In this chapter, we outline a pipeline for ortholog prediction and phylogenetic analysis in plants. This computational pipeline uses algorithms from different software to enable bioinformatic-beginner biologists to predict orthologs that can be shared with many distinct plant nonmodel and model species and identify gene loss events. Prediction of orthologs allows (1) investigation of the evolutionary relationships of plant genomes, (2) discovery of their origin, function, and (3) the impact of their adaptability to the environment.We developed a pipeline to fit, not only eukaryote but also prokaryote organisms, with small or large genomes. All results acquired from the orthologs predication will enable phylogenetic tree construction, using gene and species (phylogenomic) phylogeny approaches.

• Klíčová slova
• Bayesian inference, Coalesce phylogeny, Domain screening, Homology search, Maximum likelihood phylogeny, Molecular evolution, Orthologs assignment, Phylogenomic phylogeny,
• MeSH
• algoritmy MeSH
• fylogeneze MeSH
• genom rostlinný MeSH
• molekulární evoluce * MeSH
• software * MeSH
• výpočetní biologie metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Considerable controversy exists about which hypotheses and variables best explain mammalian brain size variation. We use a new, high-coverage dataset of marsupial brain and body sizes, and the first phylogenetically imputed full datasets of 16 predictor variables, to model the prevalent hypotheses explaining brain size evolution using phylogenetically corrected Bayesian generalized linear mixed-effects modelling. Despite this comprehensive analysis, litter size emerges as the only significant predictor. Marsupials differ from the more frequently studied placentals in displaying a much lower diversity of reproductive traits, which are known to interact extensively with many behavioural and ecological predictors of brain size. Our results therefore suggest that studies of relative brain size evolution in placental mammals may require targeted co-analysis or adjustment of reproductive parameters like litter size, weaning age or gestation length. This supports suggestions that significant associations between behavioural or ecological variables with relative brain size may be due to a confounding influence of the extensive reproductive diversity of placental mammals.

• Klíčová slova
• Bayesian, brain, comparative, imputations, marsupials, phylogenetic,
• MeSH
• Bayesova věta MeSH
• biologická evoluce MeSH
• fylogeneze MeSH
• těhotenství MeSH
• vačnatí * genetika   MeSH
• velikost orgánu MeSH
• zvířata MeSH
• Check Tag
• těhotenství MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

BACKGROUND: Farsetia hamiltonii Royle is a medicinally important annual plant from the Cholistan desert that belongs to the tribe Anastaticeae and clade C of the Brassicaceae family. We provide the entire chloroplast sequence of F.hamiltonii, obtained using the Illumina HiSeq2500 and paired-end sequencing. We compared F. hamiltonii to nine other clade C species, including Farsetia occidentalis, Lobularia libyca, Notoceras bicorne, Parolinia ornata, Morettia canescens, Cochlearia borzaeana, Megacarpaea polyandra, Biscutella laevigata, and Iberis amara. We conducted phylogenetic research on the 22 Brassicaceae species, which included members from 17 tribes and six clades. RESULTS: The chloroplast genome sequence of F.hamiltonii of 154,802 bp sizes with 36.30% GC content and have a typical structure comprised of a Large Single Copy (LSC) of 83,906 bp, a Small Single Copy (SSC) of 17,988 bp, and two copies of Inverted Repeats (IRs) of 26,454 bp. The genomes of F. hamiltonii and F. occidentalis show shared amino acid frequencies and codon use, RNA editing sites, simple sequence repeats, and oligonucleotide repeats. The maximum likelihood tree revealed Farsetia as a monophyletic genus, closely linked to Morettia, with a bootstrap score of 100. The rate of transversion substitutions (Tv) was higher than the rate of transition substitutions (Ts), resulting in Ts/Tv less than one in all comparisons with F. hamiltonii, indicating that the species are closely related. The rate of synonymous substitutions (Ks) was greater than non-synonymous substitutions (Ka) in all comparisons with F. hamiltonii, with a Ka/Ks ratio smaller than one, indicating that genes underwent purifying selection. Low nucleotide diversity values range from 0.00085 to 0.08516, and IR regions comprise comparable genes on junctions with minimal change, supporting the conserved status of the selected chloroplast genomes of the clade C of the Brassicaceae family. We identified ten polymorphic regions, including rps8-rpl14, rps15-ycf1, ndhG-ndhI, psbK-psbI, ccsA-ndhD, rpl36-rps8, petA-psbJ, ndhF-rpl32, psaJ-rpl3, and ycf1 that might be exploited to construct genuine and inexpensive to solve taxonomic discrepancy and understand phylogenetic relationship amongst Brassicaceae species. CONCLUSION: The entire chloroplast sequencing of F. hamiltonii sheds light on the divergence of genic chloroplast sequences among members of the clade C. When other Farsetia species are sequenced in the future, the full F. hamiltonii chloroplast will be used as a source for comprehensive taxonomical investigations of the genus. The comparison of F. hamiltonii and other clade C species adds new information to the phylogenetic data and evolutionary processes of the clade. The results of this study will also provide further molecular uses of clade C chloroplasts for possible plant genetic modifications and will help recognise more Brassicaceae family species.

