Alternative models of vertebrate speciation in Amazonia: an overview

The main hypotheses proposed to explain barrier formation separating populations and causing the differentiation of vertebrate species in Amazonia are based on different (mostly historical) factors, as follows. (1) Changes in the distribution of land and sea or in the landscape due to tectonic movements or sea-level fluctuations (Paleogeography hypothesis). (2) The barrier effect of Amazonian rivers (River hypothesis). (3) A combination of the barrier effect of broad rivers and vegetational changes in Northern and Southern Amazonia (River-refuge hypothesis). (4) The isolation of forest blocks near areas of surface relief in the periphery of Amazonia during dry climatic periods of the Tertiary and Quaternary (Refuge theory). (5) Competitive species interactions and local species isolations in peripheral regions of Amazonia due to invasion and counterinvasion during cold/warm periods of the Pleistocene (Disturbance-vicariance hypothesis). (6) Parapatric speciation across steep environmental gradients without separation of the representative populations (Gradient hypothesis). Several of these hypotheses are probably relevant to a different degree for the speciation processes in different faunal groups or during different geological periods. The paleogeography hypothesis refers mainly to faunal differentiation during the Tertiary and in combination with the Refuge hypothesis; Milankovitch cycles leading to global climatic-vegetational changes affected the biomes of the world not only during the Pleistocene but also during the Tertiary and earlier geological periods. New geoscientific evidence for the effect of dry climatic periods in Amazonia supports the predictions of the Refuge theory.     

Beta diversity of frogs in the forests of New Guinea, Amazonia and Europe: contrasting tropical and temperate communities

Aim To test the hypothesis that animal communities within environmentally relatively uniform lowland forests are characterized by low beta diversity, both in tropical and in temperate areas. Location Lowland forests in the basins of the Sepik and Ramu rivers in New Guinea, the Amazon river in Bolivia, and the Elbe and Dyje rivers in the Czech Republic. Methods A network of 5–6 study sites spanning distances from 20–80 to 300–500 km in each study area was systematically surveyed for all frogs, using visual detection and call tracking. The community data were analysed for alpha and beta diversity. Results Local (alpha) diversity of frog communities was similar in the two tropical areas, New Guinea (mean ± SE of 22 ± 1.4 species per site) and Amazonia (24 ± 1.7 species), but was significantly lower in Europe (8 ± 0.8 species). In Amazonia, 36 of the total of 70 species were recorded from single sites. In contrast, widespread species dominated in Europe, whereas New Guinea exhibited an intermediate pattern with both local and widespread species well represented. The rate of species accumulation across different sites was lowest in Europe, intermediate in New Guinea and highest in Amazonia. The regional species diversity, expressed as the combined number of species from five study sites, was 1.5 times higher than the local species diversity at a single site in Europe, 2.0 times higher in New Guinea and 2.7 times higher in Amazonia. The proportion of species shared between communities decreased with geographic distance in New Guinea and Europe, but not in Amazonia. Main conclusions Frog communities in the lowland tropical rain forests of New Guinea and Amazonia had similar numbers of species, but differed in their beta diversity. More species in Amazonia had restricted distributions than in New Guinea. Both tropical areas had markedly higher alpha and beta diversity than the temperate area in Europe.     

First report on new evidence for the occurrence of Podocarpus and possible human presence at the mouth of the Amazon during the Late-glacial

Palynological studies on late Quaternary lake sediments from the region of the Amazon estuary, 100 km north-east of Belém, Pará State, Brazil, enable reconstruction of lowland Amazonian rain forest during the Late-glacial and Holocene periods. Late-glacial forests included populations of Podocarpus which suggests a distinct climatic cooling. Ilex was abundant in the early Holocene. Records of the mangrove taxon, Rhizophora, indicate rapid Atlantic sea-level rise in the beginning of the Holocene. High charcoal representation may reflect the first arrival of Amerindians in the Amazon coastal area, probably about 10 800 B.P.     

