INVESTIGATING PROCESSES OF NEOTROPICAL RAIN FOREST TREE DIVERSIFICATION BY EXAMINING THE EVOLUTION AND HISTORICAL BIOGEOGRAPHY OF THE PROTIEAE (BURSERACEAE)

Andean uplift and the collision of North and South America are thought to have major implications for the diversification of the Neotropical biota. However, few studies have investigated how these geological events may have influenced diversification. We present a multilocus phylogeny of 102 Protieae taxa (73% of published species), sampled pantropically, to test hypotheses about the relative importance of dispersal, vicariance, habitat specialization, and biotic factors in the diversification of this ecologically dominant tribe of Neotropical trees. Bayesian fossil‐calibrated analyses date the Protieae stem at 55 Mya. Biogeographic analyses reconstruct an initial late Oligocene/early Miocene radiation in Amazonia for Neotropical Protieae, with several subsequent late Miocene dispersal events to Central America, the Caribbean, Brazil's Atlantic Forest, and the Chocó. Regional phylogenetic structure results indicate frequent dispersal among regions throughout the Miocene and many instances of more recent regional in situ speciation. Habitat specialization to white sand or flooded soils was common, especially in Amazonia. There was one significant increase in diversification rate coincident with colonization of the Neotropics, followed by a gradual decrease consistent with models of diversity‐dependent cladogenesis. Dispersal, biotic interactions, and habitat specialization are thus hypothesized to be the most important processes underlying the diversification of the Protieae.     

The Great American Interchange in birds: a phylogenetic perspective with the genus Trogon

The 'Great American Interchange' (GAI) is recognized as having had a dramatic effect on biodiversity throughout the Neotropics. However, investigation of patterns in Neotropical avian biodiversity has generally been focused on South American taxa in the Amazon Basin, leaving the contribution of Central American taxa under-studied. More rigorous studies of lineages distributed across the entire Neotropics are needed to uncover phylogeographical patterns throughout the area, offering insights into mechanisms that contribute to overall Neotropical biodiversity. Here we use mitochondrial DNA sequence data and intensive geographical sampling from the widespread Neotropical avian genus Trogon to investigate the role of the GAI in shaping its phylogeographical history. Our results show that genetic diversity in Trogon exceeds the perceived biodiversity, and that the GAI resulted in lineage diversification within the genus. Despite greater diversity in South America, a Central American centre of origin with multiple and independent dispersals into South America is indicated. These dispersals were followed by the evolution of divergent lineages associated with the Andes Mountains and other South American geographical features. According to our phylogenetic reconstructions, several species, which were originally defined by morphological characters, are nonmonophyletic. In sum, our results elucidate the evolutionary history of Trogon , reveal patterns obscured by extant biodiversity, and serve as a biogeographical model to consider in future studies.     

A rapid diversification of rainforest trees (Guatteria; Annonaceae) following dispersal from Central into South America

Several recent studies have suggested that a substantial portion of today's plant diversity in the Neotropics has resulted from the dispersal of taxa into that region rather than vicariance, but more data are needed to substantiate this claim. Guatteria (Annonaceae) is, with 265 species, the third largest genus of Neotropical trees after Inga (Fabaceae) and Ocotea (Lauraceae), and its widespread distribution and frequent occurrence makes the genus an excellent model taxon to study diversification patterns. This study reconstructed the phylogeny of Guatteria and inferred three major biogeographical events in the history of the genus: (1) a trans-oceanic Miocene migration from Central into South America before the closing of the Isthmus of Panama; (2) a major diversification of the lineage within South America; and (3) several migrations of South American lineages back into Central America via the closed Panamanian land bridge. Therefore, Guatteria is not an Amazonian centred-genus sensu Gentry but a major Miocene diversification that followed its dispersal into South America. This study provides further evidence that migration into the Neotropics was an important factor in the historical assembly of its biodiversity. Furthermore, it is shown that phylogenetic patterns are comparable to those found in Ocotea and Inga and that a closer comparison of these genera is desirable.     

