Optimum chance phylogenetic relationships of control area haplotypes produced from market purchased eyeball samples and sequences acquired from understood people.
Phylogenetic relationships had been identical in Bayesian inference, maximum likelihood and maximum parsimony estimates (?lnL = 1399.28612; parsimony size = 141). Help values listed above nodes are Bayesian probabilities centered on 5,000,000 resamples, maximum chance bootstrap help values predicated on 1,000 bootstrap replicates, and maximum parsimony bootstrap help values according to 2,000 bootstrap replicates. Help values are shown just for clades of Sotalia guianensis and Sotalia fluviatilis haplotypes, and also for the monophyly of Sotalia. Branch lengths are proportional to maximum chance sequence divergence; scale shows portion of series divergence. Haplotypes 1–14, highlighted in bold, had been present in our research and correspond to GenBank accession #EU022531–EU022544.
To advance confirm the relationships regarding the unknown sequences, we performed a nonphylogenetic analysis that is cladistic. We constructed a matrix of autapomorphies for Sotalia fluviatilis, Sotalia guianensis, Inia g. Geoffrensis, Inia g. Humboltiana, and Inia g. Boliviensis predicated on available series information in Genbank and our guide people, and completed a populace aggregation analysis ( Davis and Nixon 1992 ).
All eyeball?derived sequences decided by BLAST to be of cetacean origin provided species?specific autapomorphic character states indicative of molecular positional homologies with Sotalia guianensis with no other types, unambiguously assigning all eyeballs of cetacean origin to Sotalia guianensis. The control area and Cytochrome b information sets have two and six diagnostic internet web sites, correspondingly, that assign all cetacean eyeball examples to Sotalia guianensis and unambiguously differentiate it from Sotalia fluviatilis and Inia spp. ( dining dining Table 1; online Appendix S1, S2).
| Control area | BEL | MAO | PVH | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variable position | 39 | 136 | 139 | 160 | 175 | 231 | 256 | 269 | 270 | 362 | 381 | 387 | 404 | 463 | 504 | 559 | Haplotype occurence | ||
| Inia spp. | A | T | the | G | C | G | G/A | A | A | T | C | C/T | C/T | C | C/T | A | ? | ? | ? |
| Sotalia fluviatilis | T | T | A | G | C/T | G | C/T | T | C | C/T | C | T | T | C | T | A | ? | ? | ? |
| Sotalia guianensis | C | G/T | A/C | A | C/T | G/A | C/T | C/T | C/T | C/T | C/G | C/T | C/T | C/T | C/T | C/A | 22 | 11 | 1 |
| CR_Hap01 | C | T | A | A | T | A | C | C | C | C | C | T | C | C | T | the | 1 | ? | ? |
| CR_Hap02 | C | T | A | A | T | A | C | T | C | C | C | C | T | C | T | A | 2 | ? | ? |
| CR_Hap03 | C | T | A | A | T | A | C | C | bbw cam modelsC | C | C | C | T | C | T | the | 6 | 2 | ? |
| CR_Hap04 | C | T | A | A | T | A | C | T | C | C | C | T | C | C | T | A | 3 | 5 | 1 |
| CR_Hap05 | C | T | A | A | T | A | C | T | C | T | C | T | C | C | T | the | 1 | 2 | ? |
| CR_Hap06 | C | T | the | A | C | the | T | T | T | C | C | T | T | C | T | the | 1 | ? | ? |
| CR_Hap07 | C | T | A | A | T | A | C | T | C | C | C | C | C | C | T | A | 3 | ? | ? |
| CR_Hap08 | C | G | C | A | T | G | C | T | C | C | C | T | C | C | T | the | 1 | ? | ? |
| CR_Hap09 | C | T | A | A | T | G | C | T | C | C | C | T | C | C | T | the | 1 | ? | ? |
| CR_Hap10 | C | T | A | A | T | A | C | C | C | C | C | T | T | C | T | the | 1 | ? | ? |
| CR_Hap11 | C | T | A | A | T | A | C | C | C | C | C | C | T | T | T | A | ? | 1 | ? |
| CR_Hap12 | C | T | A | A | T | A | C | C | C | C | C | C | T | C | T | C | ? | 1 | ? |
| CR_Hap13 | C | T | A | A | C | the | C | T | T | C | C | T | T | C | C | the | 1 | ? | ? |
| CR_Hap14 | C | T | A | A | T | A | C | C | C | C | G | C | T | C | T | the | 1 | ? | ? |
| Cytochrome b | |||||||||||||||||||
| Variable position | 49 | 78 | 124 | 297 | 367 | 396 | 462 | 501 | 528 | 531 | 561 | ||||||||
| Inia spp. | G | T | A | C | G | C | T | T | A | C | T | ? | ? | ? | |||||
| Sotalia fluviatilis | G | C | A | G | G | C | T | the | A | C | T | ? | ? | ? | |||||
| Sotalia guianensis | G/A | C/T | G/A | A | G/A | C/T | C | G | C | T | C | 16 | 7 | 1 | |||||
| CB_Hap01 | G | C | A | A | G | C | C | G | C | T | C | 8 | 4 | 1 | |||||
| CB_Hap02 | A | C | A | the | G | C | C | G | C | T | C | 1 | ? | ? | |||||
| CB_Hap03 | G | T | A | A | G | C | C | G | C | T | C | 1 | ? | ? | |||||
| CB_Hap04 | G | C | G | A | G | T | C | G | C | T | C | 3 | 1 | ? | |||||
| CB_Hap05 | G | C | G | A | A | T | C | G | C | T | C | 3 | 2 | ? | |||||
- Internet web internet Sites highlighted in bold unambiguously assign the unknown eyeball examples to Sotalia guianensis. Those perhaps not highlighted differentiate noticed haplotypes. Control area haplotypes 1–14 match GenBank accession numbers EU022531?EU022544, while cytochrome b haplotypes 1–5 match GenBank accession numbers EU022545?EU022549. BEL = Belem, MAO = Manaus, PVH = Porto Velho.