Geological and climatic forces driving speciation in the continentally distributed trilling chorus frogs (Pseudacris)

Tertiary geological events and Quaternary climatic fluctuations have been proposed as important factors of speciation in the North American flora and fauna. Few studies, however, have rigorously tested hypotheses regarding the specific factors driving divergence of taxa. Here, we test explicit speciation hypotheses by correlating geologic events with divergence times among species in the continentally distributed trilling chorus frogs (Pseudacris). In particular, we ask whether marine inundation of the Mississippi Embayment, uplift of the Appalachian Mountains, or modification of the ancient Teays-Mahomet River system contributed to speciation. To examine the plausibility of ancient rivers causing divergence, we tested whether modern river systems inhibit gene flow. Additionally, we compared the effects of Quaternary climatic factors (glaciation and aridification) on levels of genetic variation. Divergence time estimates using penalized likelihood and coalescent approaches indicate that the major lineages of chorus frogs diversified during the Tertiary, and also exclude Quaternary climate change as a factor in speciation of chorus frogs. We show the first evidence that inundation of the Mississippi Embayment contributed to speciation. We reject the hypotheses that Cenozoic uplift of the Appalachians and that diversion of the Teays-Mahomet River contributed to speciation in this clade. We find that by reducing gene flow, rivers have the potential to cause divergence of lineages. Finally, we demonstrate that populations in areas affected by Quaternary glaciation and aridification have reduced levels of genetic variation compared to those from more equable regions, suggesting recent colonization.     

Multiple quaternary refugia in the eastern Guiana shield revealed by comparative phylogeography of 12 frog species

The Guiana Shield (GS) is one of the most pristine regions of Amazonia and biologically one of the richest areas on Earth. How and when this massive diversity arose remains the subject of considerable debate. The prevailing hypothesis of Quaternary glacial refugia suggests that a part of the eastern GS, among other areas in Amazonia, served as stable forested refugia during periods of aridity. However, the recently proposed disturbance-vicariance hypothesis proposes that fluctuations in temperature on orbital timescales, with some associated aridity, have driven Neotropical diversification. The expectations of the temporal and spatial organization of biodiversity differ between these two hypotheses. Here, we compare the genetic structure of 12 leaf-litter inhabiting frog species from the GS lowlands using a combination of mitochondrial and nuclear sequences in an integrative analytical approach that includes phylogenetic reconstructions, molecular dating, and Geographic Information System methods. This comparative and integrated approach overcomes the well-known limitations of phylogeographic inference based on single species and single loci. All of the focal species exhibit distinct phylogeographic patterns highlighting taxon-specific historical distributions, ecological tolerances to climatic disturbance, and dispersal abilities. Nevertheless, all but one species exhibit a history of fragmentation/isolation within the eastern GS during the Quaternary with spatial and temporal concordance among species. The signature of isolation in northern French Guiana (FG) during the early Pleistocene is particularly clear. Approximate Bayesian Computation supports the synchrony of the divergence between northern FG and other GS lineages. Substructure observed throughout the GS suggests further Quaternary fragmentation and a role for rivers. Our findings support fragmentation of moist tropical forest in the eastern GS during this period when the refuge hypothesis would have the region serving as a contiguous wet-forest refuge.     

The ecogeographical differentiation of Amazonian inundation forests

Due to the considerable annual fluctuations of water level of the Amazonian rivers, their river banks are fringed with periodically flooded forests of vast extension. The biota of these communities are adapted to annual inundations that can last for more than half a year. Water chemistry is most important for the floristic differentiation of these flooded forests. White water rivers, which carry a rich load of suspended material originating from the erosion of the Andes, have a floristic composition related to that of the noninundatable Amazonian forest. Clear water and black water rivers, which originate in the Amazon Basin or its adjacent crystalline shields, are nutrient-poor and more or less acidic; their flora is related to that of peculiar woodland and savannah vegetation on oligotrophic white sand. The distribution patterns of floodplain species of nutrient-poor waters point to a centre of diversity in the Upper Rio Negro region, and another one in the Guayana lowland. These coincide with diversity centres for species of non-flooded habitats. Hence it seems unlikely that species diversity is directly influenced by pluviosity. The flooded forests have developed biotic interactions with the fish fauna of the Amazon Basin, which are vital for their continued existence. It is assumed that the origin of these habitats, their biota and their interactions dates back long into the Tertiary.     

