Experimental evidence for rapid genomic adaptation to a new niche in an adaptive radiation

Abstract

A substantial part of biodiversity is thought to have arisen from adaptive radiations in which one lineage rapidly diversified into multiple lineages specialized to many different niches. However, selection and drift reduce genetic variation during adaptation to new niches and may thus prevent or slow down further niche shifts. We tested whether rapid adaptation is still possible from a highly derived ecotype in the adaptive radiation of threespine stickleback on the Haida Gwaii archipelago, Western Canada. In a 19-year selection experiment, we let giant sticklebacks from a large blackwater lake evolve in a small clearwater pond without vertebrate predators. A total of 56 whole genomes from the experiment and 26 natural populations revealed that adaptive genomic change was rapid in many small genomic regions and encompassed 75% of the change between 12,000-year-old ecotypes. Genomic change was as fast as phenotypic change in defence and trophic morphology, and both were largely parallel between the short-term selection experiment and long-term natural adaptive radiation. Our results show that functionally relevant standing genetic variation can persist in derived radiation members, allowing adaptive radiations to unfold very rapidly.

Classic and introgressed selective sweeps shape mimicry loci across a butterfly adaptive radiation

“…Many studies have used naive genome scans to identify selection in natural populations, but such an approach can lead to false positives 86 . More integrative approaches, which combine selection scans with information on phenotypic selection in the wild and genetic trait mapping, can give a more complete picture of how selection shapes specific loci and phenotypes 10,12,14,16,87 . Such studies are increasingly common, but with few exceptions focus on a single locus, or a limited set of populations or phenotypes, often because of the high sampling and sequencing effort required.…”

“…While many classic examples of selective sweeps have been found in domesticated populations, such as maize 6 , chicken 7 , and cattle 8 , or in humans 9 , increasingly natural populations are also studied. Using genomic data, these latter studies can reveal the genetic architecture and evolutionary history of ecologically relevant traits [10][11][12][13] and provide insights into the action of natural selection by complementing field and experimental studies [14][15][16] . However, to date few molecular studies of natural populations have used broad sampling across adaptive radiations with varying selection pressures and sources of adaptive variation for the same trait.…”

New environment, new invaders - repeated horizontal transfer of LINEs to sea snakes

“…However, the Aipysurus-Emydocephalus lineage has continued to evolve at the same rate as terrestrial lineages of Hydrophiinae, diverging into 9 species, while the Hydrophis lineage has rapidly radiated into 48 species (21) . Following major changes in habitat ecology, such as sea snakes transition from a terrestrial to a marine habitat, organisms must adapt to their new environment, with transposons potentially contributing to adaptations (22,23) . Here we report an analysis of transposons in sea snake genomes, where the marine environment appears to have fostered the repeated, independent acquisition of these transposons through horizontal transfer of transposons (HTT).…”

Ecological speciation in European whitefish is driven by a large-gaped predator

“…The best way to avoid confounding the causes and consequences of speciation is to study the process at its earliest stages 4,[32][33][34][35][36][37][38][39] . Unfortunately, this approach may lead us to study cases of early population divergence that are unrepresentative of the speciation process, or will never lead to speciation 4,40 .…”