The combined role of dispersal and niche evolution in the diversification of Neotropical lizards

Ecological requirements and environmental conditions can influence diversification across temporal and spatial scales. Understanding the role of ecological niche evolution under phylogenetic contexts provides insights on speciation mechanisms and possible responses to future climatic change. Large‐scale phyloclimatic studies on the megadiverse Neotropics, where biomes with contrasting vegetation types occur in narrow contact, are rare. We integrate ecological and biogeographic data with phylogenetic comparative methods, to investigate the relative roles of biogeographic events and niche divergence and conservatism on the diversification of the lizard genus Kentropyx Spix, 1825 (Squamata: Teiidae), distributed in South American rainforests and savannas. Using five molecular markers, we estimated a dated species tree, which recovered three clades coincident with previously proposed species groups diverging during the mid‐Miocene. Biogeography reconstruction indicates a role of successive dispersal events from an ancestral range in the Brazilian Shield and western Amazonia. Ancestral reconstruction of climatic tolerances and niche overlap metrics indicates a trend of conservatism during the diversification of groups from the Amazon Basin and Guiana Shield, and a strong signal of niche divergence in the Brazilian Shield savannas. Our results suggest that climatic‐driven divergence at dynamic forest‐savanna borders might have resulted in adaptation to new environmental niches, promoting habitat shifts and shaping speciation patterns of Neotropical lizards. Dispersal and ecological divergence could have a more important role in Neotropical diversification than previously thought.     

Biogeographic and diversification patterns of Neotropical Troidini butterflies (Papilionidae) support a museum model of diversity dynamics for Amazonia

ABSTRACT: BACKGROUND: The temporal and geographical diversification of Neotropical insects remains poorly understood because of the complex changes in geological and climatic conditions that occurred during the Cenozoic. To better understand extant patterns in Neotropical biodiversity, we investigated the evolutionary history of three Neotropical swallowtail Troidini genera (Papilionidae). First, DNA-based species delimitation analyses were conducted to assess species boundaries within Neotropical Troidini using an enlarged fragment of the standard barcode gene. Molecularly delineated species were then used to infer a time-calibrated species-level phylogeny based on a three-gene dataset and Bayesian dating analyses. The corresponding chronogram was used to explore their temporal and geographical diversification through distinct likelihood-based methods. RESULTS: The phylogeny for Neotropical Troidini was well resolved and strongly supported. Molecular dating and biogeographic analyses indicate that the extant lineages of Neotropical Troidini have a late Eocene (33-42 Ma) origin in North America. Two independent lineages (Battus and Euryades+Parides) reached South America via the GAARlandia connection, and later became extinct in North America. They only began substantive diversification during the Miocene in Amazonia. Macroevolutionary analysis supports the "museum model" of diversification, rather than Pleistocene refugia, as the best explanation for the diversification of these lineages. CONCLUSIONS: This study demonstrates that: (i) current Neotropical biodiversity may have originated ex situ; (ii) the GAARlandia bridge was important in facilitating invasions of South America; (iii) colonization of Amazonia initiated the crown diversification of these swallowtails; and (iv) Amazonia is not only a species-rich region but also acted as a sanctuary for the dynamics of this diversity. In particular, Amazonia probably allowed the persistence of old lineages and contributed to the steady accumulation of diversity over time with constant net diversification rates, a result that contrasts with previous studies on other South American butterflies.     

Areas of endemism and distribution patterns for Neotropical Piper species (Piperaceae)

Aim The study aimed to establish areas of endemism and distribution patterns for Neotropical species of the genus Piper in the Neotropical and Andean regions by means of parsimony analysis of endemicity (PAE) and track‐compatibility analysis. Location The study area includes the Neotropical region and the Northern Andean region (Páramo‐Punan subregion). Methods We used distribution information from herbarium specimens and recent monographic revisions for 1152 species of Piper from the Neotropics. First, a PAE was attempted in order to delimit the areas of endemism. Second, we performed a track‐compatibility analysis to establish distribution patterns for Neotropical species of Piper. Terminology for grouping Piper is based on recent phylogenetic analyses. Results The PAE yielded 104 small endemic areas for the genus Piper, 80 of which are in the Caribbean, Amazonian and Paranensis subregions of the Neotropical region, and 24 in the Páramo‐Punan subregion of the Andean region. Track‐compatibility analysis revealed 26 generalized tracks, one in the Páramo‐Punan subregion (Andean region), 19 in the Neotropical region, and six connecting the Andean and Neotropical regions. Both the generalized tracks and endemic areas indicate that distribution of Piper species is restricted to forest areas in the Andes, Amazonia, Chocó, Central America, the Guayana Shield and the Brazilian Atlantic coast. Main conclusions Piper should not be considered an Andean‐centred group as it represents two large species components with distributions centred in the Amazonian and Andean regions. Furthermore, areas of greater species richness and/or endemism are restricted to lowland habitats belonging to the Neotropical region. The distribution patterns of Neotropical species of Piper could be explained by recent events in the Neotropical region, as is the case for the track connecting Chocó and Central America, where most of the species rich groups of the genus are found. Two kinds of event could explain the biogeography of a large part of the Piper taxa with Andean–Amazonian distribution: pre‐Andean and post‐Andean events.     