Accounting for data heterogeneity in patterns of biodiversity: an application of linear mixed effect models to the oceanic island biogeography of spore‐producing plants

The general dynamic model of oceanic island biogeography describes the evolution of species diversity properties, including species richness (SR), through time. We investigate the hypothesis that SR in organisms with high dispersal capacities is better predicted by island area and elevation (as a surrogate of habitat diversity) than by time elapsed since island emergence and geographic isolation. Linear mixed effect models (LMMs) subjected to information theoretic model selection were employed to describe moss and liverwort SR patterns from 67 oceanic islands across 12 archipelagos. Random effects, which are used to modulate model parameters to take differences among archipelagos into account, included only a random intercept in the best‐fit model for liverworts and in one of the two best‐fit models for mosses. In this case, the other coefficients are constant across archipelagos, and we interpret the intercept as a measure of the intrinsic carrying capacity of islands within each archipelago, independently of their size, age, elevation and geographic isolation. The contribution of area and elevation to the models was substantially higher than that of time, with the least contribution made by measures of geographic isolation. This reinforces the idea that oceanic barriers are not a major impediment for migration in bryophytes and, together with the almost complete absence of in situ insular diversification, explains the comparatively limited importance of time in the models. We hence suggest that time per se has little independent role in explaining bryophyte SR and principally features as a variable accounting for the changing area and topographic complexity during the life‐cycle of oceanic islands. Simple area models reflecting habitat availability and diversity might hence prevail over more complex temporal models reflecting in‐situ speciation and dispersal (time, geographic connectivity) in explaining patterns of biodiversity for exceptionally mobile organisms.     

1492 and the loss of amazonian crop genetic resources. ii. crop Biogeography at contact

Fifty seven percent of the 138 cultivated plant species present in Amazonia at contact probably originated in the Amazon Basin and another 27% originated in lowland northern South America. The relationship between probable indigenous human population density and resultant agricultural intensification and crop diversity is used to propose the existence of a mosaic of crop genetic resource concentrations in Amazonia at contact, including two centers of diversity, four outlying minor centers, and five regions of diversity. This methodology is extrapolated to present a synthesis of South American crop genetic biogeography at contact.     

Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages

Background

Understanding the forces that shaped Neotropical diversity is central issue to explain tropical biodiversity and inform conservation action; yet few studies have examined large, widespread species. Lowland tapir (Tapirus terrrestris, Perissodactyla, Tapiridae) is the largest Neotropical herbivore whose ancestors arrived in South America during the Great American Biotic Interchange. A Pleistocene diversification is inferred for the genus Tapirus from the fossil record, but only two species survived the Pleistocene megafauna extinction. Here, we investigate the history of lowland tapir as revealed by variation at the mitochondrial gene Cytochrome b, compare it to the fossil data, and explore mechanisms that could have shaped the observed structure of current populations.

Results

Separate methodological approaches found mutually exclusive divergence times for lowland tapir, either in the late or in the early Pleistocene, although a late Pleistocene divergence is more in tune with the fossil record. Bayesian analysis favored mountain tapir (T. pinchaque) paraphyly in relation to lowland tapir over reciprocal monophyly, corroborating the inferences from the fossil data these species are sister taxa. A coalescent-based analysis rejected a null hypothesis of allopatric divergence, suggesting a complex history. Based on the geographic distribution of haplotypes we propose (i) a central role for western Amazonia in tapir diversification, with a key role of the ecological gradient along the transition between Andean subcloud forests and Amazon lowland forest, and (ii) that the Amazon river acted as an barrier to gene flow. Finally, the branching patterns and estimates based on nucleotide diversity indicate a population expansion after the Last Glacial Maximum.

