Revisiting Amazonian phylogeography: insights into diversification hypotheses and novel perspectives

From forest to savanna and back to forest: Evolutionary history of the genus Dimorphandra (Fabaceae)

The tree genus Dimorphandra (Fabaceae), which contains 26 species divided into three subgenera, was studied using DNA sequence data from six chloroplast genome regions (cpDNA) and the nuclear internal transcribed spacer (ITS). The analyses, which included Bayesian phylogenies and haplotype networks, ancestral area reconstructions, and ecological niche modeling, allowed for exploring the evolutionary history of Dimorphandra. Within the subgenus Phaneropsia, the cpDNA sequence data were more closely-related to species from the genus Mora, while the ITS sequence data displayed a closer phylogenetic relationship with the subgenus Pocillum. This incongruence may be due to incomplete lineage sorting associated with ancient polymorphisms. The Amazonian Dimophandra lineages were highly polymorphic and divergent, while those from the Cerrado and the Atlantic Forest had low levels of polymorphisms. The Amazon likely gave rise to the Dimophandra lineage that produced the Cerrado species, while a Cerrado lineage likely gave rise to the Atlantic Forest species. Habitat shifts were identified as a key factor in shaping the late evolutionary history of Dimorphandra.

Phylogenomics and species delimitation of an abundant and little-studied Amazonian forest spiny rat

Species delimitation studies based on integrating different datasets such as genomic, morphometric, and cytogenetics data are rare in studies focused on Neotropical rodents. As a consequence, the evolutionary history of most of these genera remains poorly understood. Proechimys is a highly diverse and widely distributed genus of Neotropical spiny rats with unique traits like multiple sympatry, micro-habitat segregation, and fuzzy species limits. Here, we applied RAD-Seq to infer the phylogenetic relationships, estimate the species boundaries, and estimate the divergence times for Proechimys, one of the most common and least studied small mammals in the Amazon. We tested whether inferred lineages in the phylogenetic trees could be considered distinct species based on the genomic dataset and morphometric data. Analyses revealed the genus is not monophyletic, with Proechimys hoplomyoides sister to a group of Hoplomys gymnurus + all other Proechimys species, contesting the generic status of Hoplomys. There are five main clades in Proechimys stricto sensu (excluding H. gymnurus and P. hoplomyoides). Species delimitation analyses supported 25 species within the genus Proechimys. The five main clades in Proechimys stricto sensu also showed similar ages for their origins, and two rapid diversification events were identified in the Early Pliocene and in the Early Pleistocene. Most cases of sympatry in Proechimys occur among species from the different main clades, and although Proechimys is an inhabitant of the Amazon, three species occupied the Cerrado biome during the Pleistocene. We could associate available nominal taxon, cytogenetics information, and DNA sequences in Genbank to most of the 25 species we hypothesized from our delimitation analyses. Based on our analyses, we estimate that eight forms represent putative new species that need a taxonomic revision.

Genetic diversity analysis in the Brazilian Amazon reveals a new evolutionary lineage and new karyotype for the genus Mesomys (Rodentia, Echimyidae, Eumysopinae)

Morphological, molecular and chromosomal studies in the genera Lonchothrix and Mesomys have contributed to a better understanding of taxonomic design, phylogenetic relationships and karyotypic patterns. Recent molecular investigations have shown a yet undescribed diversity, suggesting that these taxa are even more diverse than previously assumed. Furthermore, some authors have questioned the limits of geographic distribution in the Amazon region for the species M. hispidus and M. stimulax. In this sense, the current study sought to understand the karyotypic evolution and geographic limits of the genus Mesomys, based on classical (G- and C-banding) and molecular cytogenetic analysis (FISH using rDNA 18S and telomeric probes) and through the sequencing of mitochondrial genes Cytochrome b (Cytb) and Cytochrome Oxidase-Subunit I (CO using phylogeny, species delimitation and time of divergence, from samples of different locations in the Brazilian Amazon. The species M. stimulax and Mesomys sp. presented 2n = 60/FN = 110, while M. hispidus presented 2n = 60/FN = 112, hitherto unpublished. Molecular dating showed that Mesomys diversification occurred during the Plio-Pleistocene period, with M. occultus diverging at around 5.1 Ma, followed by Mesomys sp. (4.1 Ma) and, more recently, the separation between M. hispidus and M. stimulax (3.5 Ma). The ABGD and ASAP species delimiters support the formation of 7 and 8 potential species of the genus Mesomys, respectively. Furthermore, in both analyzes Mesomys sp. was recovered as a valid species. Our multidisciplinary approach involving karyotypic, molecular and biogeographic analysis is the first performed in Mesomys, with the description of a new karyotype for M. hispidus, a new independent lineage for the genus and new distribution data for M. hispidus and M. stimulax.

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.

