How Phenograms and Cladograms Became Molecular Phylogenetic Trees.

Tree diagrams are the prevailing form of visualization in biological classification and phylogenetics. Already during the time of the so-called Systematist Wars from the mid-1960s until the 1980s most journal articles and textbooks published by systematists contained tree diagrams. Although this episode of systematics is well studied by historians and philosophers of biology, most analyses prioritize scientific theories over practices and tend to emphasize conflicting theoretical assumptions. In this article, I offer an alternative perspective by viewing the conflict through the lens of representational practices with a case study on tree diagrams that were used by numerical taxonomists (phenograms) and cladists (cladograms). I argue that the current state of molecular phylogenetics should not be interpreted as the result of a competition of views within systematics. Instead, molecular phylogenetics arose independently of systematics and elements of cladistics and phenetics were integrated into the framework of molecular phylogenetics, facilitated by the compatibility of phenetic and cladistic practices with the quantitative approach of molecular phylogenetics. My study suggests that this episode of scientific change is more complex than common narratives of battles and winners or conflicts and compromises. Today, cladograms are still used and interpreted as specific types of molecular phylogenetic trees. While phenograms and cladograms represented different forms of knowledge during the time of the Systematist Wars, today they are both used to represent evolutionary relationships. This indicates that diagrams are versatile elements of scientific practice that can change their meaning, depending on the context of use within theoretical frameworks.

Clinical interpretation of CNVs with cross-species phenotype data.

BACKGROUND: Clinical evaluation of CNVs identified via techniques such as array comparative genome hybridisation (aCGH) involves the inspection of lists of known and unknown duplications and deletions with the goal of distinguishing pathogenic from benign CNVs. A key step in this process is the comparison of the individual's phenotypic abnormalities with those associated with Mendelian disorders of the genes affected by the CNV. However, because often there is not much known about these human genes, an additional source of data that could be used is model organism phenotype data. Currently, almost 6000 genes in mouse and zebrafish are, when knocked out, associated with a phenotype in the model organism, but no disease is known to be caused by mutations in the human ortholog. Yet, searching model organism databases and comparing model organism phenotypes with patient phenotypes for identifying novel disease genes and medical evaluation of CNVs is hindered by the difficulty in integrating phenotype information across species and the lack of appropriate software tools. METHODS: Here, we present an integrated ranking scheme based on phenotypic matching, degree of overlap with known benign or pathogenic CNVs and the haploinsufficiency score for the prioritisation of CNVs responsible for a patient's clinical findings. RESULTS: We show that this scheme leads to significant improvements compared with rankings that do not exploit phenotypic information. We provide a software tool called PhenogramViz, which supports phenotype-driven interpretation of aCGH findings based on multiple data sources, including the integrated cross-species phenotype ontology Uberpheno, in order to visualise gene-to-phenotype relations. CONCLUSIONS: Integrating and visualising cross-species phenotype information on the affected genes may help in routine diagnostics of CNVs.

Is There a Minimum Number of Landmarks That Optimizes the Geometric Morphometric Analysis of Mosquito (Diptera, Culicidae) Wings?

Culicids are the most significant arthropods affecting human health. Thus, their correct identification is critical. The use of Geometric Morphometrics (GM) has been recently incorporated into mosquito taxonomy and has begun to complement classic diagnostic techniques. Since sampling size depends on the number of Landmarks (LMs) used, this study aimed to establish the minimum number of wing LMs needed to optimize GM analysis of mosquito species and/or genera from urban and peri-urban areas of Argentina. Female left wings were used for the optimization phase, in which 17 LMs were reduced to four by iterative LM exclusion. To verify its efficiency, Principal Component Analysis (PCA), Discriminant Analysis (DA), and Canonical Variate Analysis (CVA) were performed. Additionally, a phenogram was constructed to visualize the results. We observed that five LMs for the PCA, CVA, and phenogram and nine for the DA enabled discrimination and/or clustering of almost all species and genera. Therefore, we tested the LM selection by using nine LMs and adding new species. The resulting PCA showed little overlap between species and almost all species clustered as expected, which was also reflected in the phenogram. Significant differences were found between wing shape among all species, together with a low total error rate in the DA. In conclusion, the number of LMs can be reduced and still be used to effectively differentiate and cluster culicids. This is helpful for better exploitation of available material and optimization of data processing time when classic taxonomy methods are inadequate or the material is scarce.

A Trans-Omics Comparison Reveals Common Gene Expression Strategies in Four Model Organisms and Exposes Similarities and Differences between Them.

