A reference genome for the Harpy Eagle reveals steady demographic decline and chromosomal rearrangements in the origin of Accipitriformes.

The Harpy Eagle (Harpia harpyja) is an iconic species that inhabits forested landscapes in Neotropical regions, with decreasing population trends mainly due to habitat loss, and currently classified as vulnerable. Here, we report on a chromosome-scale genome assembly for a female individual combining long reads, optical mapping, and chromatin conformation capture reads. The final assembly spans 1.35 Gb, with N50scaffold equal to 58.1 Mb and BUSCO completeness of 99.7%. We built the first extensive transposable element (TE) library for the Accipitridae to date and identified 7,228 intact TEs. We found a burst of an unknown TE ~ 13-22 million years ago (MYA), coincident with the split of the Harpy Eagle from other Harpiinae eagles. We also report a burst of solo-LTRs and CR1 retrotransposons ~ 31-33 MYA, overlapping with the split of the ancestor to all Harpiinae from other Accipitridae subfamilies. Comparative genomics with other Accipitridae, the closely related Cathartidae and Galloanserae revealed major chromosome-level rearrangements at the basal Accipitriformes genome, in contrast to a conserved ancient genome architecture for the latter two groups. A historical demography reconstruction showed a rapid decline in effective population size over the last 20,000 years. This reference genome serves as a crucial resource for future conservation efforts towards the Harpy Eagle.

Preliminary profile of the gut microbiota from amerindians in the Brazilian amazon experiencing a process of transition to urbanization.

The Yanomami are one of the oldest indigenous tribes in the Amazon and are direct descendants of the first people to colonize South America 12,000 years ago. They are located on the border between Venezuela and Brazil, with the Venezuelan side remaining uncontacted. While they maintain a hunter-gatherer society, they are currently experiencing contact with urbanized populations in Brazil. The human gut microbiota of traditional communities has become the subject of recent studies due to the Westernization of their diet and the introduction of antibiotics and other chemicals, which have affected microbial diversity in indigenous populations, thereby threatening their existence. In this study, we preliminarily characterized the diversity of the gut microbiota of the Yanomami, a hunter-gatherer society from the Amazon, experiencing contact with urbanized populations. Similarly, we compared their diversity with the population in Manaus, Amazonas. A metabarcoding approach of the 16 S rRNA gene was carried out on fecal samples. Differences were found between the two populations, particularly regarding the abundance of genera (e.g., Prevotella and Bacteroides) and the higher values of the phyla Bacteroidetes over Firmicutes, which were significant only in the Yanomami. Some bacteria were found exclusively in the Yanomami (Treponema and Succinivibrio). However, diversity was statistically equal between them. In conclusion, the composition of the Yanomami gut microbiota still maintains the profile characteristic of a community with a traditional lifestyle. However, our results suggest an underlying Westernization process of the Yanomami microbiota when compared with that of Manaus, which must be carefully monitored by authorities, as the loss of diversity can be a sign of growing danger to the health of the Yanomami.

Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates.

Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high-quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic phylogeny based on these samples along with additional published platyrrhine mitogenomes, and use this to assess support for the long-standing riverine barrier hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Along the Amazon, Negro, and Madeira rivers, we found mixed support for the RBH. While we identified divergences that coincide with a river barrier, only some occur synchronously and also overlap with the proposed dates of river formation. The most compelling evidence is for the Amazon river potentially driving speciation within bearded saki monkeys (Chiropotes spp.) and within the smallest extant platyrrhines, the marmosets and tamarins. However, we also found that even large rivers do not appear to be barriers for some primates, including howler monkeys (Alouatta spp.), uakaris (Cacajao spp.), sakis (Pithecia spp.), and robust capuchins (Sapajus spp.). Our results support a more nuanced, clade-specific effect of riverine barriers and suggest that other evolutionary mechanisms, besides the RBH and allopatric speciation, may have played an important role in the diversification of platyrrhines.

Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea (Spix, 1823) resolves a taxonomic conundrum.