• Klíčová slova
• Brassicaceae, Farsetia hamiltonii, Farsetiaoccidentalis, Monophyletic, Polymorphic regions, Synonymous substitutions,
• MeSH
• Brassicaceae * genetika   MeSH
• chloroplasty genetika   MeSH
• fylogeneze MeSH
• genom chloroplastový * genetika   MeSH
• kodon MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• kodon MeSH

Post-marital residence patterns are an important aspect of human social organization. However, identifying such patterns in prehistoric societies is challenging since they leave almost no direct traces in archaeological records. Cross-cultural researchers have attempted to identify correlates of post-marital residence through the statistical analysis of ethnographic data. Several studies have demonstrated that, in agricultural societies, large dwellings (over ca. 65 m2) are associated with matrilocality (spouse resides with or near the wife's family), whereas smaller dwellings are associated with patrilocality (spouse resides with or near the husband's family). In the present study, we tested the association between post-marital residence and dwelling size (average house floor area) using phylogenetic comparative methods and a global sample of 86 pre-industrial societies, 22 of which were matrilocal. Our analysis included the presence of agriculture, sedentism, and durability of house construction material as additional explanatory variables. The results confirm a strong association between matrilocality and dwelling size, although very large dwellings (over ca. 200 m2) were found to be associated with all types of post-marital residence. The best model combined dwelling size, post-marital residence pattern, and sedentism, the latter being the single best predictor of house size. The effect of agriculture on dwelling size becomes insignificant once the fixity of settlement is taken into account. Our results indicate that post-marital residence and house size evolve in a correlated fashion, namely that matrilocality is a predictable response to an increase in dwelling size. As such, we suggest that reliable inferences about the social organization of prehistoric societies can be made from archaeological records.

• MeSH
• antropologie MeSH
• archeologie * MeSH
• bydlení * dějiny   MeSH
• charakteristiky bydlení dějiny   MeSH
• charakteristiky rodiny * dějiny   MeSH
• dějiny starověku MeSH
• demografie dějiny   MeSH
• fylogeneze * MeSH
• lidé MeSH
• manželství * dějiny   MeSH
• populační dynamika dějiny   MeSH
• Check Tag
• dějiny starověku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• historické články MeSH
• práce podpořená grantem MeSH

• Klíčová slova
• ACETATES *, AMINO ACIDS *, BARIUM *, BIOCHEMISTRY *, CATTLE *, COLLAGEN *, EVOLUTION *, EXPERIMENTAL LAB STUDY *, MAGNESIUM *, MICROSCOPY, ELECTRON *, PHYSIOLOGY, COMPARATIVE *, PRESERVATION, BIOLOGICAL *, SHARKS *, SODIUM HYDROXIDE *, TRYPSIN *, VERTEBRATES *, WATER *,
• MeSH
• acetáty * MeSH
• aminokyseliny * MeSH
• baryum * MeSH
• biochemické jevy * MeSH
• biochemie * MeSH
• biologická evoluce * MeSH
• elektronová mikroskopie * MeSH
• elektrony * MeSH
• fylogeneze * MeSH
• hořčík * MeSH
• hydroxid sodný * MeSH
• kolagen * MeSH
• mikroskopie * MeSH
• obratlovci * MeSH
• ochrana biologická * MeSH
• skot MeSH
• srovnávací fyziologie * MeSH
• trypsin * MeSH
• voda * MeSH
• výzkum * MeSH
• žraloci * MeSH
• zvířata MeSH
• Check Tag
• skot MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• acetáty * MeSH
• aminokyseliny * MeSH
• baryum * MeSH
• hořčík * MeSH
• hydroxid sodný * MeSH
• kolagen * MeSH
• trypsin * MeSH
• voda * MeSH

A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.