Historical biogeography highlights the role of Miocene landscape changes on the diversification of a clade of Amazonian tree frogs

The diversification processes underlying why Amazonia hosts the most species-rich vertebrate fauna on earth remain poorly understood. We studied the spatio-temporal diversification of a tree frog clade distributed throughout Amazonia (Anura: Hylidae: Osteocephalus, Tepuihyla, and Dryaderces) and tested the hypothesis that Miocene mega wetlands located in western and central Amazonia impacted connectivity among major biogeographic areas during extensive periods. We assessed the group’s diversity through DNA-based (16S rRNA) species delimitation to identify Operational Taxonomic Units (OTUs) from 557 individuals. We then selected one terminal for each OTU (n = 50) and assembled a mitogenomic matrix (~14,100 bp; complete for 17 terminals) to reconstruct a Bayesian, time-calibrated phylogeny encompassing nearly all described species. Ancestral area reconstruction indicates that each genus was restricted to one of the major Amazonian biogeographic areas (western Amazonia, Guiana Shield and Brazilian Shield, respectively) between ~10 and 20 Mya, suggesting that they diverged and diversified in isolation during this period around the Pebas mega wetland. After 10 Mya and the transition to the modern configuration of the Amazon River watershed, most speciation within each genus continued to occur within each area. In Osteocephalus, only three species expanded widely across Amazonia (< 6 Mya), and all were pond-breeders. Species with other breeding modes remained mostly restricted to narrow ranges. The spectacular radiation of Osteocephalus was probably driven by climatic stability, habitat diversity and the acquisition of new reproductive modes along the Andean foothills and western Amazonia. Our findings add evidence to the importance of major hydrological changes during the Miocene on biotic diversification in Amazonia.

Phylogeography of a Typical Forest Heliothermic Lizard Reveals the Combined Influence of Rivers and Climate Dynamics on Diversification in Eastern Amazonia

The formation of the Amazon drainage basin has been considered an important driver of speciation of several taxa, promoting vicariant events or reinforcement of barriers that restrict gene flow between opposite river margins. Several recent studies reported a set of miscellaneous events involving climatic fluctuations, geomorphological changes, and dispersal mechanisms as propellers of diversification of Amazonian rainforest taxa. Here, we show the results of dated phylogenetic, biogeographic, and populational analyses to investigate which events could better explain the current distribution of a heliothermic, active foraging lizard in the central and eastern portions of the Amazonian rainforest (besides a disjunct distribution in part of the Atlantic Forest). We sampled Kentropyx calcarata from most of its area of occurrence in Amazonia and used mitochondrial and nuclear markers to evaluate if the genetic structure agrees with evolutionary scenarios previously proposed for Amazonia. We performed phylogenetic and populational analyses to better understand the dynamics of this species in the Amazonia rainforest over time. Phylogenetic inference recovered ten K. calcarata structured lineages in eastern Amazonia, some of them limited by the Amazon River and its southern tributaries (Tapajós, Xingu, and Tocantins), although we detected occasional haplotype sharing across some of the river banks. According to molecular dating, K. calcarata diversified since Miocene–Pliocene, and some of the lineages presented signs of demographic expansion during the Pleistocene, supposedly triggered by climatic dynamics. The putative ancestral lineage of K. calcarata was distributed on the Guiana Shield, later spreading south and southeastward by dispersion. Our results indicate that Amazonian rivers acted as barriers to the dispersal of Kentropyx calcarata, but they were not the sole drivers of diversification.

Deep Genomic Divergence and Phenotypic Admixture of the Treefrog Dendropsophus elegans (Hylidae: Amphibia) Coincide With Riverine Boundaries at the Brazilian Atlantic Forest

The Atlantic Forest (AF) domain is one of the Earth’s biodiversity hotspots, known for its high levels of species diversity and endemism. Factors related to palaeoenvironmental dynamics, such as the establishment of vegetational refugia and river basins, have different impacts on biological communities and biodiversity patterns in this domain. Here, we sample genome-wide RADseq data from a widespread treefrog (Dendropsophus elegans), inhabiting natural and human-impacted ecosystems at the Brazilian AF to test the impact of riverine boundaries and climatic refugia on population structure and diversification. We estimate divergence times and migration rate across identified genetic breaks related to the rivers Doce, Paraíba do Sul, Ribeira de Iguape, and Paraguaçu, known to represent barriers to gene flow for other AF endemic species, and test the role of climatic refugia. Finally, we investigate the impact of spatio-temporal population history on morphological variation in this species. We recovered a phylogeographic history supporting three distinct clades separated into two geographically structured populations, corresponding to the north and south of AF. In addition, we identified an admixture zone between north and south populations in the latitude close to the Doce River. Our findings support a pattern of isolation-by-distance and the existence of a secondary contact zone between populations, which might have been promoted by gene flow during population expansion. Further, we found support for models considering migration parameters for all the tested rivers with different population divergence times. Based on the species history and the AF palaeoenvironmental dynamics, we corroborate the role of forest refugia impacting population structure for this species through recent range expansion after the Last Glacial Maximum (LGM). The Doce and Paraíba do Sul Rivers coincide with the main genetic breaks, suggesting they might also have played a role in the diversification processes. Finally, despite finding subtle correlations for phenotypic data among different populations, variation is not strongly detectable and does not seem associated with speciation-level processes that could warrant taxonomic changes. Such results can be explained by phenotypic plasticity of the evaluated traits and by recent divergence times, where there has been insufficient time and weak selective pressures to accumulate enough phenotypic differences.

