acid replacements of the SGC. Such mutations cause shifts in the reading frame during the translation process which result in more harmful consequences in coded proteins than in the case of single-point mutations. We applied a multi-objective optimization algorithm to find the best and the worst genetic codes, regarding their robustness to both single-point and frameshift mutations, for various amino acid properties. Then we compared the features of the found codes with the properties of the standard genetic code. The results show that the SGC is not fully optimized for minimizing the effects of frameshift mutations but it is, nevertheless, much closer to the best solutions than to the worst ones. It implies that a certain tendency to minimize the costs of amino acids replacements resulting from various kinds of mutations is present in the standard genetic code., (Copyright © 2019 Elsevier B.V. All rights reserved.)

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 PhyMet 2 , 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. PhyMet 2 with the MethanoGram predictor is available at http://metanogen.biotech.uni.wroc.pl., (© 2018 The Authors. Environmental Microbiology published by Society for Applied Microbiology and JohnWiley & Sons Ltd.)

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 F 1 viability observed for all crosses were not significantly different. In hybrid crosses (in F 2 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.

Parrots (Psittaciformes) are a diverse group of birds which need urgent protection. However, many taxa from this order have an unresolved status, which makes their conservation difficult. One species-rich parrot genus is Amazona , which is widely distributed in the New World. Here we describe a new Amazona form, which is endemic to the Yucatán Peninsula. This parrot is clearly separable from other Amazona species in eleven morphometric characters as well as call and behavior. The clear differences in these features imply that the parrot most likely represents a new species. In contrast to this, the phylogenetic tree based on mitochondrial markers shows that this parrot groups with strong support within A. albifrons from Central America, which would suggest that it is a subspecies of A. albifrons . However, taken together tree topology tests and morphometric analyses, we can conclude that the new parrot represents a recently evolving species, whose taxonomic status should be further confirmed. This lineage diverged from its closest relative about 120,000 years ago and was subjected to accelerated morphological and behavioral changes like some other representatives of the genus Amazona . Our phylogenies, which are so far the most comprehensive for Amazona taxa enabled us to consider the most feasible scenarios about parrot colonization of the Greater and Lesser Antilles and Central America from South America mainland. The molecular dating of these migrations and diversification rate were correlated with climatic and geological events in the last five million years, giving an interesting insight into Amazon parrot phylogeography and their evolution in general., Competing Interests: The authors declare there are no competing interests.

Cymbomonas tetramitiformis is a peculiar green alga that unites in one cell the abilities of photosynthesis and phagocytosis, which makes it a very useful model for the study of the evolution of plastid endosymbiosis. We have pondered over this issue and propose an evolutionary scenario of trophic strategies in eukaryotes, including primary and secondary plastid endosymbioses. C. tetramitiformis is a prototroph, just like the common ancestor of Archaeplastida was, and can synthesize most small organic molecules contrary to other eukaryotic phagotrophs, e.g. some metazoans, amoebozoans, and ciliates, which have not evolved tight endosymbiotic relationships. In order to establish a permanent photosynthetic endosymbiont they do not have to become prototrophs, but have to acquire the genes necessary for plastid retention via horizontal (including endosymbiotic) gene transfer. Such processes occurred successfully in the ancestors of eukaryotes with permanent secondary plastids and thus led to their great diversification. The preservation of phagocytosis in Cymbomonas (and some other prasinophytes as well) seems to result from nutrient deficiency in their oligotrophic habitats. This forces them to supplement their diet with phagocytized prey, in contrasts to the thecate amoeba Paulinella chromatophora , which also successfully transformed cyanobacteria into permanent organelles. Although Paulinella endosymbionts were acquired very recently in comparison to primary plastids, Paulinella has lost the ability to phagocytose, most probably due to the fact that it inhabits nutrient-rich environments, which renders the phagotrophy nonessential., Competing Interests: Compliance with ethical standards Competing interests Authors have no competing interests.