Conclusions

This study is the first examining lowland tapir phylogeography. Climatic events at the end of the Pleistocene, parapatric speciation, divergence along the Andean foothill, and role of the Amazon river, have similarly shaped the history of other taxa. Nevertheless further work with additional samples and loci is needed to improve our initial assessment. From a conservation perspective, we did not find a correspondence between genetic structure in lowland tapir and ecogeographic regions proposed to define conservation priorities in the Neotropics. This discrepancy sheds doubt into this scheme's ability to generate effective conservation planning for vagile species.     

The time of divergence between the two species of uacari monkeys: Cacajao calvus and Cacajao melanocephalus

It has been suggested in the literature that primates of the genus Cacajao have been restricted to flooded-forest habitats of western Amazonia since their split from the Chiropotes line in the Tertiary. It has been proposed further that the differentiation of the two species of this genus, Cacajao melanocephalus and Cacajao calvus, occurred during the Pleistocene period as a result of the fragmentation of the Amazon forest and the isolation of populations in these forest fragments or refuges. However, recent evidence has shown that at least C. melanocephalus is not dependent on flooded-forest habitats, and molecular analysis of mitochondrial DNA shows that the two species had already differentiated during the Pliocene, thus Pleistocene glaciations do not explain the speciation in Cacajao. Considering that C. melanocephalus and its closest relative, Chiropotes, inhabit terra firme forests, it is suggested that preference for flooded-forest habitats may be an apomorphy in C. calvus.     

Genetic divergence and speciation in lowland and montane peruvian poison frogs

Amazonia is famous for high biodiversity, and the highlands of the transition zone between the Andes and the lowlands of the Amazon basin show particularly high species diversity. Hypotheses proposed to explain the high levels of diversity in the highlands include repeated parapatric speciation across ecological gradients spanning the transition zone, repeated allopatric speciation across geographic barriers between the highlands and lowlands, divergence across geographic barriers within the transition zone, and simple lineage accumulation over long periods of time. In this study, we investigated patterns of divergence in frogs of the genus Epipedobates (family Dendrobatidae) using phylogenetic and biogeographic analyses of divergence in mitochondrial DNA (1778 aligned positions from genes encoding cyt b, 12S and 16S rRNA for 60 Epipedobates and 11 outgroup specimens) and coloration (measured for 18 specimens representing nine species in Epipedobates). The majority of phenotypic and species diversity in the poison frog genus Epipedobates occurs in the transition zone, although two morphologically conserved members of the genus are distributed across the lowlands of the Amazon basin. Phylogenetic analysis reveals that there is a single highland clade derived from an ancestral colonization event in northern Peru by a population of lowland ancestry. Epipedobates trivittatus, a widespread Amazonian species, is a member of the highland clade that reinvaded the lowlands. Comparative analyses of divergence in coloration and mtDNA reveals that divergence in coloration among populations and species in the highlands has been accelerated relative to the lowlands. This suggests a role for selection in the divergence of coloration among populations and species.     

Amazonian paleoecological histories: one hill, three watersheds

Data from the Hill of Six Lakes, in the northwestern Brazilian Amazon region, provide three records of paleoclimatic and vegetation change in lowland Amazonia that span the last 170,000 years. Three lakes, Verde, Pata and Dragão, which occupy separate watersheds on the hill, provide the most detailed image yet obtained of ice-age conditions in lowland Amazonia. Well-dated sedimentary records for fossil palynological, charcoal, cation, and pigment, data are presented.The data indicate the continuous presence of mesic forest throughout the last ice age. Oscillations of lake level are recorded and the lowstands are attributed to reduced precipitation inputs to systems delicately balanced between water loss (leakage through the floor of the basin) and gain (precipitation). Gross stratigraphy, algal remains, and paleochemistry suggest that the stands of high and low lake level were cyclic, apparently correlating precessional orbital variation. Times of lake lowstand coincide with wet season (December-January-February, DJF) insolation minima. The strongest of eight lowstand cycles occurred ca. 35,000 to 27,000 cal BP.Even during lowstand episodes, pollen is well preserved and provides a clear signal of uninterrupted forest cover. The principal lowland elements are continuously present in the record, suggesting the long-term (Quaternary) availability of the lowland forest biome in this region. However, during the late Pleistocene the forest changed in composition with the expansion or invasion of montane floral elements creating communities of the mesic forest biome without modern analogs. While precipitation cycles were causing lake levels to rise and fall, the principal influence on vegetation appears to have been cooling. In the late Pleistocene, the population expansion of montane elements at lower elevations is consistent with a cooling of 4-5 °C.     

