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Evolution creates and sustains biodiversity via adaptive changes in ecologically relevant traits. Ecologically mediated selection contributes to genetic divergence both in the presence or absence of geographic isolation between populations, and is considered an important driver of speciation. Indeed, the genetics of ecological speciation is becoming increasingly studied across a variety of taxa and environments. In this paper we review the literature of ecological speciation in the tropics. We report on low research productivity in tropical ecosystems and discuss reasons accounting for the rarity of studies. We argue for research programs that simultaneously address biogeographical and taxonomic questions in the tropics, while effectively assessing relationships between reproductive isolation and ecological divergence. To contribute toward this goal, we propose a new framework for ecological speciation that integrates information from phylogenetics, phylogeography, population genomics, and simulations in evolutionary landscape genetics (ELG). We introduce components of the framework, describe ELG simulations (a largely unexplored approach in ecological speciation), and discuss design and experimental feasibility within the context of tropical research. We then use published genetic datasets from populations of five codistributed Amazonian fish species to assess the performance of the framework in studies of tropical speciation. We suggest that these approaches can assist in distinguishing the relative contribution of natural selection from biogeographic history in the origin of biodiversity, even in complex ecosystems such as Amazonia. We also discuss on how to assess ecological speciation using ELG simulations that include selection. These integrative frameworks have considerable potential to enhance conservation management in biodiversity rich ecosystems and to complement historical biogeographic and evolutionary studies of tropical biotas. [ABSTRACT FROM AUTHOR]

Ecological speciation involves the evolution of reproductive isolation and niche divergence in the absence of a physical barrier to gene flow. The process is one of the most controversial topics of the speciation debate, particularly in tropical regions. Here, we investigate ecologically based divergence across an Amazonian ecotone in the electric fish, Steatogenys elegans. We combine phylogenetics, genome scans, and population genetics with a recently developed individual-based evolutionary landscape genetics approach that incorporates selection. This framework is used to assess the relative contributions of geography and divergent natural selection between environments as biodiversity drivers. We report on two closely related and sympatric lineages that exemplify how divergent selection across a major Amazonian aquatic ecotone (i.e., between rivers with markedly different hydrochemical properties) may result in replicated ecologically mediated speciation. The results link selection across an ecological gradient with reproductive isolation and we propose that assortative mating based on water color may be driving the divergence. Divergence resulting from ecologically driven selection highlights the importance of considering environmental heterogeneity in studies of speciation in tropical regions. Furthermore, we show that framing ecological speciation in a spatially explicit evolutionary landscape genetics framework provides an important first step in exploring a wide range of the potential effects of spatial dependence in natural selection. [ABSTRACT FROM AUTHOR]

The unparalleled diversity of tropical ecosystems like the Amazon Basin has been traditionally explained using spatial models within the context of climatic and geological history. Yet, it is adaptive genetic diversity that defines how species evolve and interact within an ecosystem. Here, we combine genome scans, population genetics and sequence-based phylogeographic analyses to examine spatial and ecological arrangements of selected and neutrally evolving regions of the genome of an Amazonian fish, Triportheus albus. Using a sampling design encompassing five major Amazonian rivers, three hydrochemical settings, 352 nuclear markers and two mitochondrial DNA genes, we assess the influence of environmental gradients as biodiversity drivers in Amazonia. We identify strong divergent natural selection with gene flow and isolation by environment across craton (black and clear colour)- and Andean (white colour)-derived water types. Furthermore, we find that heightened selection and population genetic structure present at the interface of these water types appears more powerful in generating diversity than the spatial arrangement of river systems and vicariant biogeographic history. The results from our study challenge assumptions about the origin and distribution of adaptive and neutral genetic diversity in tropical ecosystems. In addition, they have important implications for measures of biodiversity and evolutionary potential in one of the world's most diverse and iconic ecosystems. [ABSTRACT FROM AUTHOR]

Accurately describing biodiversity in tropical regions such as Amazonia is difficult because of insufficient morphological inventories and the lack of studies on the distribution of genetic diversity. Aquatic organisms from Amazonian flooded forests are generally expected to move laterally along the forests during the annual inundation cycle, a behaviour that should promote admixture of populations and reduce within-drainage speciation. We used an unprecedented fine-scale sampling effort and multiple DNA markers to quantify region-wide population differentiation in an Amazonian floodplain forest specialist, the black-wing hatchet fish Carnegiella marthae (). Our study revealed three previously unsuspected and ancient cryptic species of black-wing hatchet fish in the Rio Negro floodplain (RNF), in central Amazonia. Two species produce occasional first-generation hybrids. The third and rarer species, although found in extreme sympatry with another species, appears to be reproductively isolated, and also differs in external morphology and dentition. Our findings have important implications for guiding conservation management because C. marthae is harvested commercially in the RNF ornamental fishery. They also suggest that the diversity of Amazonian ichthyofauna is vastly underestimated, including that found in landscapes lacking contemporary barriers to account for population divergence and speciation. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, , 391-403. [ABSTRACT FROM AUTHOR]

1. Historic and extant landscape structures and environmental conditions are known to influence phylogeographic patterns and population histories in organisms from Amazonia. Recent work suggests that events of the Tertiary Period have played a significant role in generating biodiversity in this exceptionally rich but understudied region. However, species distributions and population structures are also affected by recent environmental and physical changes, especially within highly dynamic ecosystems. 2. The cardinal tetra is a small luminous fish native to the dynamic flooded forest ecosystems of the Rio Negro and Orinoco basins of South America. This very popular aquarium fish represents the single most important species in the ornamental fishery of the Rio Negro, an activity of high socio-economic value for local riverine communities. Here we use a fine-scale sampling regime and sequence data from the second intron of the Ribosomal protein S7 (S7 2) to investigate population structure, colonisation history and genealogical relationships in cardinal tetras of the Rio Negro. 3. High levels of S7 2 polymorphisms revealed phylogeographic patterns across several temporal settings that appear associated with the complex dynamics of the region. Our results suggest a long history of isolation and persistence of cardinal tetra populations in the headwaters and upper regions of the Rio Negro and recent events of colonisation within the incipient Rio Negro floodplain. These colonisation events were followed by recent population expansions likely facilitated by the establishment of the extensive Rio Negro floodplain, an anabranching ecosystem of Holocene age. 4. Our reconstruction of the phylogeographic history of cardinal tetras based on S7 2 intron sequence data reflects the complex influence of both geomorphological and climatic events through time in the Rio Negro basin. Our findings also indicate that in order to maintain the cardinal tetra fishery as a sustainable activity for rural Amazonians, the fishery should be restricted to the middle Rio Negro, the region of the basin where population replenishment is more likely to occur. [ABSTRACT FROM AUTHOR]