Fishes from the Colombian Amazonia region: species composition from the river systems within the rainforest biome

Abstract The Colombian Amazon region is part of the Neotropical rainforest (humid forest biome) covering an area of 483,163 km2 and includes tributaries of both the Amazon and Orinoco River basins. The aquatic ecosystems found there include: rivers and alluvial plains originating in Andean headwaters, on eroded soils of tropical forests in the lowlands, and Guiana Shield formations, comprising a dense fluvial drainage network in the lowlands, with Paleogene/Neogene geological formations (terra firme streams in higher places that don’t usually flood) and Paleozoic (shield streams); and Andean and Guiana Shield streams above 200–250 m a.s.l. We present here an exhaustive compilation of published information, supported by fish collections, consisting of a list of 1104 species distributed in 375 genera, 53 families, and 16 orders. We include occurrence data of these species in each sub-basin. The presence/absence species matrix was analyzed using a dendrogram and non-metric multidimensional scaling (NMDS) analysis to identify patterns of similarity between basins and sub-basins. We evaluated species composition between basins and among the different geological origins using PERMANOVA. The dendrogram shows co-occurrences of 404 species in the two basins. It also shows two clear groupings of the sub-basins of the Amazon (except Guainía-Negro drainages) and those of the Orinoco. Within the Amazon Basin, there are two nodes according to the geological origin: systems of Andean origin and those of the lowlands. The dendrogram results are consistent with the NMDS analysis, which shows a clear grouping according to the connectivity of the basins; the Guainía-Negro is included in the Amazon basin. Species distribution patterns were supported by the PERMANOVA, and differed significantly between basins (F = 4.3, R = 0.26, P = 0.003) and geological origin (F = 3.6, R = 0.23, P = 0.003). The number of species in this study represents almost a fifth of the ichthyofauna of the Neotropics and about a third of that of the Amazon River basin; clearly supporting Colombia’s status among the countries with the greatest diversity of freshwater fish species of the planet. We include here a significant number of new records (75 spp), provide a first approximation of the distribution patterns, and a framework for future biogeographical studies.

Multiple evolutionary lineages for the main vector of Leishmania guyanensis, Lutzomyia umbratilis (Diptera: Psychodidae), in the Brazilian Amazon

Lutzomyia umbratilis is the main vector of Leishmania guyanensis in the Brazilian Amazon and in neighboring countries. Previous biological and molecular investigations have revealed significant differences between L. umbratilis populations from the central Brazilian Amazon region. Here, a phylogeographic survey of L. umbratilis populations collected from nine localities in the Brazilian Amazon was conducted using two mitochondrial genes. Statistical analyses focused on population genetics, phylogenetic relationships and species delimitations. COI genetic diversity was very high, whereas Cytb diversity was moderate. COI genealogical haplotypes, population structure and phylogenetic analyses identified a deep genetic differentiation and three main genetic groups. Cytb showed a shallower genetic structure, two main haplogroups and poorly resolved phylogenetic trees. These findings, allied to absence of isolation by distance, support the hypothesis that the Amazon and Negro Rivers and interfluves are the main evolutionary forces driving L. umbratilis diversification. The main three genetic groups observed represent three evolutionary lineages, possibly species. The first lineage occurs north of the Amazon River and east of Negro River, where Le. guyanensis transmission is intense, implying that L. umbratilis is an important vector there. The second lineage is in the interfluve between north of Amazon River and west of Negro River, an area reported to be free of Le. guyanensis transmission. The third lineage, first recorded in this study, is in the interfluve between south of Amazonas River and west of Madeira River, and its involvement in the transmission of this parasite remains to be elucidated.

New karyotype for Mesomys stimulax (Rodentia, Echimyidae) from the Brazilian Amazon: A case for species complex?

Mesomys Wagner, 1845 (Rodentia, Echimyidae, Eumysopinae) currently has four recognized species, three of which occur in Brazil: Mesomys hispidus (probably a species complex), M. occultus, and M. stimulax. Mesomys leniceps is found in montane forests of northern Peru. Mesomys stimulax, the focus of the present study, has a distribution that is restricted to the central and eastern Amazonia south of the Amazon River, extending from the left bank of the Tapajós River to the right bank of the Tocantins River, and south to the southeast portion of Pará State. The genus presents karyotypes with diploid number 2n = 60 and Fundamental Number (FN) = 116 for M. hispidus and M. stimulax, and 2n = 42, FN = 54 for M. occultus. We studied the karyotype of a female specimen of M. stimulax collected from the Tapirapé-Aquiri National Forest, Marabá, Pará, Brazil, in the Xingu/Tocantins interfluvium. The obtained karyotype (2n = 60 and FN = 110) differs from that described in the literature for both M. stimulax and M. hispidus by exhibiting more biarmed chromosomes, probably due to pericentric inversions and/or centromeric repositioning, and exhibiting differences in the amount and distribution of constitutive heterochromatin (CH). These results suggest that, similar to what has already been proposed for M. hispidus, M. stimulax may represent a species complex and/or cryptic species. The mechanisms of chromosomal diversification in Mesomys and the biogeographic implications are discussed reinforcing the need for broad systematic review for Mesomys.