The pygmy marmoset, the smallest of the anthropoid primates, has a broad distribution in Western Amazonia. Recent studies using molecular and morphological data have identified two distinct species separated by the Napo and Solimões-Amazonas rivers. However, reconciling this new biological evidence with current taxonomy, i.e., two subspecies, Cebuella pygmaea pygmaea (Spix, 1823) and Cebuella pygmaea niveiventris (Lönnberg, 1940), was problematic given the uncertainty as to whether Spix's pygmy marmoset ( Cebuella pygmaea pygmaea) was collected north or south of the Napo and Solimões-Amazonas rivers, making it unclear to which of the two newly revealed species the name pygmaea would apply. Here, we present the first molecular data from Spix's type specimen of Cebuella pygmaea, as well as novel mitochondrial genomes from modern pygmy marmosets sampled near the type locality (Tabatinga) on both sides of the river. With these data, we can confirm the correct names of the two species identified, i.e., C. pygmaea for animals north of the Napo and Solimões-Amazonas rivers and C. niveiventris for animals south of these two rivers. Phylogenetic analyses of the novel genetic data placed into the context of cytochrome b gene sequences from across the range of pygmy marmosets further led us to re-evaluate the geographical distribution for the two Cebuella species. We dated the split of these two species to 2.54 million years ago. We discuss additional, more recent, subdivisions within each lineage, as well as potential contact zones between the two species in the headwaters of these rivers.

An integrative analysis uncovers a new, pseudo-cryptic species of Amazonian marmoset (Primates: Callitrichidae: Mico) from the arc of deforestation.

Amazonia has the richest primate fauna in the world. Nonetheless, the diversity and distribution of Amazonian primates remain little known and the scarcity of baseline data challenges their conservation. These challenges are especially acute in the Amazonian arc of deforestation, the 2500 km long southern edge of the Amazonian biome that is rapidly being deforested and converted to agricultural and pastoral landscapes. Amazonian marmosets of the genus Mico are little known endemics of this region and therefore a priority for research and conservation efforts. However, even nascent conservation efforts are hampered by taxonomic uncertainties in this group, such as the existence of a potentially new species from the Juruena-Teles Pires interfluve hidden within the M. emiliae epithet. Here we test if these marmosets belong to a distinct species using new morphological, phylogenomic, and geographic distribution data analysed within an integrative taxonomic framework. We discovered a new, pseudo-cryptic Mico species hidden within the epithet M. emiliae, here described and named after Horacio Schneider, the pioneer of molecular phylogenetics of Neotropical primates. We also clarify the distribution, evolutionary and morphological relationships of four other Mico species, bridging Linnean, Wallacean, and Darwinian shortfalls in the conservation of primates in the Amazonian arc of deforestation.

Phylogenetic relationships of the poorly known treefrog Boana hobbsi (Cochran amp; Goin, 1970) (Anura: Hylidae), systematic implications and remarks on morphological variations and geographic distribution.

Boana hobbsi is a poorly known hylid frog currently placed within the Boana punctata group. Yet, morphological, ecological and bioacoustic traits do not support this placement, with no molecular data being available to date to test this hypothesis. Based on newly collected mitochondrial DNA sequences, morphological data review and field observations, we provide new insight into the phylogenetic relationships, morphological variations and geographic distribution of B. hobbsi. Our findings reveal that B. hobbsi is nested (with strong support) within the Boana benitezi group, recovering once more a polyphyletic Boana punctata group. Supported by this new genetic, morphological and ecological evidence, we propose a new taxonomic arrangement which includes B. hobbsi as a member of the Boana benitezi group. Furthermore, we emphasize the importance of conducting biological inventories in remote Amazonian areas, where many taxonomic and geographic knowledge gaps persist with regards to Amphibian diversity.

A new species of Piaractus (Characiformes: Serrasalmidae) from the Orinoco Basin with a redescription of Piaractus brachypomus.

Piaractus orinoquensis, a new species of serrasalmid fish, is described from the Orinoco River basin. The new species differs from congeners by having a slenderer body, relatively smaller head and snout, more compressed mid-body, fewer scales above and below the lateral line and diagnostic molecular characters in the coI mitochondrial gene region. We also provide a re-description of Piaractus brachypomus, restricting its geographic distribution to the Amazon River basin. Both species are economically important in their respective basins and need to be independently managed as distinct species.

On a new species of titi monkey (Primates: Plecturocebus Byrne et al., 2016), from Alta Floresta, southern Amazon, Brazil.

