Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites.

The Palaeognathae comprise the flightless ratites and the volant tinamous, and together with the Neognathae constitute the extant members of class Aves. It is commonly believed that Palaeognathae originated in Gondwana since most of the living species are found in the Southern Hemisphere [1-3]. However, this hypothesis has been questioned because the fossil paleognaths are mostly from the Northern Hemisphere in their earliest time (Paleocene) and possessed many putative ancestral characters [4]. Uncertainties regarding the origin and evolution of Palaeognathae stem from the difficulty in estimating their divergence times [1, 2] and their remarkable morphological convergence. Here, we recovered nuclear genome fragments from extinct elephant birds, which enabled us to reconstruct a reliable phylogenomic time tree for the Palaeognathae. Based on the tree, we identified homoplasies in morphological traits of paleognaths and reconstructed their morphology-based phylogeny including fossil species without molecular data. In contrast to the prevailing theories, the fossil paleognaths from the Northern Hemisphere were placed as the basal lineages. Combined with our stable divergence time estimates that enabled a valid argument regarding the correlation with geological events, we propose a new evolutionary scenario that contradicts the traditional view. The ancestral Palaeognathae were volant, as estimated from their molecular evolutionary rates, and originated during the Late Cretaceous in the Northern Hemisphere. They migrated to the Southern Hemisphere and speciated explosively around the Cretaceous-Paleogene boundary. They then extended their distribution to the Gondwana-derived landmasses, such as New Zealand and Madagascar, by overseas dispersal. Gigantism subsequently occurred independently on each landmass.

Genetic diversity of maternal lineage in the endangered Kiso horse based on polymorphism of the mitochondrial DNA D-loop region.

To determine genetic characteristics of the maternal lineage of the Kiso horse based on polymorphisms of the mitochondrial DNA D-loop region, we collected blood samples from 136 Kiso horses, 91% of the entire population, and sequenced 411 bp from 15,437 to 15,847 in the region. First of all, we estimated the demographic history; by searching homology between the obtained and known sequences using Basic Local Alignment Search Tool, by mismatch analysis to evaluate the mutation processes using Arlequin, and by building a phylogenetic tree showing the relationship of the mtDNA haplotypes for 24 horse breeds around the world using Molecular Evolutionary Genetics Analysis softwear. The results suggested that various horses that came to Japan stayed at Kiso region and became ancestors of Kiso horse and also genetically supported the theory that the Kiso horse was historically improved by other Japanese native horse breeds. Next, we analyzed the diversity of current maternal lineage by classifying the resulting sequences, and by calculating the haplotype diversity and nucleotide diversity using Arlequin. Then, we visualized the relationship among haplotypes by a median-joining network using NETWORK 4.6.0.0. The results suggested the diversity of maternal lineage in the Kiso horse was reasonably maintained. Lastly, we predicted future change of the diversity of maternal lineage in Kiso horse by assessing the regional distribution of the acquired haplotypes. The distribution suggested that diversity of maternal lineage would possibly be reducing.

Hematological and biochemical reference values for the endangered kiso horse.

To establish blood and biochemical references for the endangered Kiso horse, blood samples were collected from 111 adult Kiso horses, 74.5% of the existing breed. The samples were analyzed for 23 hematological and biochemical parameters to determine their means and standard deviations (SD). We compared the mean ± 2SD with the reference values cited in one of the most commonly used veterinary textbooks in Japan. The hematology of Kiso horses is characterized by lower erythrocyte count and hematocrit and hemoglobin levels. In addition, their serum biochemistry showed lower levels of aspartate transaminase, alkaline phosphatase, and γ-glutamyl transferase. Whether these propensities are attributed to breed-specific factors or are acquired factors remains unclear. Nevertheless, this study provides useful diagnostic indices for the endangered Kiso horse.

Association of BoLA-DRB3 alleles with mastitis resistance and susceptibility in Japanese Holstein cows.