Factors determining the structure of fish assemblages in Tarumã River, Jaru Biological Reserve, Machado River drainage, northern Brazil

ABSTRACT Few studies on fish assemblages and relations with environmental factors in aquatic systems in southeastern Amazonia have been carried out when compared to other areas in the Amazon. Therefore, which are the main environmental variables and processes responsible for structuring them remains unknown. We hypothesized that fish assemblages respond the variation in the physical-chemistry variables between seasons of the hydrological cycle in a pristine river in the Amazon. The study was performed on fish assemblages of the Tarumã River, Jaru Biological Reserve, Rondônia. Samplings were carried out in five sites along the river in March and September, 2015, which included fish collection and environmental data measurements. Principal component analysis was performed to ordinate the sites in high water and low water seasons, according to environmental variables. We used a similarity analysis in order to identify the individual contribution of species in hydrological period and a partial redundancy analysis for quantify the relative importance of environmental variables in the species composition. As predicted by our hypothesis, the species composition was influenced by dissolved oxygen and temperature. Myloplus rubripinnis, Serrasalmus compressus, and S. rhombeus were the most abundant during high water, while S. rhombeus, Myloplus lobatus, Prochilodus nigricans, and Hydrolycus armatus were the dominant species during the low water.

The Influence of Environmental Variation on the Genetic Structure of a Poison Frog Distributed Across Continuous Amazonian Rainforest

Biogeographic barriers such as rivers have been shown to shape spatial patterns of biodiversity in the Amazon basin, yet relatively little is known about the distribution of genetic variation across continuous rainforest. Here, we characterize the genetic structure of the brilliant-thighed poison frog (Allobates femoralis) across an 880-km-long transect along the Purus-Madeira interfluve south of the Amazon river, based on 64 individuals genotyped at 7609 single-nucleotide polymorphism (SNP) loci. A population tree and clustering analyses revealed 4 distinct genetic groups, one of which was strongly divergent. These genetic groups were concomitant with femoral spot coloration differences, which was intermediate within a zone of admixture between two of the groups. The location of these genetic groups did not consistently correspond to current ecological transitions between major forest types. A multimodel approach to quantify the relative influence of isolation-by-geographic distance (IBD) and isolation-by-environmental resistance (IBR) nevertheless revealed that, in addition to a strong signal of IBD, spatial genetic differentiation was explained by IBR primarily linked to dry season intensity (r2 = 8.4%) and canopy cover (r2 = 6.4%). We show significant phylogenetic divergence in the absence of obvious biogeographical barriers and that finer-scaled measures of genetic structure are associated with environmental variables also known to predict the density of A. femoralis.

Hidden diversity in Prochilodus nigricans: A new genetic lineage within the Tapajós River basin

Highly spread through the Amazon River basin, Prochilodus nigricans have had its taxonomic validity recently questioned, when genetic differences between Western and Eastern Amazon populations from the Brazilian shield were detected. This area has been seeing as a region of high ichthyofaunal diversity and endemism, in which the hybrid origin of the Tapajós River basin has been raised. In this paper, we report a new molecular lineage within P. nigricans of Tapajós River, highlighting this region still hides taxonomically significant diversity. Haplotype networks were reconstructed using the mitochondrial COI and ATP6/8 markers, which were also used to calculate genetic distances among clusters. We additionally conducted a delimiting species approach by employing a Generalized Mixed Yule-Coalescent model (GMYC) with COI sequences produced here, and previous ones published for individuals sampled across the Amazon River basin. In addition to the genetic differentiation within P. nigricans, our findings favor the hypothesis of hybrid origin of the Tapajós River basin and reaffirm the importance of studies aiming to investigate hidden diversity to address taxonomic and biogeographic issues, that certainly benefit better biodiversity conservation actions.