The Azores diversity enigma: why are there so few Azorean endemic flowering plants and why are they so widespread?

Aim Endemism in the flora of the Azores is high (33%) but in other respects, notably the paucity of evolutionary radiations and the widespread distribution of most endemics, the flora differs markedly from the floras of the other Macaronesian archipelagos. We evaluate hypotheses to explain the distinctive patterns observed in the Azorean endemic flora, focusing particularly on comparisons with the Canary Islands. Location Azores archipelago. Methods Data on the distribution and ecology of Azorean endemic flowering plants are reviewed to ascertain the incidence of inter‐island allopatric speciation and adaptive, ecological speciation. These are contrasted with patterns for the Canary Islands. Patterns of endemism in the Azores and Canaries are further investigated in a phylogenetic context in relation to island age. beast was used to analyse a published molecular dataset for Pericallis (Asteraceae) and to investigate the relative ages of Azorean and Canarian lineages. Results There are few examples of inter‐island allopatric speciation in the Azorean flora, despite the considerable distances between islands and sub‐archipelagos. In contrast, inter‐island allopatric speciation has been an important process in the evolution of the Canary Islands flora. Phylogenetic data suggest that Azorean endemic lineages are not necessarily recent in origin. Furthermore, in Pericallis the divergence of the Azorean endemic lineage from its closest relative pre‐dates the radiation of a Canarian herbaceous clade by inter‐island allopatric speciation. Main conclusions The data presented do not support suggestions that hypotheses pertaining to island age, age of endemic lineages and ecological diversity considered individually explain the lack of radiations and the widespread distribution of Azorean endemics. We suggest that palaeoclimatic variation, a factor rarely considered in macroecological studies of island diversity patterns, may be an important factor. Palaeoclimatic data suggest frequent and abrupt transitions between humid and arid conditions in the Canaries during the late Quaternary, and such an unstable climate may have driven the recent diversification of the flora by inter‐island allopatric speciation, a process largely absent from the climatically more stable Azores. Further phylogenetic/phylogeographic analyses are necessary to determine the relative importance of palaeoclimate and other factors in generating the patterns observed.     

Island area and species diversity in the southwest Pacific Ocean: is the lizard fauna of Vanuatu depauperate?

One island group suggested to be an exception to the species–area Relationship is the Vanuatu Archipelago, a group of 13 large and 80 small islands in the southwest Pacific Ocean. To test the hypothesis that the lizard fauna of the Vanuatu Archipelago does not meet the predictions of the species-area relationship, and thus is depauperate, we compare diversity among several island groups in the southwest Pacific: Fiji, the Loyalty Islands, New Caledonia, Samoa, the Solomon Islands, Tonga, and Vanuatu. We found that the lizard diversity of Vanuatu meets the pattern of diversity predicted by the species-area relationship. The Solomon Islands, the largest and least isolated oceanic archipelago considered, has the greatest species diversity and endemism of the oceanic islands. Inclusion or exclusion of island groups based on factors such as geologic history or faunal source affects the strength of the relationship between diversity, area, and history of emergence, and influences perceptions of diversity within individual archipelagos. In addition to island size, factors such evolutionary time scale, speciation, and archipelago complexity influence species richness on islands.     

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.     

The effects of archipelago spatial structure on island diversity and endemism: predictions from a spatially‐structured neutral model

Islands are particularly suited to testing hypotheses about the ecological and evolutionary mechanisms underpinning community assembly. Yet the complex spatial arrangements of real island systems have received little attention from both empirical studies and theoretical models. Here, we investigate the extent to which the spatial structure of archipelagos affects species diversity and endemism. We start by proposing a new spatially structured neutral model that explicitly considers archipelago structure, and then investigate its predictions under a diversity of scenarios. Our results suggest that considering the spatial structure of archipelagos is crucial to understanding their diversity and endemism, with structured island systems acting both as “museums” and “cradles” of biodiversity. These dynamics of diversification may change the traditionally expected pattern of decrease in species richness with distance from the mainland, even potentially leading to increasing patterns for taxa with high speciation rates in archipelagos off species‐poor continental areas. Our results also predict that, within spatially structured archipelagos, metapopulation dynamics and evolutionary processes can generate higher diversity on islands more centrally placed than at the periphery. We derive from our results a set of theoretical predictions, potentially testable with empirical data.     