The taxonomy of the titi monkeys (Callicebinae) has recently received considerable attention. It is now recognised that this subfamily is composed of three genera with 33 species, seven of them described since 2002. Here, we describe a new species of titi, Plecturocebus, from the municipality of Alta Floresta, Mato Grosso, Brazil. We adopt an integrative taxonomic approach that includes phylogenomic analyses, pelage characters, and locality records. A reduced representation genome-wide approach was employed to assess phylogenetic relationships among species of the eastern Amazonian clade of the Plecturocebus moloch group. Using existing records, we calculated the Extent of Occurrence (EOO) of the new species and estimated future habitat loss for the region based on predictive models. We then evaluated the species' conservation status using the IUCN Red list categories and criteria. The new species presents a unique combination of morphological characters: (1) grey agouti colouration on the crown and dorsal parts; (2) entirely bright red-brown venter; (3) an almost entirely black tail with a pale tip; and (4) light yellow colouration of the hair on the cheeks contrasting with bright red-brown hair on the sides of the face. Our phylogenetic reconstructions based on maximum-likelihood and Bayesian methods revealed well-supported species relationships, with the Alta Floresta taxon as sister to P. moloch + P. vieirai. The species EOO is 10,166,653 ha and we predict a total habitat loss of 86% of its original forest habitat under a "business as usual" scenario in the next 24 years, making the newly discovered titi monkey a Critically Endangered species under the IUCN A3c criterion. We give the new titi monkey a specific epithet based on: (1) clear monophyly of this lineage revealed by robust genomic and mitochondrial data; (2) distinct and diagnosable pelage morphology; and (3) a well-defined geographical distribution with clear separation from other closely related taxa. Urgent conservation measures are needed to safeguard the future of this newly discovered and already critically endangered primate.

A Multilocus Approach to Understanding Historical and Contemporary Demography of the Keystone Floodplain Species Colossoma macropomum (Teleostei: Characiformes).

We studied the natural populations of a flagship fish species of the Amazon, Colossoma macropomum which in recent years has been suffering from severe exploitation. Our aim was to investigate the existence or not of genetic differentiation across the wide area of its distribution and to investigate changes in its effective population size throughout its evolutionary history. We sampled individuals from 21 locations distributed throughout the Amazon basin. We analyzed 539 individuals for mitochondrial genes (control region and ATPase gene 6/8), generating 1,561 base pairs, and genotyped 604 individuals for 13 microsatellite loci obtaining, on average, 21.4 alleles per locus. Mean HE was 0.78 suggesting moderate levels of genetic variability. AMOVA and other tests used to detect the population structure based on both markers indicate that C. macropomum comprises a single and large panmitic population in the main channel of the Solimões-Amazonas River basin, on the other hand localities in the headwaters of the tributaries Juruá, Purus, Madeira, Tapajós, and localities of black water, showed genetic structure. The greatest genetic differentiation was observed between the Brazilian Amazon basin and the Bolivian sub-basin with restricted genetic flow between the two basins. Demographic analyzes of mitochondrial genes indicated population expansion in the Brazilian and Bolivian Amazon basins during the Pleistocene, and microsatellite data indicated a population reduction during the Holocene. This shows that the historical demography of C. macropomum is highly dynamic. Conservation and management strategies should be designed to respect the existing population structure and minimize the effects of overfishing by limiting fisheries C. macropomum populations.

Remarkable Geographic Structuring of Rheophilic Fishes of the Lower Araguaia River.

Rapids and waterfalls, and their associated fauna and flora are in peril. With the construction of each new hydroelectric dam, more rapids and waterfalls are destroyed, leading to the disappearance of associated fauna and flora. Areas of rapids harbor distinct, highly endemic rheophilic fauna and flora adapted to an extreme environment. Rheophilic habitats also have disjunct distribution both within and across rivers. Rheophilic habitats thus represent islands of suitable habitat separated by stretches of unsuitable habitat. In this study, we investigated to what extent, if any, species of cichlid and anostomid fishes associated with rheophilic habitats were structured among the rapids of Araguaia River in the Brazilian Amazon. We tested both for population structuring as well as non-random distribution of lineages among rapids. Eight of the nine species had multiple lineages, five of these nine species were structured, and three of the eight species with multiple lineages showed non-random distribution of lineages among rapids. These results demonstrate that in addition to high levels of endemicism of rheophilic fishes, different rapids even within the same river are occupied by different lineages. Rheophilic species and communities occupying different rapids are, therefore, not interchangeable, and this realization must be taken into account when proposing mitigatory/compensatory measures in hydroelectric projects, and in conservation planning.

One thousand DNA barcodes of piranhas and pacus reveal geographic structure and unrecognised diversity in the Amazon.

