The nature and timing of evolution of niche differentiation among closely related species remains an important question in ecology and evolution. The American live oak clade, Virentes, which spans the unglaciated temperate and tropical regions of North America and Mesoamerica, provides an instructive system in which to examine speciation and niche evolution. We generated a fossil-calibrated phylogeny of Virentes using RADseq data to estimate divergence times and used nuclear microsatellites, chloroplast sequences and an intron region of nitrate reductase (NIA-i3) to examine genetic diversity within species, rates of gene flow among species and ancestral population size of disjunct sister species. Transitions in functional and morphological traits associated with ecological and climatic niche axes were examined across the phylogeny. We found the Virentes to be monophyletic with three subclades, including a southwest clade, a southeastern US clade and a Central American/Cuban clade. Despite high leaf morphological variation within species and transpecific chloroplast haplotypes, RADseq and nuclear SSR data showed genetic coherence of species. We estimated a crown date for Virentes of 11 Ma and implicated the formation of the Sea of Cort es in a speciation event~5 Ma. Tree height at maturity, associated with fire tolerance, differs among the sympatric species, while freezing tolerance appears to have diverged repeatedly across the tropical-temperate divide. Sympatric species thus show evidence of ecological niche differentiation but share climatic niches, while allopatric and parapatric species conserve ecological niches, but diverge in climatic niches. The mode of speciation and/or degree of co-occurrence may thus influence which niche axis plants diverge along.

Cold poses major physiological challenges to plants, especially long-lived trees. In trees occurring along variable temperature clines, the expected direction and consequences of selection on cold acclimation ability and freezing tolerance are not straightforward. Here we estimated selection in cold acclimation genes at two evolutionary timescales in all seven species of the American live oaks (Quercus subsection Virentes). Two cold response candidate genes were chosen: ICE1, a key gene in the cold acclimation pathway, and HOS1, which modulates cold response by negatively regulating ICE1. Two housekeeping genes, GAPDB and CHR11, were also analyzed. At the shallow evolutionary timescale, we demonstrate that HOS1 experienced recent balancing selection in the two most broadly distributed species, Q. virginiana and Q. oleoides. At a deeper evolutionary scale, a codon-based model of evolution revealed the signature of negative selection in ICE1. In contrast, three positively selected codons have been identified in HOS1, possibly a signature of the diversification of Virentes into warmer climates from a freezing adapted lineage of oaks. Our findings indicate that evolution has favored diversity in cold tolerance modulation through balancing selection in HOS1 while maintaining core cold acclimation ability, as evidenced by purifying selection in ICE1.

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Understanding and anticipating the effects of climate change on fisheries social-ecological systems (FSESs) is central to proactive fisheries management in a changing global climate. With fisheries management increasingly striving to consider interactions and feedbacks among people, targeted species, and the broader ecological and human communities, fisheries managers and participants need tools to help them assess these complex systems. We developed a new climate vulnerability assessment framework for analyzing the impacts of a climate-induced trend or event on a FSES. The framework divides the FSES into four interrelated and interacting domains: Ecological Community, Fished Species, Fishery, and Human Community. The framework provides a systematic approach to account for indirect as well as direct effects, links among subsystems, and multiple climate change-induced stressors. We demonstrate the framework’s utility by applying it to three case studies: the effects of a marine heatwave on the Dungeness crab FSES, the effects of a marine heatwave on the red sea urchin FSES, and the effects of long-term climate trends on North Pacific albacore. We found that the effects of a climatic trend or event on a FSES are often indirect and can trigger diverse and important feedbacks. These examples also showed that the climatic trend or event may cause changes in the temporal and spatial distribution of fishing effort and fished species that have a more significant impact on the FSES than changes to species abundance per se. Unlike other climate vulnerability assessment frameworks and applications, ours is designed to enable consideration of the range of feedbacks within and among both the ecological and human communities. As such, it is a valuable tool to guide the holistic examination and assessment of potential impacts to FSESs.