Early evolution of chili peppers (Capsicum)

An hypothesis is advanced based upon geographical information and data from horizontal starch gel electrophoresis regarding the place and mode of evolution of the chili peppers (Capsicum). The hypothesis suggests a major portion of the genusCapsicum arose in a nuclear area in south central Bolivia with subsequent migration into the Andes and lowland Amazonia accompanied by radiation and speciation.     

Reductions in the mitochondrial DNA diversity of coral reef fish provide evidence of population bottlenecks resulting from Holocene sea-level change

This study investigated the influence of reproductive strategy (benthic or pelagic eggs) and habitat preferences (lagoon or outer slope) on both diversity and genetic differentiation using a set of populations of seven coral reef fish species over different geographic scales within French Polynesia. We hypothesized that a Holocene sea-level decrease contributed to severe reduction of population size for species inhabiting lagoons and a subsequent decrease of genetic diversity. Conversely, we proposed that species inhabiting stable environments, such as the outer slope, should demonstrate higher genetic diversity but also more structured populations because they have potentially reached a migration-genetic drift equilibrium. Sequences of the 5' end of the mitochondrial DNA (mtDNA) control region were compared among populations sampled in five isolated islands within two archipelagos of French Polynesia. For all the species, no significant divergences among populations were found. Significant differences in mtDNA diversity between lagoonal and outer-slope species were demonstrated both for haplotype diversity and sequence divergence but none were found between species with different egg types. Pairwise mismatch distributions suggested rapid population growth for all the seven species involved in this study, but they revealed different distributions, depending on the habitat preference of the species. Although several scenarios can explain the observed patterns, the hypothesis of population size reduction events relative to Holocene sea-level regression and its consequence on French Polynesia coral reefs is the most parsimonious. Outer-slope species have undergone a probable weak and/or old bottleneck (outer reefs persisted during low sea level, leading to reef area reductions), whereas lagoonal species suffered a strong and/or recent bottleneck since Holocene sea-level regression resulted in the drying out of all the atolls that are maximum 70 meters deep. Since present sea level was reached between 5000 and 6000 years ago, different demographic events (bottlenecks or founder events) have lead to the actual populations of lagoons in French Polynesia.     

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.     

Plant diversity in Oceanic archipelagos: realistic patterns emulated by an agent‐based computer simulation

Although islands as natural laboratories have held the attention of scientists for centuries, they continue to offer new study questions, especially in the context of the current biodiversity crisis. To date, habitat diversity on islands and spatial configuration of archipelagos have received less attention than classical island area and isolation. Moreover, in the field where experiments are impossible, correlative methods have dominated, despite the call for more mechanistic approaches. We developed an agent‐based computer simulation to study the effect of habitat diversity and archipelago configuration on plant species richness and composition in five archipelagos worldwide (Hawaii, Galapagos, Canary Islands, Cape Verde and Azores) and compared simulated diversity patterns to the empirical data. Habitat diversity proved to be an important factor to achieve realistic simulation results in all five archipelagos, whereas spatial structure of archipelagos was important in more elongated archipelagos. In most cases, simulation results correlate stronger with spermatophyte than with pteridophyte data, which we suggest can be attributed to the different dispersal and evolution rates of the two species groups. Correlation strength between simulated and observed diversity also varied among archipelagos, suggesting that geological and biogeographic histories of archipelagos have affected the species richness and composition on the islands. Our study demonstrates that a relatively simple computer simulation involving just a few essential processes can largely emulate patterns of archipelagic species richness and composition and serve as a powerful additional method to complement empirical approaches.