One of theories explaining the present structure of canonical genetic code assumes that it was optimized to minimize harmful effects of amino acid replacements resulting from nucleotide substitutions and translational errors. A way to testify this concept is to find the optimal code under given criteria and compare it with the canonical genetic code. Unfortunately, the huge number of possible alternatives makes it impossible to find the optimal code using exhaustive methods in sensible time. Therefore, heuristic methods should be applied to search the space of possible solutions. Evolutionary algorithms (EA) seem to be ones of such promising approaches. This class of methods is founded both on mutation and crossover operators, which are responsible for creating and maintaining the diversity of candidate solutions. These operators possess dissimilar characteristics and consequently play different roles in the process of finding the best solutions under given criteria. Therefore, the effective searching for the potential solutions can be improved by applying both of them, especially when these operators are devised specifically for a given problem. To study this subject, we analyze the effectiveness of algorithms for various combinations of mutation and crossover probabilities under three models of the genetic code assuming different restrictions on its structure. To achieve that, we adapt the position based crossover operator for the most restricted model and develop a new type of crossover operator for the more general models. The applied fitness function describes costs of amino acid replacement regarding their polarity. Our results indicate that the usage of crossover operators can significantly improve the quality of the solutions. Moreover, the simulations with the crossover operator optimize the fitness function in the smaller number of generations than simulations without this operator. The optimal genetic codes without restrictions on their structure minimize the costs about 2.7 times better than the canonical genetic code. Interestingly, the optimal codes are dominated by amino acids characterized by polarity close to its average value for all amino acids., (Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.)

The cave bear (Ursus spelaeus sensu lato) is a typical representative of Pleistocene megafauna which became extinct at the end of the Last Glacial. Detailed knowledge of cave bear extinction could explain this spectacular ecological transformation. The paper provides a report on the youngest remains of the cave bear dated to 20,930 ± 140 14 C years before present (BP). Ancient DNA analyses proved its affiliation to the Ursus ingressus haplotype. Using this record and 205 other dates, we determined, following eight approaches, the extinction time of this mammal at 26,100-24,300 cal. years BP. The time is only slightly earlier, i.e. 27,000-26,100 cal. years BP, when young dates without associated collagen data are excluded. The demise of cave bear falls within the coldest phase of the last glacial period, Greenland Stadial 3. This finding and the significant decrease in the cave bear records with cooling indicate that the drastic climatic changes were responsible for its extinction. Climate deterioration lowered vegetation productivity, on which the cave bear strongly depended as a strict herbivore. The distribution of the last cave bear records in Europe suggests that this animal was vanishing by fragmentation into subpopulations occupying small habitats. One of them was the Kraków-Częstochowa Upland in Poland, where we discovered the latest record of the cave bear and also two other, younger than 25,000 14 C years BP. The relatively long survival of this bear in karst regions may result from suitable microclimate and continuous access to water provided by deep aquifers, indicating a refugial role of such regions in the Pleistocene for many species.

The rhizarian amoeba Paulinella chromatophora harbors two photosynthetically active organelles of cyanobacterial origin that have been acquired independently of classic primary plastids. Because their acquisition did take place relatively recently, they are expected to provide new insight into the ancient cyanobacterial primary endosymbiosis. During the process of Paulinella endosymbiont-to-organelle transformation, more than 30 genes have been transferred from the organelle to the host nuclear genome via endosymbiotic gene transfer (EGT). The article discusses step-by-step protein import of EGT-derived proteins into Paulinella photosynthetic organelles with the emphasis on the nature of their targeting signals and the final passage of proteins through the inner organelle membrane. The latter most probably involves a simplified Tic translocon composed of Tic21- and Tic32-like proteins as well as a Hsp70-based motor responsible for pulling of imported proteins into the organelle matrix. Our results indicate that although protein translocation across the inner membrane of Paulinella photosynthetic organelles seems to resemble the one in classic primary plastids, the transport through the outer membrane does not. The differences could result from distinct integration pathways of Paulinella photosynthetic organelles and primary plastids with their respective host cells.

The rhizarian amoeba Paulinella chromatophora harbors two photosynthetically active and deeply integrated cyanobacterial endosymbionts acquired ~60 million years ago. Recent genomic analyses of P. chromatophora have revealed the loss of many essential genes from the endosymbiont's genome, and have identified more than 30 genes that have been transferred to the host cell's nucleus through endosymbiotic gene transfer (EGT). This indicates that, similar to classical primary plastids, Paulinella endosymbionts have evolved a transport system to import their nuclear-encoded proteins. To deduce how these proteins are transported, we searched for potential targeting signals in genes for 10 EGT-derived proteins. Our analyses indicate that five proteins carry potential signal peptides, implying they are targeted via the host endomembrane system. One sequence encodes a mitochondrial-like transit peptide, which suggests an import pathway involving a channel protein residing in the outer membrane of the endosymbiont. No N-terminal targeting signals were identified in the four other genes, but their encoded proteins could utilize non-classical targeting signals contained internally or in C-terminal regions. Several amino acids more often found in the Paulinella EGT-derived proteins than in their ancestral set (proteins still encoded in the endosymbiont genome) could constitute such signals. Characteristic features of the EGT-derived proteins are low molecular weight and nearly neutral charge, which both could be adaptations to enhance passage through the peptidoglycan wall present in the intermembrane space of the endosymbiont's envelope. Our results suggest that Paulinella endosymbionts/plastids have evolved several different import routes, as has been shown in classical primary plastids.