Diversity and biogeography of vascular epiphytes in Western Amazonia, Yasuní, Ecuador

Aim Although vascular epiphytes are important components of species richness and complexity of Neotropical forests, vascular epiphytes are under‐represented in large scale biogeographical analyses. We studied the diversity, biogeography and floristic relationships of the epiphytic flora of the Yasuní region (Western Amazonia) in a Neotropical context, with special emphasis on the influence of the Andean flora on floristic composition and diversity of surrounding lowland forests. Location Western Amazonian lowland rainforest, Tiputini Biodiversity Station (0°38′ S 76°09′ W, 230 m a.s.l., 650 ha), Yasuní National Park, Ecuador. Methods We compared the vascular epiphyte flora of Yasuní with 16 published Neotropical epiphyte inventories. Secondly, based on a floristic database with records of more than 70,000 specimens of vascular epiphytes from the Neotropics the elevational composition of eight selected inventories was analysed in detail. Results The vascular epiphyte flora of Yasuní is characterized by a very high species richness (313 spp.). A moderate portion of species is endemic to the Upper Napo region (c. 10%). However, this figure is much higher than previous analyses primarily based on woody species suggested. Geographical ranges of these species match with a proposed Pleistocene forest refuge. Compared with Northern and Central Amazonian sites, Western Amazonian epiphyte communities are characterized by a higher portion of montane and submontane species. Species richness of vascular epiphytes at the sites was correlated with the amount of rainfall, which is negatively correlated with the number of dry months. Main conclusion Recent and historic patterns of rainfall are the driving forces behind diversity and floristic composition of vascular epiphytes in Western Amazonia: high annual rainfall in combination with low seasonality provides suitable conditions to harbour high species richness. The proximity to the Andes, the most important centre of speciation for most Neotropical epiphytic taxa, in combination with the climatic setting has allowed a continuous supply of species richness to the region. At least for epiphytes, the borderline between the Andean and Amazonian flora is much hazier than previously thought. Moreover, the comparatively moist climate in Western Amazonia during the Pleistocene has probably led to fewer extinctions and/or more speciation than in more affected surrounding lowlands.     

Genetic structuring in a Neotropical palm analyzed through an Andean orogenesis‐scenario

Andean orogenesis has driven the development of very high plant diversity in the Neotropics through its impact on landscape evolution and climate. The analysis of the intraspecific patterns of genetic structure in plants would permit inferring the effects of Andean uplift on the evolution and diversification of Neotropical flora. In this study, using microsatellite markers and Bayesian clustering analyses, we report the presence of four genetic clusters for the palm Oenocarpus bataua var. bataua which are located within four biogeographic regions in northwestern South America: (a) Chocó rain forest, (b) Amotape‐Huancabamba Zone, (c) northwestern Amazonian rain forest, and (d) southwestern Amazonian rain forest. We hypothesize that these clusters developed following three genetic diversification events mainly promoted by Andean orogenic events. Additionally, the distinct current climate dynamics among northwestern and southwestern Amazonia may maintain the genetic diversification detected in the western Amazon basin. Genetic exchange was identified between the clusters, including across the Andes region, discarding the possibility of any cluster to diversify as a distinct intraspecific variety. We identified a hot spot of genetic diversity in the northern Peruvian Amazon around the locality of Iquitos. We also detected a decrease in diversity with distance from this area in westward and southward direction within the Amazon basin and the eastern Andean foothills. Additionally, we confirmed the existence and divergence of O. bataua var. bataua from var. oligocarpus in northern South America, possibly expanding the distributional range of the latter variety beyond eastern Venezuela, to the central and eastern Andean cordilleras of Colombia. Based on our results, we suggest that Andean orogenesis is the main driver of genetic structuring and diversification in O. bataua within northwestern South America.     

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.     

