The mega‐matrix tree of life: using genome‐scale horizontal gene transfer and sequence evolution data as information about the vertical history of life

Because horizontal gene transfer can confound the recovery of the largely prokaryotic tree of life (ToL), most genome‐based techniques seek to eliminate horizontal signal from ToL analyses, commonly by sieving out incongruent genes and data. This approach greatly limits the number of gene families analysed to a subset thought to be representative of vertical evolutionary history. However, formalized tests have not been performed to determine whether combining the massive amounts of information available in fully sequenced genomes can recover a reasonable ToL. Consequently, we used empirically defined gene homology definitions from a previous study that delineate xenologous gene families (gene families derived from a common transfer event) to generate a massively concatenated, combined‐data ToL matrix derived from 323 404 translated open reading frames arranged into 12 381 gene homologue groups coded as amino acid data and 63 336, 64 105, 65 153, 66 922 and 67 109 gene homologue groups coded as gene presence/absence data for 166 fully sequenced genomes. This whole‐genome gene presence/absence and amino acid sequence ToL data matrix is composed of 4867 184 characters (a combined data‐type mega‐matrix). Phylogenetic analysis of this mega‐matrix yielded a fully resolved ToL that classifies all three commonly accepted domains of life as monophyletic and groups most taxa in traditionally recognized locations with high support. Most importantly, these results corroborate the existence of a common evolutionary history for these taxa present in both data types that is evident only when these data are analysed in combination.
© The Willi Hennig Society 2010.     

Agricultural fertilization with poultry manure results in persistent environmental contamination with the pathogen Clostridioides difficile

During a field experiment applying broiler manure for fertilization of agricultural land, we detected viable Clostridioides (also known as Clostridium) difficile in broiler faeces, manure, dust and fertilized soil. A large diversity of toxigenic C. difficile isolates was recovered, including PCR ribotypes common from human disease. Genomic relatedness of C. difficile isolates from dust and from soil, recovered more than 2 years after fertilization, traced their origins to the specific chicken farm that had delivered the manure. We present evidence of long-term contamination of agricultural soil with manure-derived C. difficile and demonstrate the potential for airborne dispersal of C. difficile through dust emissions during manure application. Clostridioides genome sequences virtually identical to those from manure had been recovered from chicken meat and from human infections in previous studies, suggesting broiler-associated C. difficile are capable of zoonotic transmission.     

Role of ultimobranchial body and corpuscle of Stannius in regulation of the plasma calcium and phosphorus levels in the teleost Heteropneustes fossilis.

Effects of NaF, CaCl2, NaCl and mammalian calcitonin on the histology of ultimo-branchial (UTB) and corpuscle of Stannius (CS) and plasma levels of calcium and phosphorus in the teleost Heteropneustes fossilis are recorded. Administration of NaF, NaCl, and mammalian calcitonin resulted in varying degree of hypolcalcaemia and hyperphosphataemia, whereas hypercalcaemia and hypophosphataemia developed during CaCl2 treatment. These treatments also produced various histological changes in UTB and CS. It is suggested that CS and UTB are involved in metabolisms of Ca and P, and in osmoregulation. Moreover, it is an important hypocalcaemic mechanism in this fish in combating hypercalcaemia.     

Seasonal variations in the blood constituents of an air-breathing fish, Channa punctatus Bloch

A year long study based on monthly observations on the haematology of female Channa punctatus with respect to haemoglobin, haematocrit values, total erythrocyte and leucocyte numbers together with a differential enumeration of various leucocytes viz. thrombocytes small and large lymphocytes, monocytes, neutrophils, eosinophils and basophils is recorded. The study showed that the total erythrocytic number, haemoglobin and haematocrit values decrease during the breeding time i.e. July to September. The thrombocyte number significantly increased while the neutrophilic number showed a decrease. The physiological significance of these changes is discussed with reference to the available literature.