Bacteriophage KP34 is a novel virus belonging to the subfamily Autographivirinae lytic for extended-spectrum β-lactamase-producing Klebsiella pneumoniae strains. Its biological features, morphology, susceptibility to chemical and physical agents, burst size, host specificity and activity spectrum were determined. As a potential antibacterial agent used in therapy, KP34 molecular features including genome sequence and protein composition were examined. Phylogenetic analyses and clustering of KP34 phage genome sequences revealed its clear relationships with "phiKMV-like viruses". Simultaneously, whole-genome analyses permitted clustering and classification of all phages, with completely sequenced genomes, belonging to the Podoviridae.

The Trypanosomatidae is closely related to euglenids that harbor plastids acquired from a green alga via secondary endosymbiosis. This discovery led to the idea that trypanosomatid parasites contained a green alga-derived plastid in their evolutionary past, an evolutionary scenario that was criticized based on the rarity of plant/plastid/cyanobacterium-like genes in the completely sequenced genomes of Trypanosoma and Leishmania species. Because it is difficult to identify such genes, however, their apparent rarity does not preclude a previous plastid endosymbiosis in the Trypanosomatidae. The genome of the plastid-less apicomplexan Cryptosporidium parvum preserves only a handful of plant/plastid/cyanobacterium-like genes, suggesting massive loss of plastid genes after elimination of its plastid. Additional support for such wholesale gene loss comes from fucoxanthin-containing dinoflagellates. Trypanosomatid nuclear genomes contain cyanobacterium-, green plant-, and haptophyte alga-derived genes, suggesting that they could have possessed a plastid in their evolutionary past; however, these genes also could represent examples of more typical horizontal gene transfer that did not accompany a plastid endosymbiosis. Thus, the presence of host cell genes that were adapted for use in the plastid would be much stronger evidence for a past plastid endosymbiosis in the Trypanosomatidae. Good examples of such genes are those encoding superoxide dismutases (SODs). Trypanosomatid parasites possess 4 iron-containing SODs, with 2 of them, SODA and SODC, targeted to the mitochondrion. In contrast with SODAs with classical single-domain mitochondrial targeting signals, SODCs carry bipartite pre-sequences composed of a signal peptide, followed by a transit peptide. Interestingly, these N-terminal extensions show striking similarities in length, hydropathy profiles, amino acid composition, and targeting properties to pre-sequences of proteins targeted to eukaryotic alga-derived plastids of euglenids and dinoflagellates. In turn, phylogenetic analyses indicate that SODCs originated from a mitochondrion-targeted SOD via gene duplication and were inherited vertically in the trypanosomatid lineage. These data represent a new kind of evidence for a past plastid endosymbiosis in the Trypanosomatidae, but the nature of this plastid remains unclear. It is usually assumed that the trypanosomatid plastid shared a common origin with that of euglenids, but Delta 4 desaturase phylogenies suggest that it could have originated via an independent, tertiary endosymbiosis involving a haptophyte alga. It is also possible that ancestors of the Trypanosomatidae initially possessed a primary plastid that later was replaced by a secondary or tertiary plastid.

Some nuclear-encoded proteins are imported into higher plant plastids via the endomembrane (EM) system. Compared with multi-protein Toc and Tic translocons required for most plastid protein import, the relatively uncomplicated nature of EM trafficking led to suggestions that it was the original transport mechanism for nuclear-encoded endosymbiont proteins, and critical for the early stages of plastid evolution. Its apparent simplicity disappears, however, when EM transport is considered in light of selective constraints likely encountered during the conversion of stable endosymbionts into fully integrated organelles. From this perspective it is more parsimonious to presume the early evolution of post-translational protein import via simpler, ancestral forms of modern Toc and Tic plastid translocons, with EM trafficking arising later to accommodate glycosylation and/or protein targeting to multiple cellular locations. This hypothesis is supported by both empirical and comparative data, and is consistent with the relative paucity of EM-based transport to modern primary plastids.