In this study, 714 cows from 26 dairy herds were reclassified as healthy or mastitic cows on the basis of long-term somatic cell count (SCC) in milk. Cows with more than three consecutive lactation records of SCC from the first or second to fifth lactation, were selected, and their BoLA-DRB3 (DRB3) alleles were identified using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Cows with an SCC of < 200 000 cells/mL in all monthly records were classified as healthy (n=91). Cows with an SCC of > 300 000 cells/mL in two consecutive tests or four non-consecutive tests or cows with an SCC of > 500 000 cells/mL in any one test during lactation, regardless of parity, were classified as mastitic (n=201). Mastitic cows (n=153) from another 40 herds were considered to be infected if bacteriological testing revealed mastitis pathogens in milk. Their DRB3 alleles were identified using PCR-sequence-based typing (PCR-SBT). The differences in DRB3 allelic frequencies between healthy cows and cows with various degrees of mastitis were re-investigated. Moreover, the associations of various amino acid motifs in DRB3 alleles with resistance or susceptibility to mastitis pathogens were re-examined. DRB3.2*8(DRB3*1201) and DRB3.2*16(DRB3*1501) alleles were found to be associated with susceptibility, while DRB3.2*22(DRB3*1101), DRB3.2*23(DRB3*2703), and DRB3.2*24(DRB3*0101) alleles were found to be associated with resistance.

Genetic characterization of the endangered Kiso horse using 31 microsatellite DNAs.

In order to contribute to conservation of the endangered Kiso horse, we clarified their genetic information using 31 microsatellite DNAs, and genotyped 125 horses, 83% of the existing breed. First, we clarified the current status of the horses. The horses were confirmed to have experienced rapid loss of population causing a bottleneck, and their effective population size was much smaller than their census size. Moreover, the number of alleles (6.3), observed heterozygosity (0.674), and expected heterozygosity (0.662) were in the same range as other endangered horses all over the world. Therefore, although their inbreeding level was not so severe (F(is): -0.017), the Kiso horse is surely one of the endangered. Second, we obtained genetic information of individuals. This information allowed us to understand the genetic distance of individuals, and might help in development of a reproductive strategy concerning the genetic distance between the mating pairs. Moreover, there appeared to be 4 subpopulations of Kiso horse, and this result was in good agreement with their historical background. Third, we confirmed that the parentage test for identification using the 31 microsatellite DNAs was highly reliable (probability of exclusion: 0.999999993). This identification increases the reliability of stud certification, and is also helpful for effective management. Understanding the genetic diversity within the population and the relationships among individuals is important to ensuring effective management for maintenance of genetic variation, and this study may help in conservation of the endangered Kiso horse.

Population statistics and biological traits of endangered kiso horse.

The objective of this study was to clarify the current status of endangered Kiso horse, population statistics and biological traits, in order to take a step for the conservation by scientific approach. We surveyed 125 Kiso horses (86.2% of the whole breed), analyzed the construction of the population, and calculated the coefficient of inbreeding and effective population size. Moreover, we confirmed coat color variations and the traditional traits of the Kiso horse, and measured their height at the withers and chest circumference to clarify their physical characteristics. The population pyramid of the horses was stationary or contractive, suggesting a reduction of the population in the near future. The effective population size of the horse (47.9) suggested that the diversity was much less than their census size, and the high coefficient of inbreeding, 0.11 ± 0.07 on average, suggested that the horses were surely inbred. The horses had only 4 coat colors; bay, dark bay, buckskin dun, and chestnut, and 116 horses (92.8%) were bayish color, suggesting the fixation in their coat color. Moreover, the majority of them had dorsal stripe (83 horses; 66.4%), and the average heights at withers(131.9 ± 4.4 cm) and chest circumference (167.1 ± 10.1 cm) were not significantly different between males and females.

Association of BoLA-DRB3 alleles identified by a sequence-based typing method with mastitis pathogens in Japanese Holstein cows.

The association of the polymorphism of bovine leukocyte antigen (BoLA-DRB3) genes identified by the polymerase chain reaction sequence-based typing (PCR-SBT) method with resistance and susceptibility to mastitis caused by pathogenic bacteria was investigated. Blood samples for DNA extraction were collected from 194 Holstein cows (41 healthy cows and 153 mastitis cows including 24 mixed-infection cows infected with 2 or 3 species of pathogens) from 5 districts of Chiba prefecture, Japan. Sixteen BoLA-DRB3 alleles were detected. The 4 main alleles of DRB3*0101, *1501, *1201, and *1101 constituted 56.8% of the total number of alleles detected. Mastitis cows were divided into 2 groups: group 1 with single-infection cows and group 2 with all mastitis cows including 24 mixed-infection cows. The differences in the frequencies of BoLA-DRB3 alleles and the number of cows homozygous or heterozygous for each BoLA-DRB3 allele between healthy cows and the 2 groups of mastitis cows were evaluated. Furthermore, similar comparisons were performed between healthy cows and the 2 groups of mastitis cows for each mastitis pathogen. It was considered that the 4 alleles, namely, DRB3*0101, *1501, *1201, and *1101 had specific resistance and susceptibility to 4 different mastitis pathogens. Thus, DRB3*0101 might be associated with susceptibility to coagulase-negative Staphylococci and Escherichia coli, and DRB3*1501 might be associated with susceptibility to Escherichia coli. However, DRB3*1101 might be associated with resistance to Streptococci and coagulase-negative Staphylococci, and DRB3*1201, with resistance to Streptococci, Escherichia coli, and Staphylococcus aureus.

