Spatial and temporal patterns of diversification on the Amazon: A test of the riverine hypothesis for all diurnal primates of Rio Negro and Rio Branco in Brazil.

The role of Amazonian rivers as drivers of speciation through vicariance remains controversial. Here we explore the riverine hypothesis by comparing spatial and temporal concordances in pattern of diversification for all diurnal primates of Rio Negro and its largest tributary, Rio Branco. We built a comprehensive comparative phylogenetic timetree to identify sister lineages of primates based on mitochondrial cytochrome b DNA sequences from 94 samples, including 19 of the 20 species of diurnal primates from our study region and 17 related taxa from elsewhere. Of the ten primate genera found in this region, three had populations on opposite banks of Rio Negro that formed reciprocally monophyletic clades, with roughly similar divergence times (Cebus: 1.85 Ma, HPD 95% 1.19-2.62; Callicebus: 0.83 Ma HPD 95% 0.36-1.32, Cacajao: 1.09 Ma, 95% HPD 0.58-1.77). This also coincided with time of divergence of several allopatric species of Amazonian birds separated by this river as reported by other authors. Our data offer support for the riverine hypothesis and for a Plio-Pleistocene time of origin for Amazonian drainage system. We showed that Rio Branco was an important geographical barrier, limiting the distribution of six primate genera: Cacajao, Callicebus, Cebus to the west and Pithecia, Saguinus, Sapajus to the east. The role of this river as a vicariant agent however, was less clear. For example, Chiropotes sagulata on the left bank of the Rio Branco formed a clade with C. chiropotes from the Amazonas Department of Venezuela, north of Rio Branco headwaters, with C. israelita on the right bank of the Rio Branco as the sister taxon to C. chiropotes+C. sagulata. Although we showed that the formation of the Rio Negro was important in driving diversification in some of our studied taxa, future studies including more extensive sampling of markers across the genome would help determine what processes contributed to the evolutionary history of the remaining primate genera.

Diversification of Amazonian spiny tree rats in genus Makalata (Rodentia, Echimyidae): Cryptic diversity, geographic structure and drivers of speciation.

Amazonian mammal diversity is exceptionally high, yet new taxonomic discoveries continue to be made and many questions remain for understanding its diversification through time and space. Here we investigate the diversification of spiny rats in the genus Makalata, whose species are strongly associated with seasonally flooded forests, watercourses and flooded islands. We use a biogeographical approach based on a mitochondrial cytochrome b gene through divergence time estimation and reconstruction of ancestral areas and events. Our findings indicate an ancient origin of Makalata for the Guiana Shield and Eastern Amazonia as ancestral area. A first cladogenetic event led to a phylogeographic break into two broader clades of Makalata through dispersal, implying a pattern of western/Eastern Amazonian clades coinciding with the Purus Arch (middle Miocene). Most of subclades we infer originated between the late Pliocene to the early Pleistocene, with few recent exceptions in the early Pliocene through dispersal and vicariant events. The hypothesis of rivers as dispersal barriers is not corroborated for Makalata, as expected for mammalian species associated with seasonally flooded environments. We identify two key events for the expansion and diversification of Makalata species: the presence of geologically stable areas in the Guiana and Brazilian shields and the transition from lacustrine conditions in western Amazonia (Acre system) to a river system, with the establishment of the Amazon River transcontinental system and its tributaries. Our results are congruent with older geological scenarios for the Amazon basin formation (Miocene), but we do not discard the influence of recent dynamics on some speciation events and, mainly, on phylogeographic structuring processes.

The role of Pleistocene climate change in the genetic variability, distribution and demography of Proechimys cuvieri and P. guyannensis (Rodentia: Echimyidae) in northeastern Amazonia.

The spiny rats, genus Proechimys, have the highest species richness within the Echimyidae family, as well as species with high genetic variability. The genus distribution includes tropical South America and Central America south to Honduras. In this study, we evaluate the phylogeographic histories of Proechimys guyannensis and P. cuvieri using cytochrome b, in a densely sampled area in northeastern Amazon where both species are found in sympatry in different environments. For each species, Bayesian and Maximum Likelihood phylogenetic analysis were congruent and recovered similar clades in the studied area. Bayesian phylogenetic analysis using a relaxed molecular clock showed that these clusters of haplotypes diversified during Pleistocene for both species. Apparently, the large rivers of the region did not act as barriers, as some clades include specimens collected from opposite banks of Oiapoque, Araguari and Jari rivers. Bayesian skyline plot analysis showed recent demographic expansion in both species. The Pleistocene climatic changes in concert with the geologic changes in the Amazon fan probably acted as drivers in the diversification that we detected in these two spiny rats. Proechimys cuvieri and P. guyannensis show genetic structure in the eastern part of the Guiana region. Greater genetic distances observed in P. guyannensis, associated with highly structured groups, suggest that more detailed studies of systematics and ecology should be directed to this species.

Karyological analysis of Proechimys cuvieri and Proechimys guyannensis (Rodentia, Echimyidae) from central Amazon.

The aim was to characterize the karyotype of rodents of the genus Proechimys from three localities in the central Brazilian Amazon, in the search for new markers that might shed light on our understanding of the taxonomy and evolutionary history of this taxon. Two karyotypes were found, viz., 2n = 28, FN = 46 in individuals from the NRSP (Cuieiras River) and REMAN (Manaus), and 2n = 46, FN = 50 in individuals from the Balbina Hydroelectric Plant. While individuals with the karyotype with 2n = 28 chromosomes were morphologically associated with Proechimys cuvieri, their karyotype shared similarities with those of the same diploid number in two other regions. Although three karyotypes are described for Proechimys cuvieri, no geographic distribution pattern that defined a cline could be identified. Based on the morphological examination of voucher specimens and additional results from molecular analysis, the karyotype with 2n = 46 and FN = 50 could be associated with P. guyannensis.

GENE GENEALOGY AND DIFFERENTIATION AMONG ARBOREAL SPINY RATS (RODENTIA: ECHIMYIDAE) OF THE AMAZON BASIN: A TEST OF THE RIVERINE BARRIER HYPOTHESIS.

Sequence variation in the mitochondrial cytochrome b gene was examined in the arboreal spiny rat, Mesomys hispidus, collected at 15 sites along the Rio Juruá in western Amazonia, Brazil, to determine the importance of riverine barriers in the diversification of this taxon. Twenty individual haplotypes were uncovered, most of which were unique to single localities but some of which were shared among adjacent sites either along or across the river. Genealogical analyses suggest that gene flow is limited and, in combination with the unique distribution of most haplotypes, suggest that populations of this species are strongly substructured along the river. Thus, most sharing of haplotypes between adjacent localities is probably caused by historical association rather than to ongoing gene flow. Two haplotype clades were uncovered, but these correspond to headwaters versus mouth areas, not to opposite sides of the river, as would be expected by the Riverine Barrier Hypothesis. Moreover, haplotype sharing across the river was greater at its mouth than in the headwaters, a pattern opposite that expected if the river were a substantive barrier. Broader scale phylogeographic patterns of this species show that both clades have relationships to areas well outside the Rio Juruá basin. This suggests that the basin represents a relatively recent point of invasion between two more broadly distributed and differentiated geographic units of the species.