Optimum chance phylogenetic relationships of control region haplotypes produced from market purchased eyeball examples 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 mentioned above nodes are Bayesian probabilities according to 5,000,000 resamples, maximum chance bootstrap help values considering 1,000 bootstrap replicates, and maximum parsimony bootstrap help values predicated on 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 help confirm the relationships associated with unknown sequences, we performed a nonphylogenetic cladistic analysis. 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 character that is autapomorphic 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 contain two and six diagnostic web internet web sites, correspondingly, that assign all eyeball that is cetacean to Sotalia guianensis and unambiguously differentiate it from Sotalia fluviatilis and Inia spp. ( dining Table 1; online Appendix S1, S2).
| Control region | 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? that is? | |||
| 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 | C | C | C | C | T | C | T | A | 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 | A | 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 | A | 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 | the | 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 | |||||||||||||||||||
| adjustable 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 | A | 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 | ? | |||||
- Web internet Sites highlighted in bold unambiguously assign the eyeball that is unknown to Sotalia guianensis. Those perhaps perhaps not highlighted differentiate haplotypes that are observed. 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.