Association of the amino acid motifs of BoLA-DRB3 alleles with mastitis pathogens in Japanese Holstein cows.

The association of the polymorphism of bovine leukocyte antigen (BoLA-DRB3) genes, identified by the polymerase chain reaction sequence-based typing (PCR-SBT) method, with resistance and susceptibility to mastitis caused by Streptococci, coagulase-negative Staphylococci, Escherichia coli and Staphylococcus aureus was investigated. Blood samples for DNA extraction were collected from 170 Holstein cows (129 mastitis and 41 healthy cows) from 5 districts in Chiba prefecture, Japan. Susceptibility or resistance to the mastitis-causing pathogens was thought to vary by the presence of amino acid substitutions at the 9, 11, 13, and 30 positions. DRB3*0101 and DRB3*1501 had amino acid motifs of Glu(9), Ser(11), Ser(13), and Tyr(30), and they were considered to have susceptibility to all 4 mastitis pathogens. In contrast, DRB3*1101 and DRB3*1401 had amino acid motifs of Gln(9), His(11), Gly(13), and His(30) in these positions, and they also had Val(86), so these alleles were considered to have resistance to Streptococcal and coagulase-negative Staphylococcal mastitis. However, in the case of Escherichia coli mastitis, amino acid substitutions at the 9, 11, 13, and 30 positions had little effect, but rather substitutions at the 47, 67 positions of pocket 7, and at the 71, 74 positions of pocket 4, Tyr(47), Ile(67), Ala(71), and Ala(74), were associated with resistance. This motif was present in DRB3*1201.

Pralidoxime iodide (2-pAM) penetrates across the blood-brain barrier.

The in vivo rat brain microdialysis technique with HPLC/UV was used to determine the blood-brain barrier (BBB) penetration of pralidoxime iodide (2-PAM), which is a component of the current nerve agent antidote therapy. After intravenous dosage of 2-PAM (10, 50, 100 mg/kg), 2-PAM appeared dose-dependently in the dialysate; the striatal extracellular/blood concentration ratio at 1 h after 50 mg/kg dosage was 0.093 +/- 0.053 (mean +/- SEM). This finding offered conclusive evidence of the BBB penetration of 2-PAM. We also examined whether the BBB penetration of 2-PAM was mediated by a certain specific transporter, such as a neutral or basic amino acid transport system. Although it was unclear, the neural uptake of 2-PAM was Na+ dependent. The mean BBB penetration by 2-PAM was approximately 10%, indicating the intravenous administration of 2-PAM might be to a degree effective to reactivation of the blocked cholinesterase in the brain.

Production of gamma-hydroxybutyric acid in postmortem liver increases with time after death.

Gamma-hydroxybutyric (GHB) acid, which is becoming popular as a drug of abuse, was shown by means of gas chromatography-mass spectrometry (GC-MS) to increase in mouse liver with time after death. The amount detected was 0.8 +/- 1.0 microg/g at 3 h after death, 4.7 +/- 1.5 microg/g at 24 h, and 8.8 +/- 0.8 microg/g at 72 h. Furthermore, GHB was detected in samples from deceased persons, at concentrations of 2.6-12.0 microg/g in liver, 0.4-7.3 microg/ml in blood, and 0-2.6 microg/ml in urine, but was not detected in the blood and urine of living persons. Although 1,4-butanediol has been suggested to be a precursor of GHB produced after death, 1,4-butanediol was not detected in any of our samples. Additionally, succinate semialdehyde arising from gamma-aminobutyric acid (GABA) transamination to GHB was also barely detectable in any of our samples. This study supports previous reports that GHB is a product of postmortem decomposition. Production of GHB increases with time after death in postmortem liver; since we were unable to identify endogenous 1,4-butanediol and succinate semialdehyde in our samples, the pathway of GHB production after death remains unclear.