Some previous genetic studies have been performed to resolve the molecular phylogenetics of the squirrel monkeys (Saimiri). However, these studies did not show consensus in how many taxa are within this genus and what the relationships among them are. For this reason, we sequenced 2,237 base pairs of the mt COI and COII genes in 218 Saimiri individuals. All, less 12 S. sciureus sciureus from French Guyana, were sampled in the wild. These samples represented all the living Saimiri taxa recognized. There were four main findings of this study. (1) Our analysis detected 17 different Saimiri groups: albigena, cassiquiarensis, five polyphyletic macrodon groups, three polyphyletic ustus groups, sciureus, collinsi, boliviensis, peruviensis, vanzolinii, oerstedii and citrinellus. Four different phylogenetic trees showed the Central American squirrel monkey (S. oerstedii) as the most differentiated taxon. In contrast, albigena was indicated to be the most recent taxon. (2) There was extensive hybridization and/or historical introgression among albigena, different macrodon groups, peruviensis, sciureus and collinsi. (3) Different tests showed that our maximum likelihood tree was consistent with two species of Saimiri: S. oerstedii and S. sciureus. If no cases of hybridization were detected implicating S. vanzolinii, this could be a third recognized species. (4) We also estimated that the first temporal splits within this genus occurred around 1.4-1.6 million years ago, which indicates that the temporal split events within Saimiri were correlated with Pleistocene climatic changes. If the biological species concept is applied because, in this case, it is operative due to observed hybridization in the wild, the number of species within this genus is probably more limited than recently proposed by other authors. The Pleistocene was the fundamental epoch when the mitochondrial Saimiri diversification process occurred.
We sequenced the mitochondrial cytochrome b gene of 141 lowland tapirs (Tapirus terrestris) - representing the largest geographical distribution sample of this species studied across of South America to date. We compare our new data regard to two previous works on population structure and molecular systematics of T. terrestris. Our data agree with the Thoisy et al.'s work in (1) the Northern Western Amazon basin was the area with the highest gene diversity levels in T. terrestris, being probably the area of initial diversification; (2) there was no clear association between haplogroups and specific geographical areas; (3) there were clear population decreases during the last glacial maximum for the different haplogroups detected, followed by population expansions during the Holocene; and (4) our temporal splits among different T. terrestris haplogroups coincided with the first molecular clock approach carried out by these authors (fossil calibration). Nevertheless, our study disagreed regard to other aspects of the Thoisy et al.'s claims: (1) meanwhile, they detected four relevant clades in their data, we put forward six different relevant clades; (2) the Amazon River was not a strong barrier for haplotype dispersion in T. terrestris; and (3) we found reciprocal monophyly between T. terrestris and T. pinchaque. Additionally, we sequenced 42 individuals (T. terrestris, T. pinchaque, T. bairdii, and the alleged "new species", T. kabomani) for three concatenated mitochondrial genes (Cyt-b, COI, and COII) agreeing quite well with the view of Voss et al., and against of the claims of Cozzuol et al. Tapirus kabomani should be not considered as a full species with the results obtained throughout the mitochondrial sequences.
ABSTRACT. We sequenced the mitochondrial DNA (mtDNA) control region of 59 peccaries (44 white-lipped peccaries, Tayassu pecari, and 15 collared peccaries, Pecari tajacu). We also genotyped 3 DNA microsatellites from 78 white-lipped peccaries representing the 4 putative morphological subspecies (i.e., spiradens, aequatoris, pecari, and albirostris) present in northwestern South America (i.e., Colombia, Ecuador, Peru, and Bolivia). Our results showed:M. Ruiz-García et al. 5356©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (2): 5355-5378 (2015) 1) the estimated diversity of the mtDNA control region in the T. pecari population was extremely high, whereas the average genetic diversity for the microsatellites was medium to high and similar to that observed in European pig breeds; 2) there was no significant genetic heterogeneity among the quoted putative morphological subspecies at the mitochondrial marker, but we did detect significant (although relatively small) genetic heterogeneity using microsatellites, indicating that T. pecari albirostris is a uniquely differentiated group; and 3) the phylogenetic mtDNA trees showed that haplotypes were intermixed independent of their "a priori" subspecies classification. In addition, the microsatellite assignation analyses yielded low percentages of well-classified individuals when the analysis considered the geographic morphology of the subspecies. Thus, the molecular results do not support the putative morphological subspecies of T. pecari in northwestern South America. Finally, our results did not detect clear historical demographic changes using the mtDNA control region sequences. These genetic results are discussed in the context of the ecological and social characteristics of T. pecari.
The capybara (Hydrochoerus hydrochoeris) is the largest rodent on the world and it is strongly linked to the river systems of a large fraction of South America and part of Central America (Panama). Thus, it is an interesting species to test hypotheses about the origin of the high biodiversity within the Amazon Basin and in a sizeable fraction of the Neotropics. To test these hypotheses, we sequenced two mitochondrial genes (control region and Cytochrome b) of 78 wild capybaras sampled in Colombia, Peru, Ecuador and Brazil. At least, five different "populations" or ESUs were detected in well delimited geographical areas. However, our results do not support the more recent view that two different species of capybara are present (H. hydrochoeris and H. isthmus), unless chromosomal speciation (stasipatric or parapatric) can be demonstrated between these two groups. A Bayesian tree with the aforementioned two mitochondrial genes, and another Bayesian tree with a subset of 25 capybaras for 10 mitochondrial genes, showed that the initial diversification of the mitochondrial haplotype in capybaras was initiated in the Late Miocene. The trees also showed that the other haplotype diversification processes extended into the Pliocene and Pleistocene. We also detected population expansion events during different moments of the Pleistocene. Although some authors strongly suggest that the Miocene diversification explains the extreme biodiversity in the Amazon Basin and in surroundings areas (for instance, the Paleogeography hypothesis), others consider it the result of available forest refugia (Refuge hypothesis) during the Pleistocene. However, our results suggest that both hypotheses (and others, such as the Riverrefuge, the Recent Lagoon and the Hydrogeological Recent Change hypotheses) could have affected the evolution of the capybara to generate the current mitochondrial diversity. Thus, it is difficult to generalize a unique Amazon biota diversification hypothesis because each species or taxon could be affected by different processes and because the temporal antiquity of each taxon in South America is also different. Many mammalian taxa, and others, migrated into South America during the Great American Biotic Interchange (GABI) and their diversification processes in South America were mainly driven by Pleistocene events as those proposed by the Refuge hypothesis. Older taxa within this continent could have begun their current genetics diversification processes earlier, such as in the case of the capybara.
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