Phylogenomic approaches reveal how climate shapes patterns of genetic diversity in an African rain forest tree species

The world's second largest expanse of tropical rainforest is in Central Africa, and it harbours enormous species diversity. Population genetic studies have consistently revealed significant structure across Central African rainforest plants. In particular, previous studies have repeatedly demonstrated a north-south genetic discontinuity around the equatorial line, in a continuous expanse of rainforest where a climatic inversion is documented. Here, we took a phylogeographic approach by sequencing 351 nuclear markers in 112 individuals across the distribution of the African rainforest tree species Annickia affinis (Annonaceae). We showed for the first time that the north-south divide is the result of a single, major colonization event across the climatic inversion from an ancestral population located in Gabon. We suggested that differences in ecological niche of populations located on either side of this inversion may have contributed to this phylogenetic discontinuity. We found evidence for inland dispersal, predominantly in northern areas, and variable demographic histories among genetic clusters, indicating that populations responded differently to past climate change. We show how newly developed genomic tools can provide invaluable insights into our understanding of tropical rainforest evolutionary dynamics.

Systematics and historical biogeography of Neotropical foam-nesting frogs of the Adenomera heyeri clade (Leptodactylidae), with the description of six new Amazonian species

A large proportion of the biodiversity of Amazonia, one of the most diverse rainforest areas in the world, is yet to be formally described. One such case is the Neotropical frog genus Adenomera. We here evaluate the species richness and historical biogeography of the Adenomera heyeri clade by integrating molecular phylogenetic and species delimitation analyses with morphological and acoustic data. Our results uncovered ten new candidate species with interfluve-associated distributions across Amazonia. In this study, six of these are formally named and described. The new species partly correspond to previously identified candidate lineages ‘sp. F’ and ‘sp. G’ and also to previously unreported lineages. Because of their rarity and unequal sampling effort of the A. heyeri clade across Amazonia, conservation assessments for the six newly described species are still premature. Regarding the biogeography of the A. heyeri clade, our data support a northern Amazonian origin with two independent dispersals into the South American Dry Diagonal. Although riverine barriers have a relevant role as environmental filters by isolating lineages in interfluves, dispersal rather than vicariance must have played a central role in the diversification of this frog clade.

Diversification history of clown tree frogs in Neotropical rainforests (Anura, Hylidae, Dendropsophus leucophyllatus group)

General consensus emphasizes that no single biological process can explain the patterns of species' distributions and diversification in the Neotropics. Instead, the interplay of several processes across space and time must be taken into account. Here we investigated the phylogenetic relationships and biogeographic history of tree frogs in the Dendropsophus leucophyllatus species group (Amphibia: Hylidae), which is distributed across Amazonia and the Atlantic rainforests. Using Next Generation Sequencing (NGS) and double digest restriction-site associated DNA (ddRADseq), we inferred phylogenetic relationships, species limits, and temporal and geographic patterns of diversification relative to the history of these biomes. Our results indicate that the D. leucophyllatus species group includes at least 14 independent lineages, which are currently arranged into ten described species. Therefore, a significant portion of species in the group are still unnamed. Different processes were associated to the group diversification history. For instance, the Andes uplift likely caused allopatric speciation for Cis-Andean species, whereas it may also be responsible for changes in the Amazonian landscape triggering parapatric speciation by local adaptation to ecological factors. Meanwhile, Atlantic Forest ancestors unable to cross the dry diagonal biomes after rainforest's retraction, evolved in isolation into different species. Diversification in the group began in the early Miocene, when connections between Atlantic Forest and the Andes (Pacific Dominion) by way of a south corridor were possible. The historical scenario in Amazonia, characterized by several speciation events and habitat heterogeneity, helped promoting diversification, resulting in the highest species diversity for the group. This marked species diversification did not happen in Atlantic Forest, where speciation is very recent (late Pliocene and Pleistocene), despite its remarkable climatic heterogeneity.

Effect of river size on Amazonian primate community structure: A biogeographic analysis using updated taxonomic assessments

The mechanisms that underlie the diversification of Neotropical primates remain contested. One mechanism that has found support is the riverine barrier hypothesis (RBH), which postulates that large rivers impede gene flow between populations on opposite riverbanks and promote allopatric speciation. Ayres and Clutton-Brock (1992) demonstrated that larger Amazonian rivers acted as barriers, delineating the distribution limits of primate species. However, profound changes in taxonomy and species concepts have led to the proliferation of Neotropical primate taxa, which may have reduced support for their results. Using the most recent taxonomic assessments and distribution maps, we tested the effect of increasing river size on the similarity of opposite riverbank primate communities in the Amazon. First, we conducted a literature review of primate taxonomy and developed a comprehensive spatial database, then applied geographical information system to query mapped primate ranges against the riverine geography of the Amazon watershed to produce a similarity index for opposite riverbank communities. Finally, we ran models to test how measures of river size predicted levels of similarity. We found that, almost without exception, similarity scores were lower than scores from Ayres and Clutton-Brock (1992) for the same rivers. Our model showed a significant negative relationship between streamflow and similarity in all tests, and found river width significant for the segmented Amazon, but not for multiple Amazon watershed rivers. Our results support the RBH insofar as they provide evidence for the prediction that rivers with higher streamflow act as more substantial barriers to dispersal, and accordingly exhibit greater variation in community composition between riverbanks.

