Why shouldn’t Saoirse Ronan and Kate Winslet play lovers?

The love story Ammonite, starring Kate Winslet as the 19th-century fossil-hunter and palaeontologist Mary Anning, was chosen to close last year's London film festival, but its director, Francis Lee, has yet to see it with an audience. "I live in Yorkshire," he explains. Behind him are wooden beams, a kitchen table, red and yellow tulips bursting eagerly from a vase. "We were in local lockdown, and it didn't feel appropriate to travel when no one else could."

Ammonite certainly doesn’t need any additional controversy. Two years ago, before Lee had even shot a page of the script, he was pilloried in the press for having portrayed Mary Anning as a lesbian without any evidence to support his conjecture. What he still doesn’t understand is why historical figures are presumed straight until proven otherwise.

“Also, I wasn’t making a biopic!” says the sparkly-eyed 51-year-old, who has an immense grey beard in which woodland creatures could frolic unnoticed for days.

I wanted to contextualise Mary Anning in terms of a relationship. And because men had blocked and overlooked her, and reappropriated her work for themselves, I felt that this relationship couldn't be with a man

Several of Anning’s finds can be seen at the Natural History Museum in London, although comparatively little is known about her. “One description I found said she was warm and friendly and good with children,” says Lee. “The other described her as grumpy and miserable, and said she had a dirty shop. That was it.”

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His script, and Winslet’s performance, follow the second description, although things warm up gradually after Charlotte, a younger woman of higher social standing, played by Saoirse Ronan, enters the picture.

Lee considers himself an outsider. “There just aren’t that many queer working-class people in the film industry,” he says. So he was taken aback to be informed that he shouldn’t tell lesbian stories.

“It’s been a real lesson for me in identity politics. I know I can’t talk for Mary, because I’m not a 19th-century palaeontologist, but I do think I can talk with her. What I tried to do was to take this working-class woman, who hadn’t been recognised in her lifetime, and elevate her. I wanted to contextualise her in terms of a relationship. And because men had blocked and overlooked her, and reappropriated her work for themselves, I felt that this relationship couldn’t be with a man.”

Gay, rural, working-class love stories are Lee’s speciality.

God's Own Country, his exhilarating 2017 debut, was "about two queer lads on the side of a hill in Yorkshire in bad weather". But while Lee, like Johnny in that movie, is a farmer's son, he says it is Ammonite rather than its predecessor that represents the nearest he has come to self-portraiture.

“Like Mary, I have found it very difficult to find my voice, professionally and personally. I feel very closed a lot of the time. I find it hard to be me, and to be truthful about me.” The networking side of the film industry is one he finds especially traumatic. “It makes me want to die,” he says.

Success hasn’t helped. “It amplifies the discomfort and has caused issues for me. You go somewhere like a dinner party – listen to me, a dinner party! – and people want to talk about your work. Sometimes I want people to talk to me as Francis, not Francis who made some films.”

Would he like to feel more at ease socially? Or is he content to chisel away quietly at his work, the way Mary does with her fossils? He gazes out of the window, to the hill where God’s Own Country was shot. Five seconds pass, then six, then seven. Eventually, he gives a little growl, as if annoyed with himself.

“I don’t want to cry, Ryan,” he says. “I lead a very, very lonely life. I would like to be part of a group, or part of something.” His films concern introverted figures who feel unseen until they find a lover. Has that been his experience? Another thoughtful pause. “I think I’ve had some near misses. But not as yet.”

Lee spent 15 years as a jobbing actor – 'a really bad one. I always wanted to tell stories, but the frustration came from not understanding how somebody from my background, with my lack of privilege, could do that'

His isolation began in childhood. “My parents worked all the time and weren’t around. The animals were my friends.” Was it upsetting when those friends were slaughtered? “No, because you understand when you grow up with livestock that there’s always going to be dead stock. And it’s an economy, in the same way that Mary sells her most precious fossils to put food on the table.”

At first, he was content on the farm: “The hills and the woods were my playground.” Growing up, and realising he was gay, brought its own problems. “Like many queer people in rural places, I left to try to find my tribe, my family.” His comprehensive school had not led him to expect much from life. “One teacher asked us: ‘Has anyone shown you how to fill out your DSS and housing benefit forms? Because you’ll need those once you leave.’”

Nevertheless, he got into drama school in London, then spent 15 years as a jobbing actor. “A really bad one. I always wanted to tell stories, but the frustration came from not understanding how somebody from my background, with my lack of privilege, could do that.”

Along the way, he met two heroes. Victoria Wood wrote a tiny part for him in her sitcom Dinnerladies, while Mike Leigh cast him in a small role in his Gilbert and Sullivan extravaganza Topsy-Turvy. He remembers Leigh, who remains a friend, telling him how good he was. “I don’t think I could ever believe it for myself,” he says. “Acting was pretty shaming. I always felt I’d let people down.”

It is a sensation he never has as a director, where he feels “very focused and blinkered and immersed”, overseeing every detail obsessively. “It makes my brain hurt. It’s terrifying and incredibly satisfying.”

'We were in the barn and Dad said to me, 'Are you all right?' I said, 'No, I'm not. I'm in love, and it's with a man, not a woman.' And I cried. And he held me for a bit, then just said, 'You're mine. And I love you'

Queer stories tend to include scenes of homophobia or coming out, but not his. “For me, it was about trying to take the difficulty away from sexuality, and to look at the difficulty of relationships.” The nearest thing Lee had to a coming out of his own occurred when he was 30.

“I was going through a hard time in a relationship. I was back in Yorkshire, and my dad could tell something was up. We were in the barn and he said to me, ‘Are you all right?’ I said, ‘No, I’m not. I’m in love, Dad, and it’s with a man, not a woman.’ And I cried. And he held me for a bit, then just said, ‘You’re mine. And I love you.’”

That scene would never make it into one of Lee’s films. His taste is for the frugal. Any dialogue is squeezed out as if from a nearly empty toothpaste tube. He is proud of God’s Own Country: it is absolutely the film he meant to make. But he would be happier if he could remove two words from the soundtrack. When Johnny is bathing his father, who has suffered a stroke, the older man clasps his son’s hand and says: “Thank you.”

You thought the hand clasp was enough? “I did.” But you wrote those words? “I did.” Then why didn’t you cut them? “Because a very brilliant executive at the BFI, Mary Burke, kept going, ‘It resonates: people will find the emotion in it.’ I said, ‘They’ll find the emotion in the hand!’ She was, like, ‘Just keep it in!’ ”

Pressed on the matter, Lee admits that Ammonite contains several doorknobs that don’t pass muster. Though correct for the period, they are not precisely the sort that would have been seen in the bedrooms of a Georgian or early-Victorian house. When he noticed them on set, there wasn’t time to arrange replacements. “I had to let it go. But it bugged me.” And they’re visible? “Yeah.” Would you remove them if you could? “I would take them out, yeah.”

The laughter that has been building inside him for the past few moments bubbles over now. “Don’t write about that, Ryan!” he groans. “People are going to think I’m insane!” Perhaps. Or it might just make them love his films even more. – Guardian

Ammonite is available as premium video on demand from Friday, March 26th