Historic and Current Geographic Distribution of Tigers Corresponding to the Eight Traditional Subspecies Designation

<p>Geographic origin of samples and sample size (circles or squares) from each location are indicated (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020442#pbio-0020442-t301" target="_blank">Table 3</a> for sources). Three-letter codes (TIG, ALT, etc.) are indicated subspecies abbreviations. Dotted lines are approximate boundaries between tiger subspecies studied here. The Isthmus of Kra divides the traditional Indochinese tigers into the northern Indochinese tigers <i>P. t. corbetti</i> I and the Malayan tigers <i>P. t. corbetti</i> II based on the present study. We propose the Malayan tiger subspecies, COR II, be named <i>P. t. jacksoni,</i> to honor Peter Jackson, the former Chair of the IUCN's Cat Specialist Group who has contributed significantly to worldwide tiger conservation.</p

Phylogenetic Relationships among Tigers from mtDNA Haplotypes

<div><p>(A) Phylogenetic relationships based on MP among the tiger mtDNA haplotypes from the combined 4,078 bp mitochondrial sequence (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020442#pbio-0020442-t002" target="_blank">Table 2</a>). Branches of the same color represent haplotypes of the same subspecies. Trees derived from ME and ML analyses have identical topologies. Numbers above branches represent bootstrap support from 100 replicates using the MP method, followed by bootstrap values using the ME-ML analyses (only those over 70% are indicated). Numbers below branches show number of MP steps per number of homoplasies from a strict consensus tree. Numbers in parentheses represent numbers of individuals sharing the same haplotype. MP analysis using heuristic search and tree-bisection-reconnection branch-swapping approach results in two equally most-parsimonious trees and the one resembling the ME and ML trees is shown here (tree length = 60 steps; CI = 0.900). The ME tree is constructed with PAUP using Kimura two-parameter distances (transition to transversion ratio = 2) and NJ algorithm followed by branch-swapping procedure (ME = 0.0142). The ML approach is performed using a TrN (Tamura-Nei) +I (with proportion of invariable sites) model, and all nodes of the ML tree were significant (a consensus of 100 trees, –Ln likelihood = 5987.09).</p> <p>(B) Statistical parsimony network of tiger mtDNA haplotypes based on 4,078 mtDNA sequences constructed using the TCS program (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020442#pbio-0020442-Clement1" target="_blank">Clement et al. 2000</a>). The area of the circle is approximately proportional to the haplotype frequency, and the length of connecting lines is proportional to the exact nucleotide differences between haplotypes with each unit representing one nucleotide substitution. Missing haplotypes in the network are represented by dots. Haplotype codes and the number of individuals (in parentheses) with each haplotype are shown (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020442#pbio-0020442-t002" target="_blank">Table 2</a>).</p></div

Schematic of P. tigris mtDNA

<p>The position of PCR primers used for amplification of Cymt specific sequences and alignment of the homologous Numt sequence (outer, dashed line) in tiger mitochondria. Fifteen Cymt-specific primer sets spanning 6,026 bp of mtDNA were designed and screened for polymorphism in tigers (inner, solid line). Five indicated segments showed no variation among fifteen tigers that represented five traditional subspecies and therefore were excluded from further analysis. The ten variable segments (4,078 bp) were amplified in 100 tiger individuals. Primer sequences are listed in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020442#pbio-0020442-t001" target="_blank">Table 1</a>. Diamonds indicate polymorphic mtDNA segments; brackets indicate monomorphic mtDNA segments among tigers that were excluded from phylogenetic analysis.</p

Phylogenetic Relationships among the Individual Tigers from Composite Microsatellite Genotypes of 30 Loci

<p>Branches of the same color represent tiger individuals of the same subspecies. The NJ tree, which is based on Dps and Dkf with the (1 – ps/kf) option in MICROSAT (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020442#pbio-0020442-Minch1" target="_blank">Minch et al. 1995</a>), generated similar topologies, and only the Dps tree is shown here. Numbers are individual Pti codes (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020442#pbio-0020442-t301" target="_blank">Table 3</a>). Bootstrap values over 50% are shown on the divergence node.</p

NY-ESO-1 expression in DCIS: A new predictor of good prognosis

BACKGROUND: At present, it is difficult to predict which patients with ductal carcinoma-in-situ (DCIS) will subsequently develop frank invasive breast cancer (IDC). A recent survey by our group has shown that NY-ESO-1 and MAGEA are both expressed in DCIS. This study was aimed at determining whether expression of these antigens was related to the later development of IDC. RESULTS: 14 of 42 (33%) of patients developed invasive breast cancer during the follow up period. Only one of those DCIS cases that relapsed was positive for NYESO-1 at diagnosis. In contrast, DCIS samples of 15 of the 28 (54%) of those patients who remained disease-free expressed NY-ESO-1. (Permutation chi square p=0.0033). METHODS: We identified 42 patients with DCIS, and followed them up for more than 10 years. NY-ESO-1 and MAGEA were demonstrated by immunostaining as were CD8+ infiltrates on all sections together with the conventional markers, ER, PR, and HER2. CONCLUSIONS: Expression of NY-ESO-1 may predict those patients who will not subsequently develop invasive breast cancer and could therefore potentially be helpful in defining prognosis in patients with DCIS

Additional file 2: Figure S1. of Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly

Species and sub-species identification for three leopard samples. Figure S2. Distribution of K-mer frequency in the error-corrected reads. Figure S3. GC content distributions. Figure S4. Composition of mammalian orthologous genes. Figure S5. Divergence time estimation of 18 mammals. Figure S6. Contraction of the amylase gene families (AMY1 and AMY2) in carnivores. Figure S7. Frame-shift mutations in Felidae GCKR genes. Figure S8. Felidae-specific amino acid changes in DNA repair system. Figure S9. Felidae-specific amino acid change in MEP1A protein. Figure S10. Felidae-specific amino acid change in ACE2 protein. Figure S11. Felidae-specific amino acid change in PRCP protein. (DOCX 2024 kb

Additional file 3: of Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly

Tables S1-50. (DOCX 174 kb

Additional file 2: Figure S1. of Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly

Species and sub-species identification for three leopard samples. Figure S2. Distribution of K-mer frequency in the error-corrected reads. Figure S3. GC content distributions. Figure S4. Composition of mammalian orthologous genes. Figure S5. Divergence time estimation of 18 mammals. Figure S6. Contraction of the amylase gene families (AMY1 and AMY2) in carnivores. Figure S7. Frame-shift mutations in Felidae GCKR genes. Figure S8. Felidae-specific amino acid changes in DNA repair system. Figure S9. Felidae-specific amino acid change in MEP1A protein. Figure S10. Felidae-specific amino acid change in ACE2 protein. Figure S11. Felidae-specific amino acid change in PRCP protein. (DOCX 2024 kb