Diversity and evolution of Amazonian birds: implications for conservation and biogeography

Amazonia has been a focus of interest since the early days of biogeography as an intrinsically complex and extremely diverse region. This region comprises an intricate mosaic that includes diverse types of forest formations, flooded environments and open vegetation. Increased knowledge about the distribution of species in Amazonia has led to the recognition of complex biogeographic patterns. The confrontation of these biogeographic patterns with information on the geological and climatic history of the region has generated several hypotheses dedicated to explain the origin of the biological diversity. Genomic information, coupled with knowledge of Earth's history, especially the evolution of the Amazonian landscape, presents fascinating possibilities for understanding the mechanisms that govern the origin and maintenance of diversity patterns in one of the most diverse regions of the world. For this we will increasingly need more intense and coordinated interactions between researchers studying biotic diversification and the evolution of landscapes. From the interaction between these two fields of knowledge that are in full development, an increasingly detailed understanding of the historical mechanisms related to the origin of the species will surely arise.

A dynamic continental moisture gradient drove Amazonian bird diversification

The Amazon is the primary source of Neotropical diversity and a nexus for discussions on processes that drive biotic diversification. Biogeographers have focused on the roles of rivers and Pleistocene climate change in explaining high rates of speciation. We combine phylogeographic and niche-based paleodistributional projections for 23 upland terra firme forest bird lineages from across the Amazon to derive a new model of regional biological diversification. We found that climate-driven refugial dynamics interact with dynamic riverine barriers to produce a dominant pattern: Older lineages in the wetter western and northern parts of the Amazon gave rise to lineages in the drier southern and eastern parts. This climate/drainage basin evolution interaction links landscape dynamics with biotic diversification and explains the east-west diversity gradients across the Amazon.

What has become of the refugia hypothesis to explain biological diversity in Amazonia?

The spatial distribution of biodiversity and related processes is the core of Biogeography. Amazonia is the world's most diverse rainforest and the primary source of diversity to several Neotropical regions. The origins of such diversity continue to be an unresolved question in evolutionary biology. Among many competing hypotheses to explain the evolution of the Amazonian biodiversity, one stands out as the most influential: the refugia hypothesis by Jürgen Haffer. Here, we provide a chronological overview on how the refugia hypothesis evolved over the decades and how the criticism from different fields affected its acceptance. We conclude that the refugia hypothesis alone cannot explain the diversification of the complex Amazonian diversity, and perhaps it was not the most important diversification mechanism. However, the debate provoked by refugia has produced a great amount of knowledge on Amazonian climatic, geological, and evolutionary processes, as well as on species distributions, movements, and history.

Elevational differentiation accelerates trait evolution but not speciation rates in Amazonian birds

The importance of ecologically mediated divergent selection in accelerating trait evolution has been poorly studied in the most species-rich biome of the planet, the continental Neotropics. We performed macroevolutionary analyses of trait divergence and diversification rates across closely related pairs of Andean and Amazonian passerine birds, to assess whether the difference in elevational range separating species pairs - a proxy for the degree of ecological divergence - influences the speed of trait evolution and diversification rates. We found that elevational differentiation is associated with faster divergence of song frequency, a trait important for pre-mating isolation, and several morphological traits, which may contribute to extrinsic post-mating isolation. However, elevational differentiation did not increase recent speciation rates, possibly due to early bursts of diversification during the uplift of the eastern Andes followed by a slow-down in speciation rate. Our results suggest that ecological differentiation may speed up trait evolution, but not diversification of Neotropical birds.

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.

Conceptual and empirical advances in Neotropical biodiversity research

The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of "trans-disciplinary biogeography," which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow's ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.

Soil and forest structure predicts large-scale patterns of occurrence and local abundance of a widespread Amazonian frog

The distribution of biodiversity within the Amazon basin is often structured by sharp environmental boundaries, such as large rivers. The Amazon region is also characterized by subtle environmental clines, but how they might affect the distributions and abundance of organisms has so far received less attention. Here, we test whether soil and forest characteristics are associated with the occurrence and relative abundance of the forest-floor dwelling Aromobatid frog, Allobates femoralis. We applied a structured sampling regime along an 880 km long transect through forest of different density. High detection probabilities were estimated for A. femoralis in each of the sampling modules. Using generalized linear mixed-effects models and simple linear regressions that take detectability into account, we show that A. femoralis is more abundant in open forests than in dense forests. The presence and relative abundance of A. femoralis is also positively associated with clay-rich soils, which are poorly drained and therefore likely support the standing water bodies required for reproduction. Taken together, we demonstrate that relatively easy-to-measure environmental features can explain the distribution and abundance of a widespread species at different spatial scales. Such proxies are of clear value to ecologists and conservation managers working in large inaccessible areas such as the Amazon basin.

Historical connections among river basins and climatic changes explain the biogeographic history of a water rat

Background

The water ratNectomys squamipes(Cricetidae: Sigmodontinae) is a semiaquatic rodent from eastern South America that shows shallow genetic structure across space, according to some studies. We tested the influence of hydrography and climatic changes on the genetic and phylogeographic structure of this semiaquatic small mammal.