Three hundred commensal Escherichia coli recovered from healthy herbivorous, carnivorous, and omnivorous mammals from one zoo were characterized for their phylogenetic origin, intestinal virulence gene (VG) prevalence, and genomic diversity. The phylogenetic structure of the E. coli (groups A, B1, B2, and D) from the herbivores was homogenous, with a prevailing representation of group B1. In the carnivores and omnivores, the phylogenetic diversity was species specific with a higher representation of group A compared to the herbivores. Of 16 intestinal VGs in the whole set, 8 were detected and they formed 13 VG profiles. In the herbivores, all the VG-positive isolates belonged to group B1 and harboured the genes eaeA, eastI, ehxA, stx1, and stx2, which separately or in combination formed 8 VG profiles. In the carnivores and omnivores, the VG-positive isolates frequently belonged to group A and harboured the estI and estII genes or a combination of eastI and estI, forming three VG profiles. Single genes cnf2, in group B2, and eastI, in group D, were found. Similarity analysis of pulsed-field gel electrophoresis (PFGE) patterns revealed closer relatedness between the isolates from carnivores and omnivores than those from herbivores. The comparison between the prevalence of phylogenetic groups and the phylogenetic origin of VG-positive isolates in the examined E. coli suggested, that E. coli from group B1 in herbivores and E. coli from group A rather than B1 in carnivores and omnivores are "best adapted" to the host organism. The groups revealed different preferences in the acquisition and maintenance of intestinal VGs.

One of the proteins targeted to the peridinin plastid of the dinoflagellate Lingulodinium polyedrum is the iron-containing superoxide dismutase (LpSOD). Like dinoflagellate plastid proteins of class II, LpSOD carries a bipartite presequence comprising a signal peptide followed by a transit peptide. Our bioinformatic studies suggest that its signal peptide is atypical, however, and that the entire presequence may function as a mitochondrial targeting signal. It is possible that LpSOD represents a new class of proteins in algae with complex plastids, which are co-targeted to the plastid and mitochondrion. In addition to the ambiguous N-terminal targeting signal, LpSOD contains a potential type-1 peroxisome-targeting signal (PTS1) located at its C-terminus. In accordance with a peroxisome localization of this dismutase, its mRNA has two in-frame AUG codons. Our bioinformatic analyses indicate that the first start codon resides in a much weaker oligonucleotide context than the second one. This suggests that synthesis of the plastid/mitochondrion-targeted and peroxisome-targeted isoforms could proceed through so-called leaky scanning. Moreover, our results show that expression of the two isoforms could be regulated by a 'hairpin' structure located between the first and second start codons.

Many bacterial genomes are under asymmetric mutational pressure which introduces compositional asymmetry into DNA molecule resulting in many biases in coding structure of chromosomes. One of the processes affected by the asymmetry is translocation changing the position of the coding sequence on chromosome in respect to the orientation on the leading and lagging DNA strand. When analysing sets of paralogs in 50 genomes, we found that the number of observed genes which switched their positions on DNA strand is lowest for genomes with the highest DNA asymmetry. However, the number of orthologs which changed DNA strand increases with the phylogenetic distance between the compared genomes. Nevertheless, there is a fraction of coding sequences that stay on the leading strand in all analysed genomes, whereas there are no sequences that stay always on the lagging strand. Since sequences diverge very fast after switching the DNA strand, this bias in mobility of sequences is responsible, in part, for higher divergence rates among some of coding sequences located on the lagging DNA strand.

One of the common features of bacterial genomes is a strong compositional asymmetry between differently replicating DNA strands (leading and lagging). The main cause of the observed bias is the mutational pressure associated with replication. This suggests that genes translocated between differently replicating DNA strands are subjected to a higher mutational pressure, which may influence their composition and divergence rate. Analyses of groups of completely sequenced bacterial genomes have revealed that the highest divergence rate is observed for the DNA sequences that in closely related genomes are located on different DNA strands in respect to their role in replication. Paradoxically, for this group of sequences the absolute values of divergence rate are higher for closely related species than for more diverged ones. Since this effect concerns only the specific group of orthologs, there must be a specific mechanism introducing bias into the structure of chromosome by enriching the set of homologs in trans position in newly diverged species in relatively highly diverged sequences. These highly diverged sequences may be of varied nature: (1) paralogs or other fast-evolving genes under weak selection; or (2) pseudogenes that will probably be eliminated from the genome during further evolution; or (3) genes whose history after divergence is longer than the history of the genomes in which they are found. The use of these highly diverged sequences for phylogenetic analyses may influence the topology and branch length of phylogenetic trees. The changing mutational pressure may contribute to arising of genes with new functions as well.