Contrasting patterns of Andean diversification among three diverse clades of Neotropical clearwing butterflies

The Neotropical region is the most biodiverse on Earth, in a large part due to the highly diverse tropical Andean biota. The Andes are a potentially important driver of diversification within the mountains and for neighboring regions. We compared the role of the Andes in diversification among three subtribes of Ithomiini butterflies endemic to the Neotropics, Dircennina, Oleriina, and Godyridina. The diversification patterns of Godyridina have been studied previously. Here, we generate the first time‐calibrated phylogeny for the largest ithomiine subtribe, Dircennina, and we reanalyze a published phylogeny of Oleriina to test different biogeographic scenarios involving the Andes within an identical framework. We found common diversification patterns across the three subtribes, as well as major differences. In Dircennina and Oleriina, our results reveal a congruent pattern of diversification related to the Andes with an Andean origin, which contrasts with the Amazonian origin and multiple Andean colonizations of Godyridina. In each of the three subtribes, a clade diversified in the Northern Andes at a faster rate. Diversification within Amazonia occurred in Oleriina and Godyridina, while virtually no speciation occurred in Dircennina in this region. Dircennina was therefore characterized by higher diversification rates within the Andes compared to non‐Andean regions, while in Oleriina and Godyridina, we found no difference between these regions. Our results and discussion highlight the importance of comparative approaches in biogeographic studies.     

Finding needles in the haystack: where to look for rare species in the American tropics

Tropical America (the Neotropics) harbours more plant species than any other region on Earth. The contribution of rare species to this diversity has been recently recognised, but their spatial distribution remains poorly understood. Here, we use all collection records of angiosperms from the Global Biodiversity Information Facility to delineate Neotropical bioregions, and to identify putatively rare species within the Neotropics and the Amazonian rainforest. We analyse the spatial distribution of these species and validate the results on a largely independent dataset based on vegetation plots from the Amazon Tree Diversity Network. We find that rare species are homogeneously distributed through most parts of the lowland Neotropics and Amazonia, but more concentrated in highlands. The second collection of any rare species is most often found in the close vicinity of the first, but in 20% of cases they are more than 580 km apart. We also find cross‐taxonomic patterns of disjunct distributions within the Andes, the Atlantic forest in eastern Brazil, and between Amazonia and the Atlantic forest, but no clear disjunction patterns within lowland areas. These results suggest that a considerable proportion of rare plant species have surprisingly large distribution ranges, and that collections of rare species across most of the lowland Neotropics, and in particular in Amazonia, show no clear directionality. The second record of many rare species may be found virtually anywhere, urging the need for intensifying and broadening biological sampling.     

A Miocene hyperdiverse crocodylian community reveals peculiar trophic dynamics in proto-Amazonian mega-wetlands

Amazonia contains one of the world''s richest biotas, but origins of this diversity remain obscure. Onset of the Amazon River drainage at approximately 10.5 Ma represented a major shift in Neotropical ecosystems, and proto-Amazonian biotas just prior to this pivotal episode are integral to understanding origins of Amazonian biodiversity, yet vertebrate fossil evidence is extraordinarily rare. Two new species-rich bonebeds from late Middle Miocene proto-Amazonian deposits of northeastern Peru document the same hyperdiverse assemblage of seven co-occurring crocodylian species. Besides the large-bodied Purussaurus and Mourasuchus, all other crocodylians are new taxa, including a stem caiman—Gnatusuchus pebasensis—bearing a massive shovel-shaped mandible, procumbent anterior and globular posterior teeth, and a mammal-like diastema. This unusual species is an extreme exemplar of a radiation of small caimans with crushing dentitions recording peculiar feeding strategies correlated with a peak in proto-Amazonian molluscan diversity and abundance. These faunas evolved within dysoxic marshes and swamps of the long-lived Pebas Mega-Wetland System and declined with inception of the transcontinental Amazon drainage, favouring diversification of longirostrine crocodylians and more modern generalist-feeding caimans. The rise and demise of distinctive, highly productive aquatic ecosystems substantially influenced evolution of Amazonian biodiversity hotspots of crocodylians and other organisms throughout the Neogene.     