Methods

DNA sequences of two mitochondrial genetic markers (Cyt b and D-loop) and six microsatellite loci from water rats were collected at 50 localities in five river basins in the Atlantic Forest along the eastern coast of South America. We evaluated the genetic structure within and among river basins, and we estimated divergence dates. Species distribution models for the present and past were built to identify possible gene flow paths.

Results

Mitochondrial data and species distribution models showed coherent results. Microsatellite loci showed a more complex pattern of genetic differentiation. The diversification ofN. squamipeshaplotypes occurred during the Pleistocene and the river basin cannot explain most of the genetic structure. We found evidence of population expansion during the last glacial maximum, and gene flow paths indicate historical connections among rivers in the Atlantic Forest.

Discussion

Historical connections among rivers in the Atlantic Forest may have allowedN. squamipesto disperse farther across and within basins, leading to shallow genetic structure. Population expansions and gene flow through the emerged continental shelf during glacial period support the Atlantis forest hypothesis, thus challenging the forest refuge hypothesis.

Biogeography of Amazon birds: rivers limit species composition, but not areas of endemism

Amazonian rivers are usually suggested as dispersal barriers, limiting biogeographic units. This is evident in a widely accepted Areas of Endemism (AoEs) hypothesis proposed for Amazonian birds. We empirically test this hypothesis based on quantitative analyses of species distribution. We compiled a database of bird species and subspecies distribution records, and used this dataset to identify AoEs through three different methods. Our results show that the currently accepted Amazonian AoEs are not consistent with areas identified, which were generally congruent among datasets and methods. Some Amazonian rivers represent limits of AoEs, but these areas are not congruent with those previously proposed. However, spatial variation in species composition is correlated with largest Amazonian rivers. Overall, the previously proposed Amazonian AoEs are not consistent with the evidence from bird distribution. However, the fact that major rivers coincide with breaks in species composition suggest they can act as dispersal barriers, though not necessarily for all bird taxa. This scenario indicates a more complex picture of the Amazonian bird distribution than previously imagined.

The trans-riverine genetic structure of 28 Amazonian frog species is dependent on life history

Among the hypotheses formulated to explain the origin of Amazonian biodiversity, two (the riverine-barrier and the river-refuge hypotheses) focus on the role that rivers play as biotic barriers promoting speciation. However, empirical results have both supported and refuted these hypotheses. This is likely due, at least in part, to river-specific hydrologic characteristics and the biology of the focal species. The rivers of the Guiana Shield represent a model system because they have had more stable courses over time than those of the western Amazon Basin, where most tests of riverine barrier effects have taken place. We tested whether life-history traits (body size, habitat and larval development), expected to be important in determining dispersal ability, of 28 frog species are associated with genetic structure and genetic distances of individuals sampled from both banks of the Oyapock River. Thirteen of these species displayed genetic structure consistent with the river acting as a barrier to dispersal. Surprisingly, body size was not correlated with trans-riverine population structure. However, leaf-litter dwellers and species lacking free-living tadpoles were found to exhibit higher river-associated structure than open habitat/arboreal species and those with exotrophic tadpoles. These results demonstrate that rivers play an important role in structuring the genetic diversity of many frog species though the permeability of such riverine barriers is highly dependent on species-specific traits.

Biogeographic history and cryptic diversity of saxicolous Tropiduridae lizards endemic to the semiarid Caatinga

Background

Phylogeographic research has advanced in South America, with increasing efforts on taxa from the dry diagonal biomes. However, the diversification of endemic fauna from the semiarid Caatinga biome in northeastern Brazil is still poorly known. Here we targeted saxicolous lizards of the Tropidurus semitaeniatus species group to better understand the evolutionary history of these endemic taxa and the Caatinga. We estimated a time-calibrated phylogeny for the species group based on two mitochondrial and two nuclear genes and jointly estimated the species limits and species tree within the group. We also devoted a denser phylogeographic sampling of the T. semitaeniatus complex to explore migration patterns, and the spatiotemporal diffusion history to verify a possible role of the São Francisco River as a promoter of differentiation in this saxicolous group of lizards.

Results

Phylogenetic analysis detected high cryptic genetic diversity, occurrence of unique microendemic lineages associated with older highlands, and a speciation history that took place during the Pliocene-Pleistocene transition. Species delimitation detected five evolutionary entities within the T. semitaeniatus species group, albeit with low support. Thus, additional data are needed for a more accurate definition of species limits and interspecific relationships within this group. Spatiotemporal analyses reconstructed the geographic origin of the T. semitaeniatus species complex to be located north of the present-day course of the São Francisco River, followed by dispersal that expanded its distribution towards the northwest and south. Gene flow estimates showed higher migration rates into the lineages located north of the São Francisco River.