• Klíčová slova
• Repetitive DNA, continuous characters, genomics, molecular systematics, next-generation sequencing, phylogenetics,
• MeSH
• DNA rostlinná genetika   MeSH
• Drosophila klasifikace   genetika   MeSH
• fylogeneze * MeSH
• genom genetika   MeSH
• hmyzí geny genetika   MeSH
• Magnoliopsida genetika   MeSH
• repetitivní sekvence nukleových kyselin genetika   MeSH
• shluková analýza MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH

Seed germination traits in alpine grasslands are poorly understood, despite the sensitivity of these communities to climate change. We hypothesise that germination traits predict species occurrence along the alpine-subalpine elevation gradient. Phylogenetic comparative analyses were performed using fresh seeds of 22 species from alpine and subalpine grasslands (1600-2400 m) of the Cantabrian Mountains, Spain (43° N, 5° W). Laboratory experiments were conducted to characterise germinability, optimum germination temperature and effect of cold and warm stratification on dormancy breaking. Variability in these traits was reduced by phylogenetic principal component analysis (phyl.PCA). Phylogenetic generalised least squares regression (PGLS) was used to fit a model in which species average elevation was predicted from their position on the PCA axes. Most subalpine species germinated in snow-like conditions, whereas most alpine species needed accumulation of warm temperatures. Phylogenetic signal was low. PCA1 ordered species according to overall germinability, whilst PCA2 ordered them according to preference for warm or cold germination. PCA2 significantly predicted species occurrence in the alpine-subalpine gradient, as higher elevation species tended to have warmer germination preferences. Our results show that germination traits in high-mountain grasslands are closely linked to the alpine-subalpine gradient. Alpine species, especially those from stripped and wind-edge communities, prefer warmer germination niches, suggesting that summer emergence prevents frost damage during seedling establishment. In contrast, alpine snowfield and subalpine grassland plants have cold germination niches, indicating that winter emergence may occur under snow to avoid drought stress.

• Klíčová slova
• Altitude, functional traits, germination temperature, high-mountain flora, phylogenetic comparative methods, phylogenetic generalised least squares, physiological seed dormancy,
• MeSH
• fylogeneze MeSH
• klíčení * MeSH
• klimatické změny MeSH
• nízká teplota MeSH
• období sucha MeSH
• pastviny MeSH
• roční období MeSH
• semena rostlinná genetika   fyziologie   MeSH
• semenáček genetika   fyziologie   MeSH
• teplota MeSH
• tundra MeSH
• vegetační klid MeSH
• Publikační typ
• časopisecké články MeSH
• srovnávací studie MeSH
• Geografické názvy
• Španělsko MeSH

