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Mitochondrial DNA coding region sequences support the phylogenetic distinction of two Indian wolf species

2007; Wiley; Volume: 45; Issue: 2 Linguagem: Inglês

10.1111/j.1439-0469.2006.00400.x

1439-0469

R. K. Aggarwal, Toomas Kivisild, J. Ramadevi, L. Singh,

Genetic diversity and population structure

Two small endangered populations of Indian wolves were recently shown to be distant from other wolf and dog mtDNA lineages characterized so far. None of the inner branches in the tree of canid species based on partial hypervariable D-loop sequences were, however, statistically supported by the data raising the question whether the two Indian wolf lineages represent two new species, occupying an intermediate position between Canis latrans and C. lupus or have diverged from the sub-species of C. lupus due to isolation and drift. Here we report complete D-loop, cytochrome b, and 16S rRNA sequences data for 23 additional wolves from India analysed in the context of other canid species. Extended analyses of D-loop data and partial sequences of 16S rRNA showed highly reticulated pattern and were unable to resolve unambiguously the phylogenetic relationship of Indian wolves among other canid species. The phylogenetic reconstructions of cytochrome b sequences, however gave significant statistical support for the inner branches supporting genetic distinction of the two Indian wolf lineages within themselves as well as from all other wolves of the world, including individuals belonging to subspecies C. lupus chanco and C. lupus pallipes to which the two Indian wolf populations have been traditionally assigned. Their genetic differentiation relative to worldwide variation of wolves supports the suggestion to treat them as separate wolf species, C. himalayensis and C. indica. Deux petites populations en danger de loups indiens ont été démontrées récemment comme étant distantes des autres lignées mitochondriales de loups et de chiens caractérisées jusqu'à maintenant. Aucunes des branches internes de l'arbre des canidés basé sur le séquençage d'une partie de la boucle hypervariable D n'étaient cependant statistiquement soutenues par les données, soulevant la question à savoir si les deux lignées de loups indiens représentent deux nouvelles espèces, occupant une position intermédiaire entre C. latrans et C. lupus, ou bien ont divergé de la sous-espèce C. lupusà cause d'isolement et de dérive génétique. Nous rapportons ici les séquences de la boucle-D en entier, du cytochrome b et ARNr 16S de 23 loups additionnels d'Inde analysées dans le contexte d'autres espèces de canidés. Des analyses extensives des données de la boucle-D et des séquences partielles de l'ARNr 16S révèlent un modèle hautement réticulé et étaient incapables de résoudre sans ambiguïté la relation phylogénétique des loups indiens parmi les autres espèces de canidés. La reconstruction phylogénétique des séquences du cytochrome b cependant donne un soutien statistique significatif pour les branches internes, soutenant une distinction génétique des deux lignées de loups indiens entre-elles ainsi que des autres loups du monde, y compris les individus appartenant aux sous-espèces C. lupus chanco et C. lupus pallipes où les deux populations de loups indiens ont été traditionnellement assignées. Leur différentiation génétique relative aux autres loups mondiaux supporte la suggestion de les traiter comme des espèces de loups séparées, C. himlayensis et C. indica. Figure S2. ML phylogenetic tree showing relationship of HW and GW with 27 other wolf sequences/haplotypes from elsewhere and 2 dog entries. Polymorphism based on ~651 bp of d-loop control region-I. Indian jackal is used as outgroup. Note the Indian wolf haplotypes appearing as distinct clades closer to the jackal and basal to the one comprising all other global wolf haplotypes, indicating them to be representing genetically unique ancient lineages of wolf. Distance measure: Corrected K 2-P. Reference taxa are as per codes in Table S2. Numerical values near the nodes are bootstrap values (only values > 50% are shown) Figure S3. ML phylogenetic tree showing relationship of HW and GW with 19 other wolf sequences/haplotypes from elsewhere and one dog entry. Polymorphism based on complete 675 bp of d-loop control region-I. Note the Indian wolf haplotypes appearing as distinct clades closer to the jackal and basal to the one comprising all other global wolf haplotypes, indicating them to be representing genetically unique ancient lineages of wolf. Indian jackal is used as outgroup. Distance measure: Corrected K 2-P. Reference taxa are as per codes in Table S2. Numerical values near the nodes are bootstrap values (only values > 50% are shown) Table S1. Reference mitochondrial cytochrome-b and 16S RNA gene sequences retrieved from EMBL database for use in the phylogenetic analysis Table S2. Reference mitochondrial D-loop control-region sequences/haplotypes retrieved from EMBL database for use in the phylogenetic analysis Table S3. DNA substitutions observed in the partial (~332 bp) mitochondrial cytochrome-b gene sequences of Indian wolves and other reference canid species Table S4. DNA substitutions observed in the complete mitochondrial cytochrome-b gene sequences of Indian wolves and three other canids from India and elsewhere Table S5. DNA substitutions and deletions (-) in 223 bp mtD-loop CR-I region of Indian wolves and other wolf populations around the globe (sample codes are as per Supp-Table-2) Table S6. DNA substitutions and deletions (-) in 545 bp mtD-loop CR-I region of Indian wolves and other wolf sequences/haplotypes from around the globe (sequence of Indian jackal, which is used as outgroup taxa, is also included) Table S7. DNA substitutions and deletions (-) in 641 bp mtD-loop CR-I region of Indian wolves and other wolf sequences/haplotypes from around the globe (sequence of Indian jackal, which is used as outgroup taxa, is also included) Table S8. DNA substitutions and deletions (-) in 296 bp mtD-loop CR-II region of Indian wolves and other wolf sequences/haplotypes (sequence of Indian jackal, which is used as outgroup taxa, is also included) Please note: Blackwell Publishing are not responsible for the content or functionality of any supplementary materials supplied by authors. Any queries (other than missing material) should be directed to the corresponding author for the article. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.