Systematics and biogeography of Rhodniini (Heteroptera: Reduviidae: Triatominae) based on 16S mitochondrial rDNA sequences

Aim The tribe Rhodniini is one of six comprising the subfamily Triatominae (Heteroptera: Reduviidae), notorious as blood‐sucking household pests and vectors of Trypanosoma cruzi throughout Latin America. The human and economic cost of this disease in the American tropics is considerable, and these bugs are unquestionably of great importance to man. Studies of the evolution, phylogeny, biogeography, ecology, physiology and behaviour of the Rhodniini are needed to help improve existing Chagas’ disease control programmes. The objective of the study reported here was to propose biogeographical hypotheses to explain the modern geographical distribution of the species of Rhodniini. Location Neotropical region. Methods We employed mitochondrial rDNA sequences (16S) currently available in GenBank to align sequences of Rhodniini species using ClustalX. The analyses included 16S sequences from predatory reduviid subfamilies (Stenopodainae, Ectrichodiinae, Harpactorinae, Reduviinae and Salyavatinae) present in GenBank as an outgroup. Cladistic analysis used the program PAUP to derive trees based on maximum parsimony (MP) and maximum likelihood (ML). Known distribution data for Rhodniini species were obtained from reviews and plotted on maps of South and Central America using the program iMap. An area cladogram was derived from the cladistic result to show the historical connections among the studied taxa and the endemic areas. The program TreeMap (Jungle Edition) was used to deduce taxon–area associations where the optimal solutions to explain the biogeographical hypothesis of the Rhodniini in the Neotropics were those with lowest total cost. Results Parsimony and maximum‐likelihood analysis of 16S rDNA sequences included 14 species of Rhodniini, as well as five species of predatory Reduviidae representing five of the predatory subfamilies. Tanglegrams were used to show the relationship between the Neotropical areas of endemism and Rhodniini species. When TreeMap with codivergence (vicariance) events were weighted as 0 and duplication (sympatry), lineage losses (extinction) and host switching (dispersal) were all weighted as 1, 20 scenarios were found to explain the biogeographical history of Rhodniini in the Neotropical region. Twelve of the optimal solutions with the lowest total cost were used to explain the biogeography of the Rhodniini in the Neotropics. These optimal reconstructions require six vicariance events, 20 duplications (sympatry), at least three dispersals, and at least one extinction event. Main conclusions The Rhodniini have a complex biogeographical history that has involved vicariance, duplications (sympatry), dispersal and extinction events. The main geological events affecting the origin and diversification of the Rhodniini in the Neotropics were (1) uplift of the Central Andes in the Miocene or later, (2) break‐up of the Andes into three separate cordilleras (Eastern, Central and Western) in the Plio‐Pleistocene, (3) formation of a land corridor connecting South and North America in the Pliocene, and (4) uplift of the Serra do Mar and Serra da Mantiqueira mountain systems between the Oligocene and Pleistocene. The relationships and biogeographical history of the species of Rhodniini in the Neotropical region probably arose from the areas of endemism shown in our work.     

Cladistic biogeography of the Neotropical region: identifying the main events in the diversification of the terrestrial biota

A cladistic biogeographical analysis was undertaken to identify the main events in the biotic diversification of the terrestrial Neotropical biota. For the 36 animal and plant taxa analysed, a component × area matrix was constructed, associating geographical data only with informative nodes, and it was analysed under implied weights using the software TNT. The general area cladogram obtained shows that the Neotropical region constitutes a monophyletic unit, with a first split separating the Antilles and a second one dividing the continental areas into a north‐western and a south‐eastern component. Within the north‐western component the areas split following the sequence northern Amazonia, south‐western Amazonia, north‐western South America, and Mesoamerica. Within the south‐eastern component the areas split following the sequence south‐eastern Amazonia, Chaco, and Parana. The three main components are treated as subregions: Antillean, Amazonian (northern Amazonian, south‐western Amazonian, Mesoamerican, and north‐western South American dominions), and Chacoan (south‐eastern Amazonian, Chacoan, and Parana dominions). Dispersal and vicariant events postulated to explain these pattens might have occurred during the Cretaceous, when the Caribbean plate collided with the Americas, a combination of eustatic sea‐level changes and tectonic deformations of the continental platform exposed large parts of South America to episodes of marine transgressions, and the Andean uplift reconfigured the Amazonian area. Tertiary and Quaternary events are assumed to have later induced the diversification within these large biogeographical units.     