Piranhas and pacus (Characiformes: Serrasalmidae) are a charismatic but understudied family of Neotropical fishes. Here, we analyse a DNA barcode dataset comprising 1,122 specimens, 69 species, 16 genera, 208 localities, and 34 major river drainages in order to make an inventory of diversity and to highlight taxa and biogeographic areas worthy of further sampling effort and conservation protection. Using four methods of species discovery-incorporating both tree and distance based techniques-we report between 76 and 99 species-like clusters, i.e. between 20% and 33% of a priori identified taxonomic species were represented by more than one mtDNA lineage. There was a high degree of congruence between clusters, with 60% supported by three or four methods. Pacus of the genus Myloplus exhibited the most intraspecific variation, with six of the 13 species sampled found to have multiple lineages. Conversely, piranhas of the Serrasalmus rhombeus group proved difficult to delimit with these methods due to genetic similarity and polyphyly. Overall, our results recognise substantially underestimated diversity in the serrasalmids, and emphasise the Guiana and Brazilian Shield rivers as biogeographically important areas with multiple cases of across-shield and within-shield diversifications. We additionally highlight the distinctiveness and complex phylogeographic history of rheophilic taxa in particular, and suggest multiple colonisations of these habitats by different serrasalmid lineages.

Coarse- and fine-scale patterns of distribution and habitat selection places an Amazonian floodplain curassow in double jeopardy.

Patterns of habitat selection are influenced by local productivity, resource availability, and predation risk. Species have taken millions of years to hone the macro- and micro-habitats they occupy, but these may now overlap with contemporary human threats within natural species ranges. Wattled Curassow (Crax globulosa), an endemic galliform species of the western Amazon, is threatened by both hunting and habitat loss, and is restricted to white-water floodplain forests of major Amazonian rivers. In this study conducted along the Juruá River, Amazonas, Brazil, we quantified the ranging ecology and fine-scale patterns of habitat selection of the species. We estimated the home range size of C. globulosa using conventional VHF telemetry. To estimate patterns of habitat selection, we used geo-locations of day ranges to examine the extent and intensity of use across the floodplain, which were then compared to a high-resolution flood map of the study area. We captured two females and one male, which we monitored for 13 months between September 2014 and September 2015. Average home range size was 283 ha, based on the 95% aLoCoH estimator. Wattled Curassows selected areas of prolonged flood pulses (six to eight months/year) and had a consistent tendency to be near open water, usually in close proximity to river banks and lakes, especially during the dry season. Amazonian floodplains are densely settled, and the small portions of floodplain habitat used by Wattled Curassows are both the most accessible to hunters and most vulnerable to deforestation. As a result, the geographic and ecological distribution of Wattled Curassows places them at much higher extinction risk at multiple spatial scales, highlighting the need to consider habitat preferences within their conservation strategy.

Testing Wallace's intuition: water type, reproductive isolation and divergence in an Amazonian fish.

Alfred Russel Wallace proposed classifying Amazon rivers based on their colour and clarity: white, black and clear water. Wallace also proposed that black waters could mediate diversification and yield distinct fish species. Here, we bring evidence of speciation mediated by water type in the sailfin tetra (Crenuchus spilurus), a fish whose range encompasses rivers of very distinct hydrochemical conditions. Distribution of the two main lineages concords with Wallace's water types: one restricted to the acidic and nutrient-poor waters of the Negro River (herein Rio Negro lineage) and a second widespread throughout the remaining of the species' distribution (herein Amazonas lineage). These lineages occur over a very broad geographical range, suggesting that despite occurring in regions separated by thousands of kilometres, individuals of the distinct lineages fail to occupy each other's habitats, hundreds of metres apart and not separated by physical barrier. Reproductive isolation was assessed in isolated pairs exposed to black-water conditions. All pairs with at least one individual of the lineage not native to black waters showed significantly lower spawning success, suggesting that the water type affected the fitness and contributed to reproductive isolation. Our results endorse Wallace's intuition and highlight the importance of ecological factors in shaping diversity of the Amazon fish fauna.

How many pygmy marmoset (Cebuella Gray, 1870) species are there? A taxonomic re-appraisal based on new molecular evidence.

