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Oaks (Quercus, Fagaceae) are the dominant tree genus of North America in species number and biomass, and Mexico is a global center of oak diversity. Understanding the origins of oak diversity is key to understanding biodiversity of northern temperate forests. A phylogenetic study of biogeography, niche evolution and diversification patterns in Quercus was performed using 300 samples, 146 species. Next-generation sequencing data were generated using the restriction-site associated DNA (RAD-seq) method. A time-calibrated maximum likelihood phylogeny was inferred and analyzed with bioclimatic, soils, and leaf habit data to reconstruct the biogeographic and evolutionary history of the American oaks. Our highly resolved phylogeny demonstrates sympatric parallel diversification in climatic niche, leaf habit, and diversification rates. The two major American oak clades arose in what is now the boreal zone and radiated, in parallel, from eastern North America into Mexico and Central America. Oaks adapted rapidly to niche transitions. The Mexican oaks are particularly numerous, not because Mexico is a center of origin, but because of high rates of lineage diversification associated with high rates of evolution along moisture gradients and between the evergreen and deciduous leaf habits. Sympatric parallel diversification in the oaks has shaped the diversity of North American forests.

Premise of the Study Evolutionary and biogeographic history, including past environmental change and diversification processes, are likely to have influenced the expansion, migration, and extinction of populations, creating evolutionary legacy effects that influence regional species pools and the composition of communities. We consider the consequences of the diversification process in shaping trait evolution and assembly of oak‐dominated communities throughout the continental United States (U.S.). Methods Within the U.S. oaks, we tested for phylogenetic and functional trait patterns at different spatial scales, taking advantage of a dated phylogenomic analysis of American oaks and the U.S. Forest Service (USFS) Forest Inventory and Analysis (FIA). Key Results We find (1) phylogenetic overdispersion at small grain sizes throughout the U.S. across all spatial extents and (2) a shift from overdispersion to clustering with increasing grain sizes. Leaf traits have evolved in a convergent manner, and these traits are clustered in communities at all spatial scales, except in the far west, where species with contrasting leaf types co‐occur. Conclusions Our results support the hypotheses that (1) interspecific interactions were important in parallel adaptive radiation of the genus into a range of habitats across the continent and (2) that the diversification process is a critical driver of community assembly. Functional convergence of complementary species from distinct clades adapted to the same local habitats is a likely mechanism that allows distantly related species to coexist. Our findings contribute to an explanation of the long‐term maintenance of high oak diversity and the dominance of the oak genus in North America.

The Crenicichla mandelburgeri species complex from the Middle Paraná basin is a diverse group of cichlid species and contains all known ecomorphs found within the entire genus Crenicichla. Here, we study the phylogenetic relationships within the C. mandelburgeri species complex using ddRAD sequencing with focus on its two candidate species flocks endemic to the Iguazú and Urugua-í Rivers, and on two putative sympatric species in the Piray Guazú River. These species flocks include four and three syntopic species, respectively, which are strongly adapted to different trophic niches and include derived ecomorphs of Crenicichla (molluscivores, a periphyton grazer, and a crevice-feeding thick-lipped invertivore). Our phylogenomic analyses strongly support monophyly and rapid diversification of the Iguazú species flock, but reveal more complex evolutionary histories in the Urugua-í and Piray Guazú tributaries. Most species in the Middle Paraná, including one species in the Urugua-í and both species in the Piray Guazú show cytonuclear discordance, and in both of these tributaries, we also found hybridization in one of the resident species. Population-level analyses reveal complete isolation of the Iguazú species and coupled with their dramatic ecological diversity, this radiation exemplifies characteristics of a species flock that arose via ecological speciation.

The Crenicichla mandelburgeri species complex from the Middle Paraná shows parallel evolution of ecomorphs to the unrelated C. missioneira species complex from the Uruguay River. In this article, we describe a new species from the C. mandelburgeri species complex that has evolved a parallel morphology and ecology to an unrelated species from the C. missioneira species complex (C. celidochilus). The new species is a pelagic predator that feeds predominantly on fishes and together with C. celidochilus is the only known pelagic species in the large riverine genus Crenicichla. The new species is endemic solely to a small tributary (the Urugua-í) of the Middle Paraná River where it is sympatric and partly syntopic with two other closely related endemic species that, however, differ strongly in their ecomorphologies (one is a generalistic invertivore and the other a specialized molluscivore). Mitochondrial DNA phylogeny finds the new species nested within the widespread C. mandelburgeri. Reduced genome-representation ddRAD analyses, however, demonstrate that this new species is of a hybrid origin and shares ancestry with C. ypo, one of the two studied sympatric species.

Fish diversification into sympatric ecomorph pairs demonstrates a striking parallelism across a number of taxa in numerous lakes. However, there is a dearth of information on environmental conditions, which may orchestrate divergence processes across generations. Here we explore whether the environmental factors affecting food and reproductive niche distinctions could trigger the divergence of the lacustrine-riverine fish species into two morphs based on kokanee Oncorhynchus nerka of the Lake Kronotskoe. We reveal drastic differences in temperature on the tributary reproduction sites affecting the early ontogeny timing and disrupting the time of lakeward migration of the morphs. The juveniles of the benthivorous morph run into the lake in spring during the food abundance peak on the slope, while the planktivorous kokanee migrates to the lake in the summer when the pelagic zone abounds with zooplankton. The dynamics of this food niches is determined by water temperature dynamics and may be stable for long periods of time, thus making each morph adapting to similar condition throughout generations. We suggest that the pelagic-benthic divergence could be explained by the factors, which are extrinsic for fish , making our results applicable for numerous cases of this microevolutionary pathway all over the Holarctic.

A common pattern of adaptive diversification in freshwater fishes is the repeated evolution of elongated open water (limnetic) species and high‐bodied shore (benthic) species from generalist ancestors. Studies on phenotype‐diet correlations have suggested that population‐wide individual specialization occurs at an early evolutionary and ecological stage of divergence and niche partitioning. This variable restricted niche use across individuals can provide the raw material for earliest stages of sympatric divergence. We investigated variation in morphology and diet as well as their correlations along the benthic‐limnetic axis in an extremely young Midas cichlid species, Amphilophus tolteca, endemic to the Nicaraguan crater lake Asososca Managua. We found that A. tolteca varied continuously in ecologically relevant traits such as body shape and lower pharyngeal jaw morphology. The correlation of these phenotypes with niche suggested that individuals are specialized along the benthic‐limnetic axis. No genetic differentiation within the crater lake was detected based on genotypes from 13 microsatellite loci. Overall, we found that individual specialization in this young crater lake species encompasses the limnetic‐ as well as the benthic macro‐habitat. Yet there is no evidence for any diversification within the species, making this a candidate system for studying what might be the early stages preceding sympatric divergence. A common pattern of adaptive diversification in freshwater fishes is the repeated evolution of open water (limnetic) species and of shore (benthic) species. Individual specialization can reflect earliest stages of evolutionary and ecological divergence. We here demonstrate individual specialization along the benthic–limnetic axis in a young adaptive radiation of crater lake cichlid fishes.