The ultimate goal of gene expression regulation is on the protein level. However, because the amounts of mRNAs and proteins are controlled by their synthesis and degradation rates, the cellular amount of a given protein can be attained by following different strategies. By studying omics data for six expression variables (mRNA and protein amounts, plus their synthesis and decay rates), we previously demonstrated the existence of common expression strategies (CESs) for functionally related genes in the yeast Saccharomyces cerevisiae. Here we extend that study to two other eukaryotes: the yeast Schizosaccharomyces pombe and cultured human HeLa cells. We also use genomic data from the model prokaryote Escherichia coli as an external reference. We show that six-variable profiles (6VPs) can be constructed for every gene and that these 6VPs are similar for genes with similar functions in all the studied organisms. The differences in 6VPs between organisms can be used to establish their phylogenetic relationships. The analysis of the correlations among the six variables supports the hypothesis that most gene expression control occurs in actively growing organisms at the transcription rate level, and that translation plays a minor role. We propose that living organisms use CESs for the genes acting on the same physiological pathways, especially for those belonging to stable macromolecular complexes, but CESs have been modeled by evolution to adapt to the specific life circumstances of each organism.

Phylogeny, novel bacterial lineage and enzymatic potential of haloalkaliphilic bacteria from the saline coastal desert of Little Rann of Kutch, Gujarat, India.

This report describes cultivation-dependent diversity, phylogeny and enzymatic potential of the haloalkaliphilic bacteria isolated from the unvegetated desert soil of yet unexplored, saline desert of Little Rann of Kutch (LRK), India. The LRK is a unique ecosystem displaying a combination of Dry Rann and Wet Rann. A total of 25 bacteria were isolated and characterized on the basis of colony morphology, biochemical profile, sugar utilization, secretion of the extracellular enzymes and antibiotic sensitivity. Further, the identification and phylogenetic relatedness of 23 bacteria were established by the analysis of 16S rRNA gene sequences. The phylogenetic analysis indicated that the isolates belong to the phylum Firmicutes, comprising low G + C, Gram-positive bacteria, with different genera: Bacillus (~ 39%), Staphylococcus (~ 30%), Halobacillus (~ 13%), Virgibacillus (~ 13%), Oceanobacillus (~ 4%). Majority of the bacterial isolates produced proteases (30% isolates) followed by cellulases (24% isolates), CMCases (24% isolates) and amylases (20% isolates). Halobacillus, Virgibacillus and Bacillus predominantly produced hydrolases, while many produced multiple enzymes at high salinity and alkaline pH. Highest antibiotic resistance was observed against Ampicillin and Penicillin (32%) followed by Cefaclor (20%); Colistin, Cefoperazone and Cefotaxime (16%); Cefuroxime (12%); Gentamycin and Cefixime (8%); Erythromycin, Cefadroxil, Azithromycin, Co-trimoxazole, Amoxycillin, Norfloxacin, Cefpodoxime, Amikacin and Augmentin (4%). KJ1-10-99 and KJ1-10-93 representing < 97% of 16S rRNA gene sequence similarity belong to a novel lineage within the family Bacillaceae. Comparison of the phenogram and phylogram revealed the contradiction of the phenogram pattern and the phylogenetic placement of the isolates. The isolates belonging to same species have shown considerable phenotypic variation. The study on the cultivable haloalkaliphilic bacteria of an unexplored enigmatic niche reflects ecological and biotechnological significance.

Ecomorphological characterization of murines and non-arvicoline cricetids (Rodentia) from south-western Europe since the latest Middle Miocene to the Mio-Pliocene boundary (MN 7/8-MN13).

Rodents are the most speciose group of mammals and display a great ecological diversity. Despite the greater amount of ecomorphological information compiled for extant rodent species, studies usually lack of morphological data on dentition, which has led to difficulty in directly utilizing existing ecomorphological data of extant rodents for paleoecological reconstruction because teeth are the most common or often the only micromammal fossils. Here, we infer the environmental ranges of extinct rodent genera by extracting habitat information from extant relatives and linking it to extinct taxa based on the phenogram of the cluster analysis, in which variables are derived from the principal component analysis on outline shape of the upper first molars. This phenotypic "bracketing" approach is particularly useful in the study of the fossil record of small mammals, which is mostly represented by isolated teeth. As a case study, we utilize extinct genera of murines and non-arvicoline cricetids, ranging from the Iberoccitanian latest middle Miocene to the Mio-Pliocene boundary, and compare our results thoroughly with previous paleoecological reconstructions inferred by different methods. The resultant phenogram shows a predominance of ubiquitous genera among the Miocene taxa, and the presence of a few forest specialists in the two rodent groups (Murinae and Cricetidae), along with the absence of open environment specialists in either group of rodents. This appears to be related to the absence of enduring grassland biomes in the Iberian Peninsula during the late Miocene. High consistency between our result and previous studies suggests that this phenotypic "bracketing" approach is a very useful tool.