The pygmy marmoset, Cebuella pygmaea, the smallest of the New World monkeys, has one of the largest geographical distributions of the Amazonian primates. Two forms have been recognized: Cebuella pygmaea pygmaea (Spix, 1823), and C. p. niveiventris Lönnberg, 1940. In this study, we investigated if the separation of pygmy marmosets into these two clades can be corroborated by molecular data. We also examine and compare coloration of the pelage in light of the new molecular results. We analyzed the mtDNA cytochrome b gene and, for the first time for any Neotropical primate, we used a reduced representation genome sequencing approach (ddRADseq) to obtain data for recently collected, geographically representative samples from the Rio Japurá, a northern tributary of the Rio Solimões and from the Javarí, Jutaí, Juruá, Madeira and Purus river basins, all tributaries south of the Solimões. We estimated phylogenies and diversification times under both maximum likelihood and Bayesian inference criteria. Our analysis showed two highly supported clades, with intraclade divergences much smaller than interclade divergences, indicating two species of Cebuella: one from the Rio Japurá and one to the south of Solimões. The interpretation of our results in light of the current taxonomy is not trivial however. Lönnberg stated that the type of Spix's pygmy marmoset (type locality 'near Tabatinga') was obtained from the south of the Solimões, and his description of the distinct niveiventris from Lago Ipixuna, south of the Solimões and several hundred kilometres east of Tabatinga, was based on a comparison with specimens that he determined as typical pygmaea that were from the upper Rio Juruá (south of the Solimões). As such it remains uncertain whether the name pygmaea should be applicable to the pygmy marmosets north of the Rio Solimões (Tabatinga type locality) or south (near Tabatinga but across the Solimões). Finally, our analysis of pelage coloration revealed three phenotypic forms: (1) south of the Rio Solimoes, (2) Eirunepé-Acre, upper Juruá basin; and (3) Japurá. More samples from both sides of Solimões in the region of Tabatinga will be necessary to ascertain the exact type locality for Spix's pygmaea and to resolve the current uncertainties surrounding pygmy marmoset taxonomy.

A new species of Tometes Valenciennes 1850 (Characiformes: Serrasalmidae) from Tocantins-Araguaia River Basin based on integrative analysis of molecular and morphological data.

A new large serrasalmid species of Tometes is described from the Tocantins-Araguaia River Basin. Tometes siderocarajensis sp. nov. is currently found in the rapids of the Itacaiúnas River Basin, and formerly inhabited the lower Tocantins River. The new species can be distinguished from all congeners, except from T. ancylorhynchus, by the presence of lateral space between 1st and 2nd premaxillary teeth, and by the absence of lateral cusps in these two teeth. However, T. siderocarajensis sp. nov. can be differentiated from syntopic congener T. ancylorhynchus by an entirely black with mottled red body in live specimens, densely pigmented pelvic fins with a high concentration of dark chromatophores, and the presence of 39 to 41 rows of circumpeduncular scales (vs. silvery body coloration with slightly reddish overtones on middle flank during breeding period in live specimens, hyaline to slightly pale coloration on distalmost region of pelvic fins, and 30 to 36 rows of circumpeduncular scales). Additionally, molecular sequence shows that T. siderocarajensis sp. nov. is reciprocally monophyletic, and diagnosable from all congeners by having two autapomorphic molecular characters in the mitochondrial gene COI. The phylogenetic reconstruction still show that T. siderocarajensis sp. nov. is closely related to T. trilobatus. This is the first molecular study using an integrative taxonomic approach based on morphological and molecular sequence data for all described species of Tometes. These findings increase the number of formally described species of Tometes to seven. A key to the Tometes species is provided.

Host associations and turnover of haemosporidian parasites in manakins (Aves: Pipridae).

Parasites of the genera Plasmodium and Haemoproteus (Apicomplexa: Haemosporida) are a diverse group of pathogens that infect birds nearly worldwide. Despite their ubiquity, the ecological and evolutionary factors that shape the diversity and distribution of these protozoan parasites among avian communities and geographic regions are poorly understood. Based on a survey throughout the Neotropics of the haemosporidian parasites infecting manakins (Pipridae), a family of Passerine birds endemic to this region, we asked whether host relatedness, ecological similarity and geographic proximity structure parasite turnover between manakin species and local manakin assemblages. We used molecular methods to screen 1343 individuals of 30 manakin species for the presence of parasites. We found no significant correlations between manakin parasite lineage turnover and both manakin species turnover and geographic distance. Climate differences, species turnover in the larger bird community and parasite lineage turnover in non-manakin hosts did not correlate with manakin parasite lineage turnover. We also found no evidence that manakin parasite lineage turnover among host species correlates with range overlap and genetic divergence among hosts. Our analyses indicate that host switching (turnover among host species) and dispersal (turnover among locations) of haemosporidian parasites in manakins are not constrained at this scale.

