Emma Donoghue on her contentious bestseller Room and new crime fiction novel

Blanche Beunon , the erotic dancer at the heart of Emma Donoghue's new novel, rescues her son from a baby farm after her pugnacious, cross-dressing friend, Jenny, poses some "obvious questions".

Does Blanche believe young P'tit is better off without his mother? Why did she abandon him to a loveless institution? Does Blanche want P'tit back? Jenny is correct about the importance of asking obvious questions but, when I meet Donoghue at Heathrow Airport, between flights from her native Dublin to her adopted country of Canada, she beats me to it.

"Why do I write about hideous things?" she says. "It could be because my own life has been extremely easy. I'm drawn to stories where the stakes are high and people make desperate decisions."

Unless you've been locked in a shed for several years, cut off from civilisation, you probably know that Donoghue's previous novel, the Man Booker Prize-shortlisted Room (2010), was about a woman and child who suffered exactly that fate. Inspired by the Josef Fritzl case, their harrowing story is being made in to a film this year and Donoghue has written the screenplay.

Her new novel, Frog Music, is also based on a real crime, set in the sweltering summer of 1876, as smallpox sweeps San Francisco. "It was peculiarly disgusting to research," she says of the novel's sticky, sickly milieu, but is she under pressure following the million-selling Room? "No, writing Frog Music was daunting because it's the first time I've written crime fiction. I have great respect for the way writers like Lee Child satisfy readers' expectations and surprise them."

At 44, Donoghue labels herself a "veteran novelist". Frog Music is her 12th work of fiction and she plans books years in advance: "The next project is always the most desirable, the new love that hasn't made any tedious domestic demands." Readers are lured in to the novel's heady atmosphere from the moment Jenny is shot and Blanche decides to find the murderer.

"Fiction informed by the grittiness of fact," is how Donoghue describes her narrative which switches between past and present, generating intrigue about the crime and the women's unusual friendship. "Nobody wants to be forgotten so it's satisfying to put obscure, dead people in the spotlight. When I read about Jenny, she struck me as a trouble-maker, picking fights, getting arrested repeatedly for dressing like a man."

Donoghue has two children, aged six and ten, with her female partner, Chris Roulston, a professor of women's studies at the university of Western Ontario. So does she think motherhood is the subject which connects Frog Music to Room? "Definitely. After writing about a good mother in my last novel, I enjoyed exploring the early, intimate years of parenthood from the perspective of a bad mother. The roles are never fixed between mother and baby, you go from being good mother to bad mother instantly then you redeem yourself. It's the most intense relationship I've known and one of the few adult experiences that's brought me new emotions. I'm also looking at what happens when a self-consciously free 25-year-old has a child."

Donoghue spent her mid-20s with her "head down in the library" at Cambridge University, completing her PhD in 18th-century literature and writing her first novel, Stir Fry (1994), which examined a young, Irish woman's lesbian awakening and established Donoghue as an author of gay fiction. ]

Slammerkin (2000) was her first novel to use an historical setting and, like Frog Music, told the story of a prostitute: "I think I'll get grief for celebrating prostitution," she says of Blanche's casual transition from dancer to sex worker.

"She's fairly empowered, earning lots of money, and you have to look at prostitution case by case. It's the job that symbolises other jobs. I find prostitutes interesting as test cases for considering how much we choose and how much life happens to us. I wanted to see what degree of agency I could give Blanche."

Blanche is manipulated by Arthur, her "maque" (the French term for a man who lives off his girlfriend's prostitution), who is also P'tit's father.

"He's handsome, idling around town, spending Blanche's money, yet irritated with Jenny for usurping the masculine role," Donoghue explains.

Blanche suspects Arthur and his sidekick Ernest are behind the murder, especially when they vanish with P'tit, but why was Jenny determined to subvert her society's dress codes? "There's no explaining the clothes we want to wear," says Donoghue, whose pink stole compliments her blue eyes. "If Jenny dressed in crinoline, men in bars would come on to her or she'd be considered intrusive. Pants have always offered freedom." We both laugh before she adds: "I'm interested in the freakish, not just in terms of sex, but people who exist on the edge of national identities too."

Donoghue has lived in Canada since 1998 but, while Blanche and Arthur are accepted in America as French immigrants, she knows others experience harder landings. "San Francisco was supposed to be a free zone but the city introduced laws to keep the Chinese out of public places and the same went for women. California needed immigrants in 1876 as much as it needs undocumented fruit pickers today." Is writing about the past a way of indirectly examining the present? "Yes, but I don't regard historical fiction as a separate genre. I thought about The Wire while writing Frog Music. I wanted to make readers care about lowlife and The Wire expands our capacity for sympathy by showing us faces in the herd of life."

The novel's ending is shaped by Donoghue's surprising theory about the real Jenny's unsolved murder. The title refers to frogs her character catches to sell to French chefs and the circus songs and odes to drinking which soundtrack her world. "Songs spread fast then," says Donoghue, "they crossed racial lines and people weren't self-conscious about singing." Feel free, I suggest, hoping she'll burst in to "Vive la Rose" or "The Daring Young Man on the Flying Trapeze." Alas, the attention she received for Room – not all of it favourable – has taught her to draw the line and, when our time is up, she leaves to catch her flight, saying: "I'll watch out for a hatchet job, then?"

I can't help thinking that would appeal to her taste for the dark and unexpected.

An exclusive extract from Emma Donoghue's novel, 'Frog Music', (Picador , £16.99) can be read on independent.co.uk/arts-entertainment/books/ Readers can speak to her directly in a Twitter Q&A hosted by The Independent on @indybooks #AskEmma on Monday 24 March at 1pm