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The spread of PTLV-I in Africa is estimated to have occurred at least 27,300 ± 8,200 years ago. To test the robustness of the NJ and mpars tree topologies, 1,000 bootstrap replicates were performed.Using the available strains, the HTLV-If subtype appears to have emerged within the last 3,000 years, and the HTLV-Ia, HTLV-Ib, HTLV-Id, and HTLV-Ie subtypes appear to have diverged between 21,100 and 5,300 years ago. The Gen Bank accession numbers for the LTRphylogenetic analysis were AF012728–AF012730, AF035538–AF035541, AF045929, AF045931– AF045933, AF054627, AF061438, AF061441, AF061837, AF061838, AF061840, AF061847– AF061849, D00294, D23693, D23694, J02029, L02534, L36905, L47128, L58023, L60024, L60026, L75787, L76032, L76033, L76306, L76307, L76309, L76310, L76312, M33063, M33064, M92845, U12806, U12807, U86376, Y13347, Y16475, Y16481, Y17014, Y17016, Y17017, Z32527, and Z46900.ML trees generated in PAUP*, version 4.0b4a (Swofford 1998 ), were used in PAML, version 3.0 (Yang 1997 ), to reconstruct the ancestral sequences at the internal nodes of the tree with Base ML.The synonymous (silent) versus nonsynonymous (amino acid change) substitution distances (, respectively) were estimated in Dambe according to the Li93 method (Xia 2000 ) between neighboring internal nodes and between each tip of the tree and the node of its most recent common ancestor.For ideal data, this is a tree, whereas less ideal data will give rise to a treelike network that can be interpreted as possible evidence for different and conflicting phylogenies.The molecular-clock hypothesis, assuming a constant rate of evolution, was tested on the LTR- data set in Puzzle, version 4.0 (Strimmer and von Haeseler 1997 ), as previously described (Van Dooren et al. The most appropriate substitution model for HTLV-I, the Tamura-Nei substitution model with a gamma distributed rate heterogeneity (Salemi, Desmyter, and Vandamme 2000 ), was used.In the Li93 method, sequences are pairwise-compared codon by codon and divided into three categories of sites; zerofold-, twofold-, and fourfold-degenerate sites.Transitions and transversions are then scored after applying Kimura's two-parameter method to correct for multiple hits.
HTLV-I clusters are interspersed with STLV- I strains from different species, suggesting that species and genus barriers have been repeatedly crossed, at least once for each human subtype (Vandamme, Salemi, and Desmyter 1998 ). 1998 ; Vandamme, Salemi, and Desmyter 1998 ) must have occurred in the past and are likely still ongoing.
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