Whole-genome data reveal the complex history of a diverse ecological community

Abstract

SignificanceWidespread biological communities are common, but little is known about how they assemble. A key question is how sets of trophically linked species (predators and their prey, hosts and parasites) spread to occupy current distributions. Do they disperse together, preserving ecological interactions, or separately, such that interactions are interrupted? This is central to assessing the potential for coevolution in a system and requires inference of species associations both over space and through time. Here, we use de novo genomic data and likelihood-based approaches to infer the assembly history of a multispecies community of Western Palearctic insect herbivores and parasitoid natural enemies—the two trophic groups that together comprise 50% of all animal species.

Common barriers, but temporal dissonance: Genomic tests suggest ecological and paleo‐landscape sieves structure a coastal riverine fish community

“…for discussion about barriers in the region). In contrast, others have argued that in hyperdiverse communities, like the Atlantic Rainforest, congruency in species responses will be highly dependent on the degree of species interactions and ecological fitting(Bunnefeld et al, 2018). Our findings indicate that aquatic organisms may exhibit species-specific divergence histories, despite being under strong dispersal constraints imposed by riverine environments.Moreover, and perhaps somewhat counterintuitively, our results suggest that an ecological sieve contributes to temporal dissonance in the response of taxa to temporary connections despite spatial congruence, unlike conclusions about shared histories of terrestrial organisms.…”

“…Moreover, the differences in the inferred timing of divergence (i.e., temporal dissonance across species and geographic breaks) point to the episodic nature of when historical connections were traversed, or conversely differences in the effectiveness of barriers, which is a conclusion that is reached whether a common or a species-specific mutation rate are used to estimate divergence times. Nevertheless, there is some temporal clustering (e.g., LGM ~25 kya and ~100 kya; Figure 3), indicating that a null model of random divergence times can be rejected (Bunnefeld, Hearn, Stone, & Lohse, 2018).…”

The determinants of genetic diversity in butterflies

“…Genetic diversity in many European taxa has been shaped by the cycles of isolation into, and range expansion out of, glacial refugia during the Pleistocene 33,34,41 . While we have sought to minimize the effects of Pleistocene history by focusing sampling on a single Pleistocene refugium, Iberia, our inferences could be confounded in at least two ways: Firstly, rather than being solely driven by long-term N e , variation in genetic diversity in Iberia may be affected by gene flow from other refugia 42 or even species 43 . Secondly, even if Iberian populations are little affected by admixture, they may have undergone drastic (and potentially different) changes in N e in response to past climatic events.…”

From Inquilines to Gall Inducers: Genomic Signature of a Life-Style Transition in Synergus Gall Wasps

“…The genomes of four Synergus species were used for this study: Previously published genomes of the inquilines Synergus umbraculus ( Bunnefeld et al. 2018 ; Hearn 2018 ) and Synergus japonicus ( Hearn 2018 ) and de novo genomes sequenced for this study of the inquiline S. gifuensis and the gall-inducer S. itoensis .…”