Tracing the diversification history of a Neogene rodent invasion into South America

We investigated spatial patterns of evolutionary relatedness and diversification rates to test hypotheses about the historical biogeographic processes underlying the radiation of Neotropical rats and mice (Sigmodontinae, ~400 species). A negative correlation between mean phylogenetic distance and diversification rates of rodent assemblages reveals a pattern of species co‐occurrence in which assemblages of closely related species are also the fastest diversifying ones. Subregions of the Neotropics occupied by distantly related species that are on average more slowly diversifying include Central America, northern South America, and the Atlantic forest. In southern South America, recent species turnover appears to have been higher. Ancestral locations for the main tribes of sigmodontines were also estimated, suggesting eastern South America and the Amazonian lowlands were colonized before some central Andean regions, even though the latter are now centers of species richness for these rodents. Moreover, a past connection between the tropical Andes and the Atlantic Forest is suggested by our results, highlighting a role for a hypothetical arc connecting the two biomes, which would have impacted many other groups of organisms. Whether rapid, recent speciation in some regions is related to Quaternary climatic fluctuations and the young age of sigmodontines (~12.7 Ma crown age) or instead to intrinsic traits of these rodents remains an open question. If the former is true, we hypothesize that contrasting trends will characterize older Neotropical clades.     

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.     

Are the Northern Andes a species pump for Neotropical birds? Phylogenetics and biogeography of a clade of Neotropical tanagers (Aves: Thraupini)

Aim We used mitochondrial DNA sequence data to reconstruct the phylogeny of a large clade of tanagers (Aves: Thraupini). We used the phylogeny of this Neotropical bird group to identify areas of vicariance, reconstruct ancestral zoogeographical areas and elevational distributions, and to investigate the correspondence of geological events to speciation events. Location The species investigated are found in 18 of the 22 zoogeographical regions of South America, Central America and the Caribbean islands; therefore, we were able to use the phylogeny to address the biogeographical history of the entire region. Methods Molecular sequence data were gathered from two mitochondrial markers (cytochrome b and ND2) and analysed using Bayesian and maximum‐likelihood approaches. Dispersal–vicariance analysis (DIVA) was used to reconstruct zoogeographical areas and elevational distributions. A Bayesian framework was also used to address changes in elevation during the evolutionary history of the group. Results Our phylogeny was similar to previous tanager phylogenies constructed using fewer species; however, we identified three genera that are not monophyletic and uncovered high levels of sequence divergence within some species. DIVA identified early diverging nodes as having a Northern Andean distribution, and the most recent common ancestor of the species included in this study occurred at high elevations. Most speciation events occurred either within highland areas or within lowland areas, with few exchanges occurring between the highlands and lowlands. The Northern Andes has been a source for lineages in other regions, with more dispersals out of this area relative to dispersals into this area. Most of the dispersals out of the Northern Andes were dispersals into the Central Andes; however, a few key dispersal events were identified out of the Andes and into other zoogeographical regions. Main conclusions The timing of diversification of these tanagers correlates well with the main uplift of the Northern Andes, with the highest rate of speciation occurring during this timeframe. Central American tanagers included in this study originated from South American lineages, and the timing of their dispersal into Central America coincides with or post‐dates the completion of the Panamanian isthmus.     

HISTORICAL DIVERSIFICATION OF BIRDS IN NORTHWESTERN SOUTH AMERICA: A MOLECULAR PERSPECTIVE ON THE ROLE OF VICARIANT EVENTS

Studies of South American biodiversity have identified several areas of endemism that may have enhanced historical diversification of South American organisms. Hypotheses concerning the derivation of birds in the Chocó area of endemism in northwestern South America were evaluated using protein electrophoretic data from 14 taxonomically diverse species groups of birds. Nine of these groups demonstrated that the Chocó area of endemism has a closer historical relationship to Central America than to Amazonia, a result that is consistent with phytogeographic evidence. Within species groups, genetic distances between cis-Andean (east of the Andes) and trans-Andean (west of the Andes) taxa are, on average, roughly twice that between Chocó and Central American taxa. The genetic data are consistent with the hypotheses that the divergence of most cis-Andean and trans-Andean taxa was the result of either the Andean uplift fragmenting a once continuous Amazonian-Pacific population (Andean Uplift Hypothesis), the isolation of the two faunas in forest refugia on opposite sides of the Andes during arid climates (Forest Refugia Hypothesis), or dispersal of Amazonian forms directly across the Andes into the trans-Andean region (Across-Andes Dispersal Hypothesis). Disentangling these hypotheses is difficult due to the complexity of the Andean uplift and to the scant geologic and paleoclimatic information that elucidates diversification events in northwestern South America. Regarding the divergence of cis- and trans-Andean taxa, the genetic, geologic, and paleoclimatic data allow weak rejection of the Andean Uplift Hypothesis and weak support for the Forest Refugia and Andean Dispersal Hypotheses. The subsequent diversification of Chocó and Central American taxa was the result of Pleistocene forest refugia, marine transgressions, or parapatric speciation.     