BACKGROUND: Despite the excellent fossil record of cephalopods, their early evolution is poorly understood. Different, partly incompatible phylogenetic hypotheses have been proposed in the past, which reflected individual author's opinions on the importance of certain characters but were not based on thorough cladistic analyses. At the same time, methods of phylogenetic inference have undergone substantial improvements. For fossil datasets, which typically only include morphological data, Bayesian inference and in particular the introduction of the fossilized birth-death model have opened new possibilities. Nevertheless, many tree topologies recovered from these new methods reflect large uncertainties, which have led to discussions on how to best summarize the information contained in the posterior set of trees. RESULTS: We present a large, newly compiled morphological character matrix of Cambrian and Ordovician cephalopods to conduct a comprehensive phylogenetic analysis and resolve existing controversies. Our results recover three major monophyletic groups, which correspond to the previously recognized Endoceratoidea, Multiceratoidea, and Orthoceratoidea, though comprising slightly different taxa. In addition, many Cambrian and Early Ordovician representatives of the Ellesmerocerida and Plectronocerida were recovered near the root. The Ellesmerocerida is para- and polyphyletic, with some of its members recovered among the Multiceratoidea and early Endoceratoidea. These relationships are robust against modifications of the dataset. While our trees initially seem to reflect large uncertainties, these are mainly a consequence of the way clade support is measured. We show that clade posterior probabilities and tree similarity metrics often underestimate congruence between trees, especially if wildcard taxa are involved. CONCLUSIONS: Our results provide important insights into the earliest evolution of cephalopods and clarify evolutionary pathways. We provide a classification scheme that is based on a robust phylogenetic analysis. Moreover, we provide some general insights on the application of Bayesian phylogenetic inference on morphological datasets. We support earlier findings that quartet similarity metrics should be preferred over the Robinson-Foulds distance when higher-level phylogenetic relationships are of interest and propose that using a posteriori pruned maximum clade credibility trees help in assessing support for phylogenetic relationships among a set of relevant taxa, because they provide clade support values that better reflect the phylogenetic signal.

• Klíčová slova
• Bayesian phylogenetics, Cephalopoda, Endoceratoidea, Fossilized birth-death process, Multiceratoidea, Nautiloidea, Orthoceratoidea, Phylogeny, Posterior clade probabilities, Tree similarities,
• MeSH
• Bayesova věta MeSH
• fylogeneze MeSH
• hlavonožci * genetika   MeSH
• pravděpodobnost MeSH
• zkameněliny MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Reconstruction of the evolutionary history of specific protein-coding genes is an essential component of the biological sciences toolkit and relies on identification of orthologs (a gene in different organisms related by vertical descent from a common ancestor and usually presumed to have the same or similar function) and paralogs (a gene related to another in the same organism by descent from a single ancestral gene which may, or may not, retain the same/similar function) across a range of taxa. While obviously essential for the reconstruction of evolutionary histories, ortholog identification is of importance for protein expression, modeling for drug discovery programs, identification of critical residues and other studies. Here we describe an automated system for searching for orthologs and paralogs in eukaryotic organisms. Unlike manual methods the system is fast, requiring minimal user input while still being highly configurable.

• Klíčová slova
• Automation, Drug discovery, Evolution, Homology, Ortholog, Phylogenetics, Sequence searching,
• MeSH
• fylogeneze * MeSH
• molekulární evoluce MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Mandibles of representatives of the Holarctic crayfish families Astacidae, Cambaridae, and Cambaroididae were examined using SEM, and the results were analyzed in a phylogenetic framework. The intraspecific variability of the incisor process was found to be higher than its interspecific variability, mainly due to extensive abrasion of its ridge during intermolt periods. The plesiomorphic state of the crayfish mandibles highlights the dentate-crenate type of the incisor process and the extensive ribbed molar field with a multicuspidate caudal part, typical of the two parastacid crayfish examined for comparison. For Holarctic crayfish, the initial evolutionary type of the incisor is also the dentate-crenate one, but the molar field has a bowl-shaped caudal part and reduced cephalic part, both of which have been shown, for example, for Cambaroides. Similar mandibles are also widely present in American cambarids, which further evolved a blade-like incisor process (some Faxonius spp.) or a tricuspidate or double-bladed caudal molar field (some Procambarus spp.). The molar field in Astacidae crayfish is subdivided and rugose. The results of the present study indicate that little phylogenetic information is conveyed by the mandible shape at the species or genus level. Evolutionary changes are indicated mainly on the level of the main crayfish families. RESEARCH HIGHLIGHTS: Mandible shape can be an additional characteristic to distinguish crayfish families and selected genera. Obvious differences exist in the molar process rather than in the incisor ridge.

• Klíčová slova
• astacidae, cambaridae, cambaroididae, crustacea, decapoda, parastacidae,
• MeSH
• anatomie srovnávací * MeSH
• biologická evoluce * MeSH
• druhová specificita MeSH
• fylogeneze MeSH
• mandibula anatomie a histologie   diagnostické zobrazování   MeSH
• řezáky diagnostické zobrazování   MeSH
• severní raci anatomie a histologie   MeSH
• shazování tělního pokryvu MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH