Morphology and molecular phylogeny of Pauciconfibuloides amazonica gen. n. sp. n. (Platyhelminthes,Monogenoidea) parasitizing the Amazonian croaker Plagioscion squamosissimus

An integrative study was performed to understand the phylogenetic relationships of an undescribed, freshwater species of microcotylid parasitizing Plagioscion squamosissimus from the Amazon River Basin. Based on morphological and molecular analysis (18S rDNA and partial 28S rDNA genes), a new genus is proposed to accommodate this new species, Pauciconfibuloides amazonica gen. n. sp. n. The new genus is closely related to Protastomicrocotylinae and Pauciconfibula by sharing the vagina, male copulatory organ, and genital atrium all unarmed. However, Pauciconfibuloides gen. n. can be distinguished from those taxa by the prostatic system and position of the vaginal pore. Molecular phylogenetic inference suggests a sister relationship with species of Polylabris (Prostatomicrocotylinae), but to date, there are no available 18S or 28S rDNA sequences of Pauciconfibula to be compared. This is the first report of a microcotylid parasitizing a freshwater sciaenid from South America.     

Vergleichende Wachstumsuntersuchungen an zwei Sciaenidenarten (Plagioscion squamosissimus Heckel und Plagioscion monti Soares) in verschiedenen Gewässertypen Zentralamazoniens

A comparative growth analysis of two sciaenid species (Plagioscion squamosissimus Heckel and Plagioscion monti Soares) in different water types of the Central Amazon The growth of two sciaenid species P. squamosissimus and P. monti was comparatively described in black and white water of the Amazon by determining the age by means of daily rings on otoliths. Growth was described according to v. Bertalanffy's and Pauly's equations. A comparison between black and white water proved the expected faster growth of white water fishes.     

Tracking the history of an invasion: the freshwater croakers (Teleostei: Sciaenidae) in South America

In this study, the competing hypotheses of single vs. double colonisation events for freshwater Pachyurinae (Sciaenidae) in South America is tested and the historical biogeography of the expansion of this clade within the continent is reconstructed based on phylogenetic analysis. Parsimony and Bayesian inference (BI) for 19 marine and freshwater species assigned to Sciaenidae, Haemulidae and Polypteridae were determined based on partial sequences of the mitochondrial 16S and cytochrome b genes and fragments of the nuclear Tmo‐4C4 and rhodopsin genes. A parsimonious ancestral character reconstruction of euryhalinity was performed on a clade of families of closely related fishes to evaluate the role of ecological fitting in the colonisation of freshwater by a marine sciaenid. The parsimony and BI phylogenetic hypotheses for the concatenated sequences supported the monophyly of the freshwater Sciaenidae. Divergence of the two freshwater clades of Sciaenidae, Pachyurinae and Plagioscion, occurred within the Amazon Basin. Within Pachyurinae, two clades were recovered: one composed of species from the Amazon and the Paraná Basin and a second with representatives from the São Francisco and south‐eastern Atlantic basins. The results were compatible with the hypothesis of a single colonisation event of South American freshwater habitats by a marine lineage. The hypothesis of gradual adaptation to freshwater was rejected in favour of the hypothesis of ecological fitting. Sciaenidae, or a subordinate lineage within the family, is ancestrally capable of withstanding exposure to low‐salinity habitats, which putatively facilitated the colonisation of freshwater habitats. The subsequent diversification and expansion of Pachyurinae across South America followed this colonisation and replicated the general pattern of the area relationships of South American river basins for several other fish groups.     

Genetic relationships of Plagioscion squamosissimus (Perciformes,Sciaenidae) from five Neotropical river basins evaluated using mitochondrial atpase6/8 gene sequences

The genetic relationships of native or introduced Plagioscion squamosissimus in five Brazilian Neotropical basins were evaluated using the mitochondrial atpase6/8 genes. Results revealed that the population of the Tocantins River basin is more basal than the native populations of the Amazon and Parnaíba River basins. Moreover, the populations of P. squamosissimus that were introduced in the São Francisco and upper Paraná River basins originated from the population of the Parnaíba River.     

Molecular phylogenetics of Atlantic Shield Platynectes diving beetles (Coleoptera: Dytiscidae): a first glance at the evolution of the genus in the Amazon Basin

Neotropical diving beetles of the genus Platynectes are distributed across Central America, the Andes and different Precambrian shields in the Amazon Basin. Species from the northern Guiana Shield form a monophyletic clade, yet the phylogenetic relationships of the eastern Atlantic Shield species remain unknown. Here, we augmented an existing molecular dataset with a species from the Atlantic Shield that was not previously sampled. We reconstructed the phylogenetic relationships and estimated divergence times to understand the evolution of lineages dwelling in this region. The newly sampled specimens from the Atlantic Shield are recovered as sister taxa to Guiana Shield species. The dating analyses suggest a split between these two lineages in the late Oligocene to mid-Miocene, contemporary with the Miocenic geological remodeling of the Amazon Basin. Additional sampling in the Atlantic and Central Brazilian Shields will be determinant to test the monophyly of Platynectes species distributed in these ancient shields, and to fully understand the biogeographical history of diving beetles in the Amazon Basin.     

Length‐weight relationship of 11 fish species from a tributary of the Amazon River system in northern Brazil

The length–weight relationships (LWRs) of 11 freshwater fish for eight families (Leporinus friderici, Pterophyllum scalare, Geophagus camopiensis, Curimata incompta, Astyanax bimaculatus, Tetragonopterus chalceus, Moenkhausia lepidura, Metynnis lippincottianus, Plagioscion squamosissimus, Hemiodus unimaculatus and Colomesus asellus) captured in tributary of the Amazon River system (Brazil) were investigated. These results represent the first reference on the LWRs for all 11 species in the eastern Amazon.     

Phylogeny and biogeography of the Rhinella marina species complex (Amphibia,Bufonidae) revisited: implications for Neotropical diversification hypotheses

Vallinoto, M., Sequeira, F., Sodré, D., Bernardi, J. A. R., Sampaio, I. & Schneider, H. (2009). Phylogeny and biogeography of the Rhinella marina species complex (Amphibia, Bufonidae) revisited: implications for Neotropical diversification hypotheses. —Zoologica Scripta, 39, 128–140. A number of distinct hypotheses have been proposed to account for the origin of the considerable biological diversity found in the Neotropics, which is still a matter of intense debate. Here, we conducted a phylogenetic analysis of the Rhinella marina complex, a group of species widely distributed in Central and South America, combining published data with new sequences of three mtDNA genes (12S, 16S and cyt b) in order to clarify the evolutionary relationships and biogeographical history of the group. We included eight of the ten currently recognized R. marina group species and several outgroups. Maximum parsimony, maximum likelihood, and Bayesian inference analyses produced similar topologies, with two well‐supported main clades, each characterized by a deep subdivision. One of these major clades includes the samples of R. marina from Central America and Ecuador (west of the Andes), whereas the other comprises the remaining species of the group and samples of R. marina from the Amazon basin and other areas east of the Andes. A Bayesian coalescent‐based method (BEAST) dated the divergence between the two major clades, and between the Central American and Ecuadorian clades to the Miocene, matching the timing of other Central‐South American faunal divergences. Taken together, the results highlight the importance of Tertiary events such as the Pebas/marine incursions into the Amazon basin and Andean uplift for the diversification and historical biogeography of R. marina, making such taxa paraphyletic, and provide new perspectives on the debate on its species status.     

Therodamas tamarae, a new species of copepod (Poecilostomatoida: Ergasilidae) parasitic on Plagioscion squamosissimus (Heckel) from the Araguaia River, Brazil; with a key to the species of the genus

Therodamas tamarae n.sp. is described based on females removed from branchial filaments of Plagioscion squamosissimus (Teleostei, Sciaenidae) caught in a lake near the Araguaia River, State of Goiás, Brazil. The new species shares with Therodamas elongatus (Thatcher, 1986) the same host, a similar reaction from the host to the presence of the parasites, and the same general shape of body; in addition, the two species are from the Amazon basin. On the other hand, it resembles T. fluviatilis Paggi, 1976 in the structure of legs 1 to 4. An identification key for Therodamas species, as well as comments on the distribution of the species, are included.     

Distribution of Miogypsinoides in the Zagros Basin,in southwest Iran

In the present study three species of Miogypsinoides are described from the Oligocene–Miocene Asmari Formation of the Zagros Basin in the southwest of Iran. This is the explanation of the morphological recognition and distribution of Miogypsinoides complanatus, Miogypsinoides formosensis (Upper Oligocene, Chattian) and Miogypsinoides dehaartii (Lower Miocene, Aquitanian). Nepionic acceleration is the most important factor for recognition of Miogypsinoides species. Also it is applied in stratigraphic correlation. Examination of samples indicates a decreasing number of nepionic chambers (Mx) as time passes so M. dehaartii with Mx < 10 belong to the Aquitanian age. The study of microfacies shows that these species lived in an open marine environment with normal salinity and medium hydraulic energy in a middle ramp position.     

Explosive Pleistocene range expansion leads to widespread Amazonian sympatry between robust and gracile capuchin monkeys

Aim Capuchin monkey species are widely distributed across Central and South America. Morphological studies consistently divide the clade into robust and gracile forms, which show extensive sympatry in the Amazon Basin. We use genetic data to test whether Miocene or Plio‐Pleistocene processes may explain capuchin species’ present distributions, and consider three possible scenarios to explain widespread sympatry. Location The Neotropics, including the Amazon and Atlantic Coastal Forest. Methods We sequenced the 12S ribosomal RNA and cytochrome b genes from capuchin monkey specimens. The majority were sampled from US museum collections and were wild‐caught individuals of known provenance across their distribution. We applied a Bayesian discrete‐states diffusion model, which reconstructed the most probable history of invasion across nine subregions. We used comparative methods to test for phylogeographic association and dispersal rate variation. Results Capuchins contained two well supported monophyletic clades, the morphologically distinct ‘gracile’ and ‘robust’ groups. The time‐tree analysis estimated a late Miocene divergence between Cebus and Sapajus and a subsequent Plio‐Pleistocene diversification within each of the two clades. Bayesian analysis of phylogeographic diffusion history indicated that the current wide‐ranging sympatry of Cebus and Sapajus across much of the Amazon Basin was the result of a single explosive late Pleistocene invasion of Sapajus from the Atlantic Forest into the Amazon, where Sapajus is now sympatric with gracile capuchins across much of their range. Main conclusions The biogeographic history of capuchins suggests late Miocene geographic isolation of the gracile and robust forms. Each form diversified independently, but during the Pleistocene, the robust Sapajus expanded its range from the Atlantic Forest to the Amazon, where it has now encroached substantially upon what was previously the exclusive range of gracile Cebus. The genus Cebus, as currently recognized, should be split into two genera to reflect the Miocene divergence and two subsequent independent Pliocene radiations: Cebus from the Amazon and Sapajus from the Atlantic Forest.     

Phylogeography of West Indies Coral snakes (Micrurus): Island colonisation and banding patterns

In this study, we analyse New World coral snakes in a phylogenetic framework based upon an increased molecular data set, including novel sequences for the only two sympatric species known from an island (Trinidad, West Indies). Their presence in Trinidad and absence in Tobago offers a unique system to study the phylogeography of the region. We assess the tempo and mode of colonisation of Micrurus on the island, in addition to discussing the phylogenetic relationships for the genus Micrurus concerning two phenotypic traits, body and tail banding patterns. These relationships are analysed for the first time on statistical coalescent phylogeographic discrete ancestral reconstruction. We find a robust phylogenetic component in these characteristics, where strongly supported clades are recovered: prior to the onset of the Early Miocene, a triadal and tricolour tail clade composed of species from South America, and a second clade dating to the Middle‐Late‐ Miocene with monadal and bicolour tails widely distributed from North to South America. The divergence between clades dates to the Oligocene and suggests an ancient pre‐isthmus divergence supporting the arrival of the triadal clade into South America, before the connection between Central and South America was established. We find the two coral snakes present in the West Indies, M. diutius and M. circinalis, belong to the triadal and monadal clades, respectively. Guyana and Trinidad Micrurus diutius share the same haplotypes suggesting a Late Pleistocene–Holocene vicariance when sea level rises separated Trinidad from the mainland. A second lineage of diutius‐like snakes is present in Guyana and is confirmed as M. lemniscatus which is assigned as a voucher and restricts the type locality for M. lemniscatus.     

Molecular systematics and historical biogeography of tree boas (Corallus spp.)

Inferring the evolutionary and biogeographic history of taxa occurring in a particular region is one way to determine the processes by which the biodiversity of that region originated. Tree boas of the genus Corallus are an ancient clade and occur throughout Central and South America and the Lesser Antilles, making it an excellent group for investigating Neotropical biogeography. Using sequenced portions of two mitochondrial and three nuclear loci for individuals of all recognized species of Corallus, we infer phylogenetic relationships, present the first molecular analysis of the phylogenetic placement of the enigmatic C. cropanii, develop a time-calibrated phylogeny, and explore the biogeographic history of the genus. We found that Corallus diversified within mainland South America, via over-water dispersals to the Lesser Antilles and Central America, and via the traditionally recognized Panamanian land bridge. Divergence time estimates reject the South American Caribbean-Track as a general biogeographic model for Corallus and implicate a role for events during the Oligocene and Miocene in diversification such as marine incursions and the uplift of the Andes. Our findings also suggest that recognition of the island endemic species, C. grenadensis and C. cookii, is questionable as they are nested within the widely distributed species, C. hortulanus. Our results highlight the importance of using widespread taxa when forming and testing biogeographic hypotheses in complex regions and further illustrate the difficulty of forming broadly applicable hypotheses regarding patterns of diversification in the Neotropical region.     

Paleodistributions and comparative molecular phylogeography of leafcutter ants (Atta spp.) provide new insight into the origins of Amazonian diversity

The evolutionary basis for high species diversity in tropical regions of the world remains unresolved. Much research has focused on the biogeography of speciation in the Amazon Basin, which harbors the greatest diversity of terrestrial life. The leading hypotheses on allopatric diversification of Amazonian taxa are the Pleistocene refugia, marine incursion, and riverine barrier hypotheses. Recent advances in the fields of phylogeography and species-distribution modeling permit a modern re-evaluation of these hypotheses. Our approach combines comparative, molecular phylogeographic analyses using mitochondrial DNA sequence data with paleodistribution modeling of species ranges at the last glacial maximum (LGM) to test these hypotheses for three co-distributed species of leafcutter ants (Atta spp.). The cumulative results of all tests reject every prediction of the riverine barrier hypothesis, but are unable to reject several predictions of the Pleistocene refugia and marine incursion hypotheses. Coalescent dating analyses suggest that population structure formed recently (Pleistocene-Pliocene), but are unable to reject the possibility that Miocene events may be responsible for structuring populations in two of the three species examined. The available data therefore suggest that either marine incursions in the Miocene or climate changes during the Pleistocene--or both--have shaped the population structure of the three species examined. Our results also reconceptualize the traditional Pleistocene refugia hypothesis, and offer a novel framework for future research into the area.     

Molecular phylogenetics unveils the ancient evolutionary origins of the enigmatic fairy armadillos

Fairy armadillos or pichiciegos (Xenarthra, Dasypodidae) are among the most elusive mammals. Due to their subterranean and nocturnal lifestyle, their basic biology and evolutionary history remain virtually unknown. Two distinct species with allopatric distributions are recognized: Chlamyphorus truncatus is restricted to central Argentina, while Calyptophractus retusus occurs in the Gran Chaco of Argentina, Paraguay, and Bolivia. To test their monophyly and resolve their phylogenetic affinities within armadillos, we obtained sequence data from modern and museum specimens for two mitochondrial genes (12S RNA [MT-RNR1] and NADH dehydrogenase 1 [MT-ND1]) and two nuclear exons (breast cancer 1 early onset exon 11 [BRCA1] and von Willebrand factor exon 28 [VWF]). Phylogenetic analyses provided a reference phylogeny and timescale for living xenarthran genera. Our results reveal monophyletic pichiciegos as members of a major armadillo subfamily (Chlamyphorinae). Their strictly fossorial lifestyle probably evolved as a response to the Oligocene aridification that occurred in South America after their divergence from Tolypeutinae around 32 million years ago (Mya). The ancient divergence date (～17Mya) for separation between the two species supports their taxonomic classification into distinct genera. The synchronicity with Middle Miocene marine incursions along the Paraná river basin suggests a vicariant origin for pichiciegos by the disruption of their ancestral range. Their phylogenetic distinctiveness and rarity in the wild argue in favor of high conservation priority.     

Lepadiform and scalpelliform barnacles from the Oligocene and Miocene of the Paratethys sea

Abstract: A review on the Oligocene and Miocene stalked barnacles of the Paratethys Sea is presented. The fauna comprises two lepadiform and eight scalpelliform species. Only two species are known from Oligocene deposits, four are documented from Lower Miocene formations, and another four species occur in the Middle Miocene. Only one Oligocene and one Miocene species occur in two different Paratethyan basins in roughly coeval environments, and only a single Middle Miocene species is also known from the adjacent Mediterranean Sea. This low degree of biogeographical similarity is probably a result from the still low number of publications dealing with this group. Stalked barnacles are often indicating bathyal or at least deep sublittoral environments. Especially, the abundance of the benthic deep‐water lepadiform Poecilasma in evaporitic deposits of the Middle Miocene Badenian Salinity Crisis may serve as new evidence for a deeper marine depositional environment. Scalpellum paratethyianum sp. nov. and Lepas sattmanni sp. nov. are described as new species; Arcoscalpellum renevieri (Mayer and Gümbel in Gümbel, 1861) is introduced as new combination.     

Phylogenetic systematics and historical biogeography of the Neotropical electric fish Sternopygus (Teleostei: Gymnotiformes)

Interrelationships among 10 extant species of the Neotropical electric fish Sternopygus are inferred from phylogenetic analysis of 66 morphological characters, including features of pigmentation, body proportions, meristics and osteology. A total of 287 lots containing 677 specimens were examined. The important findings of this study are: (1) S. branco is the most basal species unique among congeners in being restricted to whitewater rivers in the Central Amazon Basin, (2) S. sp. ‘cau’ from the Rio Caura of Venezuela is the sister taxon to (S. obtusirostris + S. astrabes), (3) S. castroi is a junior synonym of S. astrabes, (4) S. macrurus is the sister taxon to (S. arenatus + S. xingu + S. aequilabiatus species group) and (5) S. arenatus is the sister taxon to (S. xingu + S. aequilabiatus species group). A key to the adults of Sternopygus species is provided. Several features of S. astrabes previously thought to be plesiomorphic are now considered derived, including: short body cavity, paedomorphic cranial osteology, and the habitat restriction to terra firme streams. Sternopygus species assemblages in the Pacific (trans‐Andean) and Atlantic (cis‐Andean) slopes of northwestern South America are not monophyletic and do not result exclusively from local or regional radiations. The clade composed of S. macrurus, S. arenatus, S. xingu and the S. aequilabiatus species group is inferred to predate the Middle Miocene uplift of the Eastern Cordillera (c. 11.8–12.2 Ma). As currently recognized S. macrurus is the most widely distributed and most eurytopic gymnotiform species, inhabiting all hydrogeographical regions of tropical South America and most lowland aquatic habitats. Other Sternopygus species have much more restricted geographic and ecological distributions. Perceptions of phylogenetic patterns in Sternopygus are shown to be highly sensitive to taxon sampling.     

Historical biogeography of South American freshwater fishes

Aim To investigate biogeographical patterns of the obligate freshwater fish order Characiformes. Location South America. Methods Parsimony analysis of endemicity, likelihood analysis of congruent geographical distribution, and partition Bremer support were used. Results Areas of endemism are deduced from parsimony analysis of endemicity, and putative dispersal routes from a separate analysis of discordant patterns of distribution. Main conclusions Our results demonstrate the occurrence of 11 major areas of endemism and support a preferential eastern–western differentiation of the characiforms in the Amazonian region, contrasting with the southern–northern differentiation of terrestrial organisms. The areas of endemism identified seem to be deeply influenced by the distribution of the emerged land during the 100‐m marine highstand that occurred during the late Miocene and allow us to hypothesize the existence of eight aquatic freshwater refuges at that time. The raw distribution of non‐endemic species supports nine patterns of species distribution across the 11 areas of endemism, two of which support a southern–northern differentiation in the eastern part of the Amazon. This result shows that the main channel of the Amazon limited dispersal between tributaries from each bank of the river. The levels of endemism further demonstrate that the aquatic freshwater refuges promoted allopatric speciation and later allowed the colonization of the lowlands. By contrast, the biogeographical pattern found in the western part of the Amazon is identified as a result of the Miocene Andean foreland dynamic and the uplift of the palaeoarches that promoted allopatric divergence across several sedimentary basins by the establishment of disconnected floodplains. The assessment of conflicting species distributions also shows the presence of seven putative dispersal routes between the Amazon, Orinoco and Paraná rivers. Our findings suggest that, rather than there being a single predominant process, the establishment of the modern South American freshwater fish biotas is the result of an interaction between marine incursions, uplift of the palaeoarches, and historical connections allowing cross‐drainage dispersal.     

Trachemys medemi n. sp. from northwestern Colombia turns the biogeography of South American slider turtles upside down

South America was invaded by slider turtles (Trachemys spp.) twice, with one immigration wave estimated to have reached South America 8.6–7.1 million years ago (mya) and a second wave, 2.5–2.2 mya. The two widely disjunct South American subspecies of Trachemys dorbigni (northeastern and southern Brazil, Río de la Plata region of Argentina and Uruguay) are derived from the first dispersal pulse, while the two South American subspecies of Trachemys venusta (Colombia, Venezuela) originated from the second immigration event. We describe a new species of slider turtle from the lower Atrato river basin of Antioquia and Chocó departments, northwestern Colombia. This new species, the Atrato slider (Trachemys medemi n. sp.), is the first representative of the older immigration wave inhabiting northern South America. Using phylogenetic analyses of 3,242 bp of mitochondrial and 3,396 bp of nuclear DNA, we show that T. medemi is more closely related to T. dorbigni than to the geographically neighboring subspecies of Trachemys grayi and T. venusta from Central America and northern South America. The two subspecies of T. dorbigni are separated from the Atrato slider by the Andes and the Amazon Basin, and occur approximately 4,600 km and 3,700 km distant from T. medemi. According to molecular clock calculations, T. medemi diverged from the last common ancestor of the two subspecies of T. dorbigni during the Pliocene (4.1–2.8 mya), with T. dorbigni diversifying later (2.3–1.9 mya) in eastern South America beyond the Amazon basin. The divergence of the T. dorbigni subspecies overlaps with the estimated arrival of T. venusta in South America (2.5–2.2 mya). This time is characterized by massive climatic and environmental fluctuations with intermittent dispersal corridors in South America. According to their distribution, it seems likely that the ancestors of the extant subspecies of T. dorbigni dispersed along the eastern corridor, leaving a relict population northwest of the Andes with T. medemi. The distribution range of T. medemi is surrounded by taxa derived from the second southern range expansion of slider turtles, so that it can be concluded that T. venusta circumvented the habitats occupied by the ancestors of the Atrato slider when entering South America.     

Amazonian lowland, white sand areas as ancestral regions for South American biodiversity: Biogeographic and phylogenetic patterns in Potalia (Angiospermae: Gentianaceae)

Present-day white sand areas in South America are thought to be relictual areas of earlier, widespread habitats now covered by more recent sediments mainly from the Andean orogeny. These ancient, nutrient-poor areas have been suggested to be possible ancestral regions for neotropical plant diversity. Members of the genus Potalia of the Gentianaceae grow in the New World tropics from Costa Rica in the north to southern Bolivia. Until recently, only one Potalia species was accepted, but a new revision identifies eight others. Three species are endemic to lowland, white sand areas in the Amazon and Orinoco basins and share morphological characteristics with Anthocleista, the African – Malagasy sister group to Potalia. To resolve phylogenetic and biogeographic patterns in Potalia, morphological characters and sequences of the internal transcribed spacer (ITS) and the 5S non-transcribed spacer (5S-NTS) of the ribosomal nuclear DNA were collected and used for phylogenetic reconstruction using Bayesian and parsimony-based methods. Potalia species restricted to ancient, nutrient-poor white sand areas of the Amazon Basin and Guayana Shield were placed basal to other Potalia taxa from finer, lateritic, and younger soils, further suggesting that lowland white sand areas may be ancestral seats of neotropical diversity.     

Phylogenetic Relationships of Spider Monkeys (Ateles) Based on Mitochondrial DNA Variation

Our goal was to determine phylogenetic relationships among geographically and taxonomically distinct haplotypes of spider monkeys (Ateles) based on DNA sequence variation for the mitochondrial DNA control region and cytochrome c oxidase subunit II gene. We obtained samples from most previously recognized subspecies of Ateles, ranging from Central America throughout the Amazon Basin, to determine phylogenetic relationships among racially recognized groups. Comparison of DNA sequences using both parsimony analysis and genetic distance analysis produced phylogenetic relationships that were very similar for each genetic region. We analyzed the phylograms produced, along with associated bootstrap support, confidence probabilities, and genetic distances between taxonomic groups, to identify four monophyletic species of Ateles: Ateles paniscus, composed of haplotypes from the northeastern Amazon Basin; A. belzebuth in the southern Amazon Basin; A. hybridus, located primarily along the Magdalena River valley of Colombia; and A. geoffroyi, which includes two former species: A. geoffroyi and A. fusciceps. This arrangement is contradictory to long-held taxonomies of Ateles based on pelage variation and is similar to a recent analysis based on craniodental variation. Results of this investigation suggest patterns of gene flow, evolutionary relationships, and speciation patterns that are more plausible than previous pelage-based taxonomies, which required seemingly impossible patterns of gene flow. Conservation efforts aimed at protecting Ateles, one of the Neotropics most endangered genera, will also benefit from the findings presented in this paper.