Phylogenetic Patterns of Geographical and Ecological Diversification in the Subgenus Drosophila

Colonisation of new geographic regions and/or of new ecological resources can result in rapid species diversification into the new ecological niches available. Members of the subgenus Drosophila are distributed across the globe and show a large diversity of ecological niches. Furthermore, taxonomic classification of Drosophila includes the rank radiation, which refers to closely related species groups. Nevertheless, it has never been tested if these taxonomic radiations correspond to evolutionary radiations. Here we present a study of the patterns of diversification of Drosophila to test for increased diversification rates in relation to the geographic and ecological diversification processes. For this, we have estimated and dated a phylogeny of 218 species belonging to the major species groups of the subgenus. The obtained phylogenies are largely consistent with previous studies and indicate that the major groups appeared during the Oligocene/Miocene transition or early Miocene, characterized by a trend of climate warming with brief periods of glaciation. Ancestral reconstruction of geographic ranges and ecological resource use suggest at least two dispersals to the Neotropics from the ancestral Asiatic tropical disribution, and several transitions to specialized ecological resource use (mycophagous and cactophilic). Colonisation of new geographic regions and/or of new ecological resources can result in rapid species diversification into the new ecological niches available. However, diversification analyses show no significant support for adaptive radiations as a result of geographic dispersal or ecological resource shift. Also, cactophily has not resulted in an increase in the diversification rate of the repleta and related groups. It is thus concluded that the taxonomic radiations do not correspond to adaptive radiations.     

Phylogeography of a species complex of lowland Neotropical rain forest trees (Carapa,Meliaceae)

Aim Many tropical tree species have poorly delimited taxonomic boundaries and contain undescribed or cryptic species. We examined the genetic structure of a species complex in the tree genus Carapa in the Neotropics in order to evaluate age, geographic patterns of diversity and evolutionary relationships, and to quantify levels of introgression among currently recognized species. Location Lowland moist forests in the Guiana Shield, the Central and Western Amazon Basin, Chocó and Central America. Methods Genetic structure was analysed using seven nuclear simple sequence repeats (nuSSR), five chloroplast SSRs (cpSSR), and two chloroplast DNA (cpDNA) intergenic sequences (trnH–psbA and trnC–ycf6). Bayesian clustering analysis of the SSR data was used to infer population genetic structure and to assign 324 samples to their most likely genetic cluster. Bayesian coalescence analyses were performed on the two cpDNA markers to estimate evolutionary relationships and divergence times. Results Two genetic clusters (nu_guianensis and nu_surinamensis) were detected, which correspond to the Neotropical species C. guianensis (sensu latu) and C. surinamensis. Fourteen cpDNA haplotypes clustered into six haplogroups distributed between the two nuclear genetic clusters. Divergence between the haplogroups was initiated in the Miocene, with some haplotype structure evolving as recently as the Pleistocene. The absence of complete lineage sorting between the nuclear and chloroplast genomes and the presence of hybrid individuals suggest that interspecific reproductive barriers are incomplete. NuSSR diversity was highest in C. guianensis and, within C. guianensis, cpDNA diversity was highest in the Central and Western Amazon Basin. Regional genetic differentiation was strong but did not conform to an isolation‐by‐distance process or exhibit a phylogeographical signal. Main conclusions The biogeographical history of Neotropical Carapa appears to have been influenced by events that took place during the Neogene. Our results point to an Amazonian centre of origin and diversification of Neotropical Carapa, with subsequent migration to the Pacific coast of South America and Central America. Gene flow apparently occurs among species, and introgression events are supported by inconsistencies between chloroplast and nuclear lineage sorting. The absence of phylogeographical structure may be a result of the ineffectiveness of geographical barriers among populations and of reproductive isolation mechanisms among incipient and cryptic species in this species complex.