Delimiting Evolutionarily Significant Units of the Fish, Piaractus brachypomus (Characiformes: Serrasalmidae), from the Orinoco and Amazon River Basins with Insight on Routes of Historical Connectivity.

The freshwater fish Piaractus brachypomus is an economically important for human consumption both in commercial fisheries and aquaculture in all South American countries where it occurs. In recent years the species has decreased in abundance due to heavy fishing pressure. The species occurs in the Amazon and Orinoco basins, but lack of meristic differences between fishes from the 2 basins, and extensive migration associated with reproduction, have resulted in P. brachypomus being considered a single panmictic species. Analysis of 7 nuclear microsatellites, mitochondrial DNA sequences (D-loop and COI), and body shape variables demonstrated that each river basin is populated by a distinct evolutionarily significant unit (ESU); the 2 groups had an average COI divergence of 3.5% and differed in body depth and relative head length. Historical connection between the 2 basins most probably occurred via the Rupununi portal rather than via the Casiquiare canal. The 2 ESUs will require independent fishery management, and translocation of fisheries stocks between basins should be avoided to prevent loss of local adaptations or extinction associated with outbreeding depression. Introductions of fishes from the Orinoco basin into the Putumayo River basin, an Amazon basin drainage, and evidence of hybridization between the 2 ESUs have already been detected.

Effects of Forest Fragmentation on Genetic Diversity of the Critically Endangered Primate, the Pied Tamarin (Saguinus bicolor): Implications for Conservation.

We analyzed DNA at 9 microsatellite loci from hair samples of 73 pied tamarins (Saguinus bicolor) located in 3 urban forest fragments and a biological reserve in the city of Manaus, Amazonas, Brazil. The forest fragments had become isolated from the continuous forest 6-15 years prior to the time of sampling. Tests for reduction in population size showed that all groups from the urban forest fragments had undergone genetic bottlenecks. Pied tamarins in this region historically formed one biological population, and the fragments were connected by high levels of gene flow. These results indicate the need to implement a conservation plan that allows for connectivity between the urban fragments, as well as protection from further constriction. Such connectivity could be achieved via the creation and protection of corridors. In addition to the current population trends explained by anthropogenic actions, the species also shows a trend of long-term demographic decline that has resulted in approximately an order of magnitude decrease and began 13 thousand years ago.

Biogeography of squirrel monkeys (genus Saimiri): South-central Amazon origin and rapid pan-Amazonian diversification of a lowland primate.

The squirrel monkey, Saimiri, is a pan-Amazonian Pleistocene radiation. We use statistical phylogeographic methods to create a mitochondrial DNA-based timetree for 118 squirrel monkey samples across 68 localities spanning all Amazonian centers of endemism, with the aim of better understanding (1) the effects of rivers as barriers to dispersal and distribution; (2) the area of origin for modern Saimiri; (3) whether ancestral Saimiri was a lowland lake-affiliated or an upland forest taxa; and (4) the effects of Pleistocene climate fluctuation on speciation. We also use our topology to help resolve current controversies in Saimiri taxonomy and species relationships. The Rondônia and Inambari centers in the southern Amazon were recovered as the most likely areas of origin for Saimiri. The Amazon River proved a strong barrier to dispersal, and squirrel monkey expansion and diversification was rapid, with all speciation events estimated to occur between 1.4 and 0.6Ma, predating the last three glacial maxima and eliminating climate extremes as the main driver of squirrel monkey speciation. Saimiri expansion was concentrated first in central and western Amazonia, which according to the "Young Amazon" hypothesis was just becoming available as floodplain habitat with the draining of the Amazon Lake. Squirrel monkeys also expanded and diversified east, both north and south of the Amazon, coincident with the formation of new rivers. This evolutionary history is most consistent with a Young Amazon Flooded Forest Taxa model, suggesting Saimiri has always maintained a lowland wetlands niche and was able to greatly expand its range with the transition from a lacustrine to a riverine system in Amazonia. Saimiri vanzolinii was recovered as the sister group to one clade of Saimiri ustus, discordant with the traditional Gothic vs. Roman morphological division of squirrel monkeys. We also found paraphyly within each of the currently recognized species: S. sciureus, S. ustus, and S. macrodon. We discuss evidence for taxonomic revision within the genus Saimiri, and the need for future work using nuclear markers.

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.