Brenna Aubrey self-published her debut romance novel At Any Price on the Amazon Kindle on 9 December 2013. One month later At Any Price had netted a total profit of £16,588. Aubrey's success is far from unique – 2013 was a breakout year for "indie authors" led by the phenomenal success of Hugh Howey. But Aubrey is among the first in a wave of authors to do what, until very recently, would have been unthinkable; turn down a $120,000 (£72,000) deal from one of the big five publishing houses and decide to do their job herself.

"Ebooks have changed everything and the traditional publishing establishment is not quite keeping up," Brenna Aubrey answered when I asked her about some of the negative responses to her decision from traditionally-published authors. "I also think that in some ways authors who have been chasing their own dream deals take my rejection of the dream deal as a rejection of their core values and aspirations."

The six-figure deal has been the aspiration of many authors for decades. A major advance – such as the $2m deal announced for Garth Risk Holdberg – can cement a literary career. But the reality is that advances for mid-list writers are often no more than $5,000. Aubrey's deal of $120,000 was significant, but would have been split across three novels, divided with her agent and paid in instalments. When she cranked the figures Aubrey realised that – even as a debut author – self-publishing offered far more potential reward.

But it was the sticky issue of copyright that swung Aubrey towards self-publishing. "The clauses being written into contracts these days call for a reversion of rights if the yearly sales of an ebook are under a certain amount, and usually that amount is very very low." The effect of this for authors like Brenna Aubrey is that once you sign a publishing deal, you give up control of your work for up to 35 years. And three-and-a-half decades is a very long time in digital publishing.

The freedom indie authors have to market and price their own books has allowed them to dominate the digital marketplace for the last three years. As Hugh Howey observed in a typically contentious blogpost, a look at the Amazon Kindle bestseller lists in any key genre show them dominated by two kinds of writers. Established bestsellers like George RR Martin, and unknown indie writers like AG Riddle. Almost entirely absent are debut authors and mid-listers from the big five. Howey has built on this observation with the data-driven Author Earnings report, which suggests indie authors account for 39% of Kindle daily unit sales in the most popular genres of commercial fiction.

Publishers are now racing to recapture the digital ebook market from self-published authors, particularly in pivotal genres like science fiction, fantasy and romance that have proved so popular with ebook readers. New digital-only imprints like Hydra seem designed to compete in that space, but it's an open question why any author would sign deals that have been staunchly challenged by professional writers' organisations. The more natural strategy seems to be for major publishers to cherry-pick the most successful self-published authors and promote them to genuine bestseller status, as they have done with EL James and Hugh Howey. The "hybrid" author, who retains control of ebook rights while signing print-only publishing deals, may now become the new standard for publishing.

But it may be too little to late. Already this year Quercus – the successful independent publisher of Stieg Larsson's The Girl with the Dragon Tattoo – has placed itself up for sale citing "a lower than expected upturn in digital sales" among its reasons. It's a trend reflected across the big five publishers. Ebooks provided a much needed cash infusion for publishers struggling with a declining print market. But as the process of making backlist material available in ebook reaches completion, publishers need new bestsellers to keep their growth going. But the authors who could provide those new books, like Brenna Aubrey, are increasingly choosing to self-publish and keep both creative and financial control of their work.