Statistical analyses were performed within each haplotype
Following maternal plasma DNA sequencing and relative haplotype
dosage (RHDO) analysis was used to infer the mutational status of the fetus for inheritance of Mendelian disorders.
1) and 99% homology with Anas zonorhyncha isolate ZH-18 haplotype
A-56 (GenBank Acc Number AY506969.
To better assess minimum numbers of independent native matrilines, we combined the cytochrome b and D-loop fragments into a single concatenated haplotype
, which we denoted as X-Y, where X represents the cytochrome b fragment and Y represents the D-loop fragment; the concatenated haplotypes
provided greater resolution than the cytochrome b fragment alone, enabling us to infer independent native and nonnative matrilines (for example, Sacks and others 2010, 2016).
SL1 was the only sublineage not originating from the basal haplotype
but directly from the earliest NS-405.
The other was that the tumor necrosis factor-a (TNF-a) gene is polymorphic and the association of TNF-a haplotype
with different HLA alleles leads to different TNF-a secretion level and induces hypo- or hyper-immune reactivity.
was compared to previously assigned haplotypes
and named using the standardized nomenclature conventions recently established for the hawksbill turtles (LeRoux et al.
For the haplotype
/nucleotide diversity, the following measures were calculated: S, as the number of segregating (polymorphic) sites; haplotype
(gene) diversity and its sampling variance (Nei 1987); the standard deviation (or standard error) as the square root of the variance; nucleotide diversity, Pi ([Pi]), as the average number of nucleotide differences per site between two sequences and its sampling variance (Nei 1987); the mutation parameter Theta ([theta], per site or per gene) from S or Eta ([eta]), as the total number of mutations (Watterson 1975, Nei 1987); and k, the average number of nucleotide differences between two sequences (Tajima 1993).
network was constructed using TCS (Clement et al.
In RHDO analysis, maternal haplotype
information is required.
Based on the eight MCIR haplotypes
recovered during this study, 36 expected haplotype
combinations were constructed.
were compared in phylogenetic trees with 347 additional mtDNA D-loop sequences already reported for river and swamp buffaloes.
frequencies were estimated using the expectation-maximization (em) algorithm implemented in Arlequin software v.
But one variant of the protein, haplotype
V, staves off destruction, Rokusuke Yoshikawa of Kyoto University in Japan and colleagues report online October 21 in the Journal of Virology.
Results: Of the total 133 haplotypes
studied, 52(39%) were Haplotype