Conclusions

The phylogenetic and population structures are intrinsically associated with stable rock surfaces and landscape rearrangements, such as the establishment of drainage basins located to the northern and southern distribution ranges. The T. semitaeniatus complex preserved high genetic diversity during range expansion, possibly as a result of frequent long-distance dispersal events. Our results indicate that both the current course of the São Francisco River and its paleo-courses had an important role in promoting diversification of the Caatinga endemic T. semitaeniatus species group.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0368-3) contains supplementary material, which is available to authorized users.

Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow

The demographic and phylogeographic histories of species provide insight into the processes responsible for generating biological diversity, and genomic datasets are now permitting the estimation of species histories with unprecedented accuracy. We used a genomic single nucleotide polymorphism (SNP) dataset generated using a RAD-Seq method to investigate the historical demography and phylogeography of a widespread lowland Neotropical bird (Xenops minutus). As expected, we found that prominent landscape features that act as dispersal barriers, such as Amazonian rivers and the Andes Mountains, are associated with the deepest phylogeographic breaks, and also that isolation by distance is limited in areas between these barriers. In addition, we inferred positive population growth for most populations and detected evidence of historical gene flow between populations that are now physically isolated. Although we were able to reconstruct the history of Xenops minutus with unprecedented resolution, we had difficulty conclusively relating this history to the landscape events implicated in many Neotropical diversification hypotheses. We suggest that even if many traditional diversification hypotheses remain untestable, investigations using genomic datasets will provide greater resolution of species histories in the Neotropics and elsewhere.

Transitions between Andean and Amazonian centers of endemism in the radiation of some arboreal rodents

Background

The tropical Andes and Amazon are among the richest regions of endemism for mammals, and each has given rise to extensive in situ radiations. Various animal lineages have radiated ex situ after colonizing one of these regions from the other: Amazonian clades of dendrobatid frogs and passerine birds may have Andean ancestry, and transitions from the Amazon to Andes may be even more common. To examine biogeographic transitions between these regions, we investigated the evolutionary history of three clades of rodents in the family Echimyidae: bamboo rats (Dactylomys-Olallamys-Kannabateomys), spiny tree-rats (Mesomys-Lonchothrix), and brush-tailed rats (Isothrix). Each clade is distributed in both the Andes and Amazonia, and is more diverse in the lowlands. We used two mitochondrial (cyt-b and 12S) and three nuclear (GHR, vWF, and RAG1) markers to reconstruct their phylogenetic relationships. Tree topologies and ancestral geographic ranges were then used to determine whether Andean forms were basal to or derived from lowland radiations.

Results

Four biogeographic transitions are identified among the generic radiations. The bamboo rat clade unambiguously originated in the Amazon ca. 9 Ma, followed by either one early transition to the Andes (Olallamys) and a later move to the Amazon (Dactylomys), or two later shifts to the Andes (one in each genus). The Andean species of both Dactylomys and Isothrix are sister to their lowland species, raising the possibility that highland forms colonized the Amazon Basin. However, uncertainty in their reconstructed ancestral ranges obscures the origin of these transitions. The lone Andean species of Mesomys is confidently nested within the lowland radiation, thereby indicating an Amazon-to-Andes transition ca. 2 Ma.

Conclusions

Differences in the timing of these biogeographic transitions do not appear to explain the different polarities of these trees. Instead, even within the radiation of a single family, both Andean and Amazonian centers of endemism appear enriched by lineages that originated in the other region. Our survey of other South American lineages suggests a pattern of reciprocal exchange between these regions—among mammals, birds, amphibians, and insects we found no fewer than 87 transitions between the Andes and Amazon from Miocene-Pleistocene. Because no clear trend emerges between the timing and polarity of transitions, or in their relative frequency, we suggest that reciprocal exchange between tropical highland and lowland faunas in South America has been a continual process since ca. 12 Ma.

Taxonomic revision of the olingos (Bassaricyon), with description of a new species, the Olinguito

We present the first comprehensive taxonomic revision and review the biology of the olingos, the endemic Neotropical procyonid genus Bassaricyon, based on most specimens available in museums, and with data derived from anatomy, morphometrics, mitochondrial and nuclear DNA, field observations, and geographic range modeling. Species of Bassaricyon are primarily forest-living, arboreal, nocturnal, frugivorous, and solitary, and have one young at a time. We demonstrate that four olingo species can be recognized, including a Central American species (Bassaricyon gabbii), lowland species with eastern, cis-Andean (Bassaricyon alleni) and western, trans-Andean (Bassaricyon medius) distributions, and a species endemic to cloud forests in the Andes. The oldest evolutionary divergence in the genus is between this last species, endemic to the Andes of Colombia and Ecuador, and all other species, which occur in lower elevation habitats. Surprisingly, this Andean endemic species, which we call the Olinguito, has never been previously described; it represents a new species in the order Carnivora and is the smallest living member of the family Procyonidae. We report on the biology of this new species based on information from museum specimens, niche modeling, and fieldwork in western Ecuador, and describe four Olinguito subspecies based on morphological